Mass Spectrometry Engine

The MassSpecEngine R6 class is a framework for parsing, processing and inspecting mass spectrometry (MS) data. MS data (i.e., spectra and chromatograms, including chromatograms produced by UV detection) can be loaded from mzML and mzXML. If msconvert from ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF / WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS.

Details

The MassSpecEngine is using several patRoon patRoon for assembly of Non-Target Analysis (NTA) data processing workflows.

References

Helmus R, ter Laak TL, van Wezel AP, de Voogt P, Schymanski EL (2021). “patRoon: open source software platform for environmental mass spectrometry based non-target screening.” Journal of Cheminformatics, 13(1). doi:10.1186/s13321-020-00477-w .

Helmus R, van de Velde B, Brunner AM, ter Laak TL, van Wezel AP, Schymanski EL (2022). “patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening.” Journal of Open Source Software, 7(71), 4029. doi:10.21105/joss.04029 .

Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008). “ProteoWizard: open source software for rapid proteomics tools development.” Bioinformatics, 24(21), 2534–2536. doi:10.1093/bioinformatics/btn323 , http://www.ncbi.nlm.nih.gov/pubmed/18606607.

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak M, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P (2012). “A cross-platform toolkit for mass spectrometry and proteomics.” Nature Biotechnology, 30(10), 918–920. https://doi.org/10.1038/nbt.2377.

Super class

StreamFind::CoreEngine -> MassSpecEngine

Active bindings

NonTargetAnalysisResults: Get/Set for the NonTargetAnalysisResults results class.
Spectra: Get/set for the Spectra results class.
Chromatograms: Get/set for the chromatograms results class.

Methods

Public methods

MassSpecEngine$new()
MassSpecEngine$add_analyses()
MassSpecEngine$remove_analyses()
MassSpecEngine$add_replicate_names()
MassSpecEngine$add_blank_names()
MassSpecEngine$get_analysis_names()
MassSpecEngine$get_replicate_names()
MassSpecEngine$get_blank_names()
MassSpecEngine$get_files()
MassSpecEngine$get_formats()
MassSpecEngine$get_instruments()
MassSpecEngine$get_software()
MassSpecEngine$get_spectra_number()
MassSpecEngine$get_spectra_mode()
MassSpecEngine$get_spectra_level()
MassSpecEngine$get_spectra_lowest_mz()
MassSpecEngine$get_spectra_highest_mz()
MassSpecEngine$get_spectra_lowest_rt()
MassSpecEngine$get_spectra_highest_rt()
MassSpecEngine$get_spectra_polarity()
MassSpecEngine$get_spectra_headers()
MassSpecEngine$get_spectra_tic()
MassSpecEngine$get_spectra_bpc()
MassSpecEngine$get_raw_spectra()
MassSpecEngine$get_spectra_eic()
MassSpecEngine$get_spectra_ms1()
MassSpecEngine$get_spectra_ms2()
MassSpecEngine$plot_spectra_tic()
MassSpecEngine$plot_spectra_bpc()
MassSpecEngine$plot_spectra_eic()
MassSpecEngine$plot_spectra_xic()
MassSpecEngine$plot_spectra_ms1()
MassSpecEngine$plot_spectra_ms2()
MassSpecEngine$get_chromatograms_number()
MassSpecEngine$get_chromatograms_headers()
MassSpecEngine$get_raw_chromatograms()
MassSpecEngine$has_results_nts()
MassSpecEngine$has_results_spectra()
MassSpecEngine$has_results_chromatograms()
MassSpecEngine$get_chromatograms()
MassSpecEngine$get_chromatograms_peaks()
MassSpecEngine$plot_chromatograms()
MassSpecEngine$plot_chromatograms_baseline()
MassSpecEngine$plot_chromatograms_peaks()
MassSpecEngine$get_spectra()
MassSpecEngine$plot_spectra()
MassSpecEngine$plot_spectra_3d()
MassSpecEngine$plot_spectra_charges()
MassSpecEngine$get_spectra_peaks()
MassSpecEngine$plot_spectra_peaks()
MassSpecEngine$plot_spectra_baseline()
MassSpecEngine$get_spectra_matrix()
MassSpecEngine$get_features_count()
MassSpecEngine$plot_features_count()
MassSpecEngine$get_features()
MassSpecEngine$map_features()
MassSpecEngine$map_features_intensity()
MassSpecEngine$get_features_eic()
MassSpecEngine$plot_features()
MassSpecEngine$get_features_ms1()
MassSpecEngine$plot_features_ms1()
MassSpecEngine$get_features_ms2()
MassSpecEngine$plot_features_ms2()
MassSpecEngine$get_groups()
MassSpecEngine$plot_groups()
MassSpecEngine$plot_groups_overview()
MassSpecEngine$plot_groups_profile()
MassSpecEngine$get_groups_ms1()
MassSpecEngine$plot_groups_ms1()
MassSpecEngine$get_groups_ms2()
MassSpecEngine$plot_groups_ms2()
MassSpecEngine$get_components()
MassSpecEngine$map_components()
MassSpecEngine$get_suspects()
MassSpecEngine$plot_suspects()
MassSpecEngine$get_internal_standards()
MassSpecEngine$plot_internal_standards()
MassSpecEngine$get_fold_change()
MassSpecEngine$plot_fold_change()
MassSpecEngine$get_compounds()
MassSpecEngine$get_patRoon_features()
MassSpecEngine$get_patRoon_MSPeakLists()
MassSpecEngine$clone()

Inherited methods

Method `new()`

Creates an R6 MassSpecEngine class object.

Usage

MassSpecEngine$new(
  metadata = NULL,
  workflow = NULL,
  analyses = NULL,
  centroid = FALSE,
  levels = c(1, 2)
)

Arguments

metadata: A named list or a Metadata object. Each list element must have length one. There is no type restrictions except for name (must be type character), author (must be type character) and date (must be class POSIXct or POSIXt). A file entry must be a character string with a full path to a file.
workflow: A Workflow object, a list of ProcessingStep objects or a character string with a full path to a rds or json file containing a Workflow.
analyses: A MassSpecAnalyses S7 class object or a character vector with full file paths to mzML files or a data.frame with colnames: "file", "replicate" and "blank". The "replicate" column is used to group the analyses and the "blank" column is used to identify the blank samples. The "file" column is the full path to the mzML files. If msconvert from ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF / WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS.
centroid: Logical (length 1). Set to TRUE to centroid data when converting from vendor formats to mzML.
levels: Numeric vector with the MS levels to consider when centroiding data. Default is c(1, 2).

Returns

A new MassSpecEngine class object.

Method `add_analyses()`

Adds analyses. Note that when adding new analyses, any existing results are removed.

Usage

MassSpecEngine$add_analyses(analyses = NULL)

Arguments

analyses: A character vector with full file paths to mzML/mzXML files. f msconvert from ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF / WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS.

Method `remove_analyses()`

Removes analyses.

Usage

MassSpecEngine$remove_analyses(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `add_replicate_names()`

Adds replicate names to the analysis.

Usage

MassSpecEngine$add_replicate_names(value)

Arguments

value: Character vector with the replicate names. Must have the same length as the number of analyses.

Method `add_blank_names()`

Adds blank names to the analysis.

Usage

MassSpecEngine$add_blank_names(value)

Arguments

value: Character vector with the replicate names. Must have the same length as the number of analyses and must be one of replicate names.

Method `get_analysis_names()`

Gets a character vector with the analysis replicate names.

Usage

MassSpecEngine$get_analysis_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_replicate_names()`

Gets a character vector with the analysis replicate names.

Usage

MassSpecEngine$get_replicate_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_blank_names()`

Gets a character vector with the analysis blank replicate names.

Usage

MassSpecEngine$get_blank_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_files()`

Gets a character vector with the full file paths of each analysis.

Usage

MassSpecEngine$get_files(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_formats()`

Gets a character vector with the file format of each analysis.'

Usage

MassSpecEngine$get_formats(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_instruments()`

Gets a list of instrument information from each analysis as elements.

Usage

MassSpecEngine$get_instruments(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_software()`

Gets a list of software information from each analysis as elements.

Usage

MassSpecEngine$get_software(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_number()`

Gets a numeric vector with the number of spectra in each analysis.

Usage

MassSpecEngine$get_spectra_number(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_mode()`

Gets a character vector with the spectra mode of each analysis (i.e., profile or centroid).

Usage

MassSpecEngine$get_spectra_mode(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_level()`

Gets a character vector with the spectra levels (e.g., "1, 2") of each analysis.

Usage

MassSpecEngine$get_spectra_level(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_lowest_mz()`

Gets a numeric vector with the lower m/z value of each analysis.

Usage

MassSpecEngine$get_spectra_lowest_mz(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_highest_mz()`

Gets a numeric vector with the higher m/z value of each analysis.

Usage

MassSpecEngine$get_spectra_highest_mz(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_lowest_rt()`

Gets a numeric vector with the start retention time value of each analysis.

Usage

MassSpecEngine$get_spectra_lowest_rt(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_highest_rt()`

Gets a numeric vector with the end retention time value of each analysis.

Usage

MassSpecEngine$get_spectra_highest_rt(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_polarity()`

Gets a character vector with the polarity of each analysis.

Usage

MassSpecEngine$get_spectra_polarity(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_headers()`

Gets a data.table of the spectra headers from each analysis.

Usage

MassSpecEngine$get_spectra_headers(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_spectra_tic()`

Gets a data.table of the total ion chromatogram (TIC) from each analysis.

Usage

MassSpecEngine$get_spectra_tic(analyses = NULL, levels = c(1, 2), rt = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
rt: Numeric (length 2). The retention time range to filter the TIC.

Method `get_spectra_bpc()`

Gets a data.table of the base peak chromatogram (BPC) from each analysis.

Usage

MassSpecEngine$get_spectra_bpc(analyses = NULL, levels = c(1, 2), rt = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
rt: Numeric (length 2). The retention time range to filter the BPC.

Method `get_raw_spectra()`

Gets a data.table of spectra from the analyses based on targets.

Usage

MassSpecEngine$get_raw_spectra(
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
allTraces: Logical, when TRUE all level 2 data is returned. When FALSE and level has 2, only the MS2 traces of MS1 targets are returned, using the isolationWindow to calculate the mass window.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
minIntensityMS1: Numeric value with the minimum intensity of level 1 data (i.e., MS1 data).
minIntensityMS2: Numeric value with the minimum intensity of level 2 data (i.e., MS2 data).

Method `get_spectra_eic()`

Gets a data.table of extract ion chromatograms (EIC) from the analyses based on targets.

Usage

MassSpecEngine$get_spectra_eic(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.

Method `get_spectra_ms1()`

Gets a data.table of level 1 spectra from the analyses based on targets.

Usage

MassSpecEngine$get_spectra_ms1(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 1000
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.

Method `get_spectra_ms2()`

Gets a data.table of level 2 spectra from the analyses based on targets.

Usage

MassSpecEngine$get_spectra_ms2(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  isolationWindow = 1.3,
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 0
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.

Method `plot_spectra_tic()`

Plots the spectra total ion chromatogram (TIC) of each analysis.

Usage

MassSpecEngine$plot_spectra_tic(
  analyses = NULL,
  levels = c(1, 2),
  rt = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  legendNames = NULL,
  downsize = 1,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
downsize: An integer of length one to downsize the TIC plot. The default is 1.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_bpc()`

Plots the spectra base peak chromatogram (BPC) of each analysis.

Usage

MassSpecEngine$plot_spectra_bpc(
  analyses = NULL,
  levels = c(1, 2),
  rt = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  legendNames = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_eic()`

Plots spectra extract ion chromatograms (EIC) from the analyses based on targets.

Usage

MassSpecEngine$plot_spectra_eic(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_xic()`

Plots spectra extract ion chromatograms (EIC) and m/z vs retention time from the analyses.

Usage

MassSpecEngine$plot_spectra_xic(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  legendNames = NULL,
  plotTargetMark = TRUE,
  targetsMark = NULL,
  ppmMark = 5,
  secMark = 10,
  numberRows = 1,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
plotTargetMark: Logical (length 1), set to TRUE to plot a target mark.
targetsMark: A data.frame with columns mz and rt, defining the m/z and retention time values of each target. Note that the number of rows should match with the number of targets.
ppmMark: A numeric vector of length one to define the mass deviation, in ppm, of the target mark. The default is 5 ppm.
secMark: A numeric vector of length one to define the time deviation, in seconds, of the target mark. The default is 10 ppm.
numberRows: An integer vector of length one to define the number of rows to grid the plots. Note that each target is always plotted in one row for all selected analyses.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_ms1()`

Plots level 1 spectra from the analyses based on targets.

Usage

MassSpecEngine$plot_spectra_ms1(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 1000,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  showText = FALSE,
  interactive = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showText: Logical (length 1), set to TRUE to show the text annotations.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `plot_spectra_ms2()`

Plots level 2 spectra from the analyses based on targets.

Usage

MassSpecEngine$plot_spectra_ms2(
  analyses = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  isolationWindow = 1.3,
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 0,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  interactive = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `get_chromatograms_number()`

Gets the number of chromatograms in each analysis.

Usage

MassSpecEngine$get_chromatograms_number(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_chromatograms_headers()`

Gets the chromatograms headers data.table of each analysis.

Usage

MassSpecEngine$get_chromatograms_headers(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_raw_chromatograms()`

Gets a list of chromatograms data.table objects from each analysis.

Usage

MassSpecEngine$get_raw_chromatograms(
  analyses = NULL,
  chromatograms = NULL,
  rtmin = 0,
  rtmax = 0,
  minIntensity = NULL
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
rtmin: Numeric (length 1) with the minimum retention time.
rtmax: Numeric (length 1) with the maximum retention time.
minIntensity: Numeric (length 1) with the minimum intensity.

Method `has_results_nts()`

Checks if there are NonTargetAnalysisResults results, returning TRUE or FALSE.

Usage

MassSpecEngine$has_results_nts()

Method `has_results_spectra()`

Checks if there are spectra, returning TRUE or FALSE.

Usage

MassSpecEngine$has_results_spectra()

Method `has_results_chromatograms()`

Checks if there are chromatograms, returning TRUE or FALSE.

Usage

MassSpecEngine$has_results_chromatograms()

Method `get_chromatograms()`

Gets a list of chromatograms from the Chromatograms results.

Usage

MassSpecEngine$get_chromatograms(
  analyses = NULL,
  chromatograms = NULL,
  rtmin = 0,
  rtmax = 0,
  minIntensity = NULL
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
rtmin: Numeric (length 1) with the minimum retention time.
rtmax: Numeric (length 1) with the maximum retention time.
minIntensity: Numeric (length 1) with the minimum intensity.

Method `get_chromatograms_peaks()`

Gets a data.table of integrated peaks from the Chromatograms results.

Usage

MassSpecEngine$get_chromatograms_peaks(
  analyses = NULL,
  chromatograms = NULL,
  rtmin = 0,
  rtmax = 0,
  minIntensity = NULL
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
rtmin: Numeric (length 1) with the minimum retention time.
rtmax: Numeric (length 1) with the maximum retention time.
minIntensity: Numeric (length 1) with the minimum intensity.

Method `plot_chromatograms()`

Plots chromatograms from the Chromatograms results.

Usage

MassSpecEngine$plot_chromatograms(
  analyses = NULL,
  chromatograms = NULL,
  rtmin = 0,
  rtmax = 0,
  minIntensity = NULL,
  normalized = TRUE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses+targets",
  legendNames = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
rtmin: Numeric (length 1) with the minimum retention time.
rtmax: Numeric (length 1) with the maximum retention time.
minIntensity: Numeric (length 1) with the minimum intensity.
normalized: Logical (length 1). Set to TRUE to normalize the chromatograms.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_chromatograms_baseline()`

Plots baseline correction from the Chromatograms results.

Usage

MassSpecEngine$plot_chromatograms_baseline(
  analyses = NULL,
  chromatograms = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_chromatograms_peaks()`

Plots chromatographic peaks from the Chromatograms results.

Usage

MassSpecEngine$plot_chromatograms_peaks(
  analyses = NULL,
  chromatograms = NULL,
  rtmin = 0,
  rtmax = 0,
  minIntensity = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses+targets",
  legendNames = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
chromatograms: A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
rtmin: Numeric (length 1) with the minimum retention time.
rtmax: Numeric (length 1) with the maximum retention time.
minIntensity: Numeric (length 1) with the minimum intensity.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_spectra()`

Gets a list of data.table object with spectra each analysis.

Usage

MassSpecEngine$get_spectra(
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
allTraces: Logical, when TRUE all level 2 data is returned. When FALSE and level has 2, only the MS2 traces of MS1 targets are returned, using the isolationWindow to calculate the mass window.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
minIntensityMS1: Numeric value with the minimum intensity of level 1 data (i.e., MS1 data).
minIntensityMS2: Numeric value with the minimum intensity of level 2 data (i.e., MS2 data).

Method `plot_spectra()`

Plots spectra.

Usage

MassSpecEngine$plot_spectra(
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "mz",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
allTraces: Logical, when TRUE all level 2 data is returned. When FALSE and level has 2, only the MS2 traces of MS1 targets are returned, using the isolationWindow to calculate the mass window.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
minIntensityMS1: Numeric value with the minimum intensity of level 1 data (i.e., MS1 data).
minIntensityMS2: Numeric value with the minimum intensity of level 2 data (i.e., MS2 data).
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
xVal: Character length one. Possible values are "mz", "rt", "mobility" or "mass".
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_3d()`

Plots spectra in 3D.

Usage

MassSpecEngine$plot_spectra_3d(
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "rt",
  yVal = "mz",
  xLab = NULL,
  yLab = NULL,
  zLab = NULL,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
levels: Integer vector with the levels of MS data.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
id: Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.
allTraces: Logical, when TRUE all level 2 data is returned. When FALSE and level has 2, only the MS2 traces of MS1 targets are returned, using the isolationWindow to calculate the mass window.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
minIntensityMS1: Numeric value with the minimum intensity of level 1 data (i.e., MS1 data).
minIntensityMS2: Numeric value with the minimum intensity of level 2 data (i.e., MS2 data).
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
xVal: Character length one. Possible values are "mz", "rt" or "mobility".
yVal: Character length one. Possible values are "mz", "rt" or "mobility".
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
zLab: A string with the title for the z axis.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_charges()`

Plots charge assignment of deconvoluted spectra from analyses.

Usage

MassSpecEngine$plot_spectra_charges(
  analyses = NULL,
  legendNames = NULL,
  title = NULL,
  colorBy = "analyses",
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_spectra_peaks()`

Gets a data.table with peaks from spectra in each analysis.

Usage

MassSpecEngine$get_spectra_peaks(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `plot_spectra_peaks()`

Plots peaks from spectra in each analysis.

Usage

MassSpecEngine$plot_spectra_peaks(
  analyses = NULL,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "mz",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
xVal: Character length one. Possible values are "mz" or "mobility".
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_baseline()`

Plots spectra baseline correction.

Usage

MassSpecEngine$plot_spectra_baseline(
  analyses = NULL,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "mz",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
xVal: Character length one. Possible values are "mz" or "mobility".
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_spectra_matrix()`

Gets a matrix with spectra from analyses.

Usage

MassSpecEngine$get_spectra_matrix(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_features_count()`

Gets a data.table with the features count from NonTargetAnalysisResults results.

Usage

MassSpecEngine$get_features_count(analyses = NULL, filtered = FALSE)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Method `plot_features_count()`

Plots the features count from NonTargetAnalysisResults results.

Usage

MassSpecEngine$plot_features_count(
  analyses = NULL,
  filtered = FALSE,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  showLegend = TRUE,
  showHoverText = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showLegend: Logical (length 1). Set to TRUE to show legend.
showHoverText: Logical (length 1). Set to TRUE to show hover text.

Method `get_features()`

Gets a data.table with all features from NonTargetAnalysisResults results or as selected by the arguments.

Usage

MassSpecEngine$get_features(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Method `map_features()`

Plots a map of the retention time vs m/z of features from analyses.

Usage

MassSpecEngine$map_features(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  neutral_mass = TRUE,
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "replicates+targets",
  showLegend = TRUE,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
neutral_mass: Logical (length 1). Set to TRUE to use neutral mass.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showLegend: Logical (length 1). Set to TRUE to show legend.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `map_features_intensity()`

Plots a map of the retention time vs m/z of features from analyses.

Usage

MassSpecEngine$map_features_intensity(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "replicates+targets",
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_features_eic()`

Gets a data.table with feature EICs following the targets from the arguments.

Usage

MassSpecEngine$get_features_eic(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtExpand = 0,
  mzExpand = 0,
  filtered = FALSE,
  useLoadedData = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtExpand: Numeric (length 1) with the retention time values (in seconds) for expanding left and right the retention time range.
mzExpand: Numeric (length 1) with the mass or mass-to-charge ratio (m/z) (in Da) for expanding left and right the mass range.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.

Method `plot_features()`

Plots features from analyses.

Usage

MassSpecEngine$plot_features(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtExpand = 120,
  mzExpand = 0.001,
  useLoadedData = TRUE,
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtExpand: Numeric (length 1) with the retention time values (in seconds) for expanding left and right the retention time range.
mzExpand: Numeric (length 1) with the mass or mass-to-charge ratio (m/z) (in Da) for expanding left and right the mass range.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_features_ms1()`

Gets a data.table of averaged MS1 spectrum for features in the analyses or as selected from the arguments.

Usage

MassSpecEngine$get_features_ms1(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtWindow = c(-2, 2),
  mzWindow = c(-5, 100),
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 1000,
  filtered = FALSE,
  useLoadedData = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtWindow: Numeric (length 2) with the retention time values (in seconds) for expanding left and right the retention time range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzWindow: Numeric (length 2) with the mass or mass-to-charge ratio (m/z) values (in Da) for expanding left and right the mass range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.

Method `plot_features_ms1()`

Plots level 1 spectra from features in the analyses.

Usage

MassSpecEngine$plot_features_ms1(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtWindow = c(-2, 2),
  mzWindow = c(-5, 100),
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 1000,
  filtered = FALSE,
  useLoadedData = TRUE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  showText = FALSE,
  interactive = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtWindow: Numeric (length 2) with the retention time values (in seconds) for expanding left and right the retention time range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzWindow: Numeric (length 2) with the mass or mass-to-charge ratio (m/z) values (in Da) for expanding left and right the mass range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showText: Logical (length 1), set to TRUE to show the text annotations.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `get_features_ms2()`

Gets a data.table of averaged MS2 spectrum for features in the analyses or as selected from the arguments.

Usage

MassSpecEngine$get_features_ms2(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  isolationWindow = 1.3,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 0,
  filtered = FALSE,
  useLoadedData = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.

Method `plot_features_ms2()`

Plots level 2 spectra from features in the analyses.

Usage

MassSpecEngine$plot_features_ms2(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  isolationWindow = 1.3,
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 0,
  filtered = FALSE,
  useLoadedData = TRUE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  showText = TRUE,
  interactive = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showText: Logical (length 1), set to TRUE to show the text annotations.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `get_groups()`

Gets a data.table with feature groups from the analyses.

Usage

MassSpecEngine$get_groups(
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE,
  intensities = TRUE,
  average = FALSE,
  sdValues = FALSE,
  metadata = FALSE,
  correctIntensity = FALSE
)

Arguments

groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
intensities: Logical (length 1). When TRUE, feature intensity values are returned.
average: Logical (length 1). When TRUE, feature intensities from each group are averaged and returned for each analysis replicate group.
sdValues: Logical (length 1). Set to TRUE for returning the sd values when averaging the intensity within analysis replicates.
metadata: Logical (length 1). Set to TRUE for returning extra metadata from feature groups (e.g., presence in each analysis replicate and mass and time widths).
correctIntensity: Logical (length 1) with TRUE for correcting the intensity for matrix suppression before applying intensity based filters. Note that suppression factor as obtained by the processing method CorrectMatrixSuppression must be present. When not available the correction is ignored even if set to TRUE.

Method `plot_groups()`

Plots feature groups EIC.

Usage

MassSpecEngine$plot_groups(
  analyses = NULL,
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtExpand = 15,
  mzExpand = 0.001,
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtExpand: Numeric (length 1) with the retention time values (in seconds) for expanding left and right the retention time range.
mzExpand: Numeric (length 1) with the mass or mass-to-charge ratio (m/z) (in Da) for expanding left and right the mass range.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_groups_overview()`

Method to give an overview of the EIC, alignment and intensity variance from features within target feature groups.

Usage

MassSpecEngine$plot_groups_overview(
  analyses = NULL,
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtExpand = 120,
  mzExpand = 0.005,
  useLoadedData = TRUE,
  correctIntensity = TRUE,
  filtered = FALSE,
  legendNames = NULL,
  title = NULL,
  heights = c(0.35, 0.5, 0.15),
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtExpand: Numeric (length 1) with the retention time values (in seconds) for expanding left and right the retention time range.
mzExpand: Numeric (length 1) with the mass or mass-to-charge ratio (m/z) (in Da) for expanding left and right the mass range.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
correctIntensity: Logical (length 1). When TRUE and suppression factor is available the intensities are corrected for suppression.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
title: A string with the title.
heights: A numeric vector of length 3 to control the height of the first, second and third plot, respectively.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_groups_profile()`

Method to plot the intensity profile of feature groups across the analyses.

Usage

MassSpecEngine$plot_groups_profile(
  analyses = NULL,
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE,
  correctIntensity = TRUE,
  averaged = FALSE,
  normalized = TRUE,
  legendNames = NULL,
  yLab = NULL,
  title = NULL,
  showLegend = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
correctIntensity: Logical (length 1) with TRUE for correcting the intensity for matrix suppression before applying intensity based filters. Note that suppression factor as obtained by the processing method CorrectMatrixSuppression must be present. When not available the correction is ignored even if set to TRUE.
averaged: Logical (length 1). When TRUE the profile intensities are averaged.
normalized: Logical (length 1). When TRUE the profile intensities are normalized.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
yLab: A string with the title for the y axis.
title: A string with the title.
showLegend: Logical (length 1). Set to TRUE to show legend.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_groups_ms1()`

Gets a data.table of averaged MS1 spectrum for feature groups in the analyses.

Usage

MassSpecEngine$get_groups_ms1(
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtWindow = c(-2, 2),
  mzWindow = c(-5, 90),
  mzClustFeatures = 0.003,
  presenceFeatures = 0.8,
  minIntensityFeatures = 1000,
  useLoadedData = TRUE,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 1000,
  groupBy = "groups",
  filtered = FALSE
)

Arguments

groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtWindow: Numeric (length 2) with the retention time values (in seconds) for expanding left and right the retention time range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzWindow: Numeric (length 2) with the mass or mass-to-charge ratio (m/z) values (in Da) for expanding left and right the mass range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzClustFeatures: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces for features. Highly dependent on the mass resolution of the MS data.
presenceFeatures: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensityFeatures: Numeric (length 1) with the minimum intensity for features.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
groupBy: String with the way of grouping. Possible values are groups and replicates to group by feature groups or feature groups and replicates, respectively.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Method `plot_groups_ms1()`

Plots level 1 spectra from feature groups in the analyses.

Usage

MassSpecEngine$plot_groups_ms1(
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  rtWindow = c(-2, 2),
  mzWindow = c(-5, 90),
  mzClustFeatures = 0.005,
  presenceFeatures = 0.8,
  minIntensityFeatures = 1000,
  useLoadedData = TRUE,
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 1000,
  groupBy = "groups",
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  showText = FALSE,
  interactive = TRUE
)

Arguments

groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
rtWindow: Numeric (length 2) with the retention time values (in seconds) for expanding left and right the retention time range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzWindow: Numeric (length 2) with the mass or mass-to-charge ratio (m/z) values (in Da) for expanding left and right the mass range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.
mzClustFeatures: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces for features. Highly dependent on the mass resolution of the MS data.
presenceFeatures: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensityFeatures: Numeric (length 1) with the minimum intensity for features.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
groupBy: String with the way of grouping. Possible values are groups and replicates to group by feature groups or feature groups and replicates, respectively.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showText: Logical (length 1), set to TRUE to show the text annotations.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `get_groups_ms2()`

Gets a data.table of averaged MS2 spectrum for feature groups in the analyses.

Usage

MassSpecEngine$get_groups_ms2(
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  isolationWindow = 1.3,
  mzClustFeatures = 0.003,
  presenceFeatures = 0.8,
  minIntensityFeatures = 100,
  useLoadedData = TRUE,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 100,
  groupBy = "groups",
  filtered = FALSE
)

Arguments

groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClustFeatures: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces for features. Highly dependent on the mass resolution of the MS data.
presenceFeatures: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensityFeatures: Numeric (length 1) with the minimum intensity for features.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
groupBy: String with the way of grouping. Possible values are groups and replicates to group by feature groups or feature groups and replicates, respectively.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Method `plot_groups_ms2()`

Plots level 1 spectra from feature groups in the analyses.

Usage

MassSpecEngine$plot_groups_ms2(
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  isolationWindow = 1.3,
  mzClustFeatures = 0.003,
  presenceFeatures = 0.8,
  minIntensityFeatures = 100,
  useLoadedData = TRUE,
  mzClust = 0.003,
  presence = TRUE,
  minIntensity = 100,
  groupBy = "groups",
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  showText = TRUE,
  interactive = TRUE
)

Arguments

groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClustFeatures: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces for features. Highly dependent on the mass resolution of the MS data.
presenceFeatures: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensityFeatures: Numeric (length 1) with the minimum intensity for features.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
groupBy: String with the way of grouping. Possible values are groups and replicates to group by feature groups or feature groups and replicates, respectively.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
showText: Logical (length 1), set to TRUE to show the text annotations.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Method `get_components()`

Gets feature components (i.e., isotope and adduct related to a main feature) in the analyses.

Usage

MassSpecEngine$get_components(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Method `map_components()`

Maps feature components in the analyses.

Usage

MassSpecEngine$map_components(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE,
  legendNames = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "targets",
  interactive = TRUE,
  showLegend = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
showLegend: Logical (length 1). Set to TRUE to show legend.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_suspects()`

Gets a data.table of suspects from features according to a defined database and mass (ppm) and time (sec) deviations.

Usage

MassSpecEngine$get_suspects(
  analyses = NULL,
  database = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 5,
  sec = 10,
  millisec = 5,
  ppmMS2 = 10,
  mzrMS2 = 0.008,
  minCusiness = 0.7,
  minFragments = 3,
  filtered = FALSE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
database: A data.frame with at least the columns name and mass, indicating the name and neutral monoisotopic mass of the suspect targets.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
ppmMS2: Numeric (length 1) with the mass deviation for MS2, in ppm.
mzrMS2: Numeric (length 1). The m/z resolution for MS2 spectra.
minCusiness: Numeric (length 1). The minimum Cusiness value for the suspects.
minFragments: Integer (length 1) with the minimum number of fragments.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Details

The ppm and sec which indicate the mass (im ppm) and time (in seconds) deviations applied during the screening.

Method `plot_suspects()`

Plots suspects.

Usage

MassSpecEngine$plot_suspects(
  analyses = NULL,
  database = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 5,
  sec = 10,
  millisec = 5,
  ppmMS2 = 10,
  mzrMS2 = 0.008,
  minCusiness = 0.7,
  minFragments = 3,
  filtered = FALSE,
  rtExpand = 120,
  mzExpand = 0.005,
  useLoadedData = TRUE,
  legendNames = NULL,
  colorBy = "replicates+targets",
  heights = c(0.5, 0.5),
  interactive = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
database: A data.frame with at least the columns name and mass, indicating the name and neutral monoisotopic mass of the suspect targets.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
ppmMS2: Numeric (length 1) with the mass deviation for MS2, in ppm.
mzrMS2: Numeric (length 1). The m/z resolution for MS2 spectra.
minCusiness: Numeric (length 1). The minimum Cusiness value for the suspects.
minFragments: Integer (length 1) with the minimum number of fragments.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
rtExpand: Numeric (length 1) with the retention time values (in seconds) for expanding left and right the retention time range.
mzExpand: Numeric (length 1) with the mass or mass-to-charge ratio (m/z) (in Da) for expanding left and right the mass range.
useLoadedData: Logical of length one. Set to TRUE for using loaded data not raw data from files.
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
colorBy: Character (length 1). One of analyses (the default), polarities, levels, targets or replicates. Mixed use (e.g. analyses+polarities) is also possible.
heights: A numeric vector of length 2 to control the height of the first and second plot, respectively.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.

Details

The ppm and sec which indicate the mass (im ppm) and time (in seconds) deviations applied during the screening.

Method `get_internal_standards()`

Gets a data.table with internal standards found by the FindInternalStandards processing method.

Usage

MassSpecEngine$get_internal_standards(average = TRUE)

Arguments

average: Logical of length one. When TRUE and groups are present, internal standards are averaged per analysis replicate group.

Method `plot_internal_standards()`

Plots the quality control assessment of the internal standards.

Usage

MassSpecEngine$plot_internal_standards(
  analyses = NULL,
  presence = TRUE,
  recovery = TRUE,
  deviations = TRUE,
  widths = TRUE,
  renderEngine = "webgl"
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
presence: Logical (length 1). When TRUE the presence of the internal standards is plotted.
recovery: Logical (length 1). When TRUE the recovery of the internal standards is plotted.
deviations: Logical (length 1). When TRUE the deviations of the internal standards is plotted.
widths: Logical (length 1). When TRUE the widths of the internal standards is plotted.
renderEngine: The engine to render the data. The default is "webgl".

Method `get_fold_change()`

Gets a data.table with fold-change analysis between the replicatesIn and replicatesOut.

Usage

MassSpecEngine$get_fold_change(
  replicatesIn = NULL,
  replicatesOut = NULL,
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 4,
  sec = 10,
  millisec = 5,
  filtered = FALSE,
  constantThreshold = 0.5,
  eliminationThreshold = 0.2,
  correctIntensity = FALSE,
  fillZerosWithLowerLimit = FALSE,
  lowerLimit = NA_real_
)

Arguments

replicatesIn: Character vector with the names of the replicates to be considered as the denominator.
replicatesOut: Character vector with the names of the replicates to be considered as the numerator.
groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
constantThreshold: Numeric of length one. The threshold to consider a feature as constant.
eliminationThreshold: Numeric of length one. The threshold to consider a feature as eliminated.
correctIntensity: Logical of length one. When TRUE the suppression factor (when available) is used to correct the intensity before fold-change analysis.
fillZerosWithLowerLimit: Logical of length one. When TRUE the zero values are filled with the lower limit.
lowerLimit: Numeric of length one. The lower limit to fill the zero values.

Method `plot_fold_change()`

Plots the fold-change analysis between the replicatesIn and replicatesOut.

Usage

MassSpecEngine$plot_fold_change(
  replicatesIn = NULL,
  replicatesOut = NULL,
  groups = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 4,
  sec = 10,
  millisec = 5,
  filtered = FALSE,
  constantThreshold = 0.5,
  eliminationThreshold = 0.2,
  correctIntensity = FALSE,
  fillZerosWithLowerLimit = FALSE,
  lowerLimit = NA_real_,
  normalized = TRUE,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  showLegend = TRUE
)

Arguments

replicatesIn: Character vector with the names of the replicates to be considered as the denominator.
replicatesOut: Character vector with the names of the replicates to be considered as the numerator.
groups: A numeric or character vector with the number or ID of feature groups, respectively.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
constantThreshold: Numeric of length one. The threshold to consider a feature as constant.
eliminationThreshold: Numeric of length one. The threshold to consider a feature as eliminated.
correctIntensity: Logical of length one. When TRUE the suppression factor (when available) is used to correct the intensity before fold-change analysis.
fillZerosWithLowerLimit: Logical of length one. When TRUE the zero values are filled with the lower limit.
lowerLimit: Numeric of length one. The lower limit to fill the zero values.
normalized: Logical of length one. When TRUE the fold-change values are normalized.
yLab: A string with the title for the y axis.
title: A string with the title.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
showLegend: Logical (length 1). Set to TRUE to show legend.

Method `get_compounds()`

Gets a data.table with compounds from the analyses.

Usage

MassSpecEngine$get_compounds(
  analyses = NULL,
  features = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  filtered = FALSE,
  averaged = TRUE
)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
features: A character vector with the feature IDs or a data.frame or data.table with a column named feature with the feature IDs. A column named analysis can be given to specify from which analyses the features matched.
mass: A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
mz: A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.
rt: A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
mobility: A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
millisec: Numeric of length one with the drift time deviation, in milliseconds.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
averaged: Logical of length one. When TRUE the compounds are averaged per analysis replicate group.

Method `get_patRoon_features()`

Creates an S4 class features or featureGroupsfrom the patRoon package.

Usage

MassSpecEngine$get_patRoon_features(filtered = FALSE, featureGroups = TRUE)

Arguments

filtered: Logical (length 1). When TRUE, filtered features/groups are considered.
featureGroups: Logical of length one. When TRUE the featureGroups class is returned.

Method `get_patRoon_MSPeakLists()`

Creates S4 class MSPeakLists. Note that feature groups are required. The MS and MSMS spectra of each feature are then average by patRoon to produce the feature group spectra using the parameters of the function getDefAvgPListParams.

Usage

MassSpecEngine$get_patRoon_MSPeakLists(
  clusterMzWindow = 0.005,
  topMost = 100,
  minIntensityPre = 50,
  minIntensityPost = 50,
  avgFun = "mean",
  method = "distance"
)

Arguments

clusterMzWindow: m/z window (in Da) used for clustering m/z values when spectra are averaged. For method="hclust" this corresponds to the cluster height, while for method="distance" this value is used to find nearby masses (+/- window). Too small windows will prevent clustering m/z values (thus erroneously treating equal masses along spectra as different), whereas too big windows may cluster unrelated m/z values from different or even the same spectrum together.
topMost: Only retain this maximum number of MS peaks when generating averaged spectra. Lowering this number may exclude more irrelevant (noisy) MS peaks and decrease processing time, whereas higher values may avoid excluding lower intense MS peaks that may still be of interest.
minIntensityPre: MS peaks with intensities below this value will be removed (applied prior to selection by topMost) before averaging.
minIntensityPost: MS peaks with intensities below this value will be removed after averaging.
avgFun: Function that is used to calculate average m/z values.
method: Method used for producing averaged MS spectra. Valid values are "hclust", used for hierarchical clustering (using the fastcluster package), and "distance", to use the between peak distance. The latter method may reduces processing time and memory requirements, at the potential cost of reduced accuracy.

Method `clone()`

The objects of this class are cloneable with this method.

Usage

MassSpecEngine$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Details

References

See also

Super class

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method add_analyses()

Usage

Arguments

Method remove_analyses()

Usage

Arguments

Method add_replicate_names()

Usage

Arguments

Method add_blank_names()

Usage

Arguments

Method get_analysis_names()

Usage

Arguments

Method get_replicate_names()

Usage

Arguments

Method get_blank_names()

Usage

Arguments

Method get_files()

Usage

Arguments

Method get_formats()

Usage

Arguments

Method get_instruments()

Usage

Arguments

Method get_software()

Usage

Arguments

Method get_spectra_number()

Usage

Arguments

Method get_spectra_mode()

Usage

Arguments

Method get_spectra_level()

Usage

Arguments

Method get_spectra_lowest_mz()

Usage

Arguments

Method get_spectra_highest_mz()

Usage

Arguments

Method get_spectra_lowest_rt()

Usage

Arguments

Method get_spectra_highest_rt()

Usage

Arguments

Method get_spectra_polarity()

Usage

Arguments

Method get_spectra_headers()

Usage

Arguments

Method get_spectra_tic()

Usage

Arguments

Method get_spectra_bpc()

Usage

Arguments

Method get_raw_spectra()

Usage

Method `new()`

Method `add_analyses()`

Method `remove_analyses()`

Method `add_replicate_names()`

Method `add_blank_names()`

Method `get_analysis_names()`

Method `get_replicate_names()`

Method `get_blank_names()`

Method `get_files()`

Method `get_formats()`

Method `get_instruments()`

Method `get_software()`

Method `get_spectra_number()`

Method `get_spectra_mode()`

Method `get_spectra_level()`

Method `get_spectra_lowest_mz()`

Method `get_spectra_highest_mz()`

Method `get_spectra_lowest_rt()`

Method `get_spectra_highest_rt()`

Method `get_spectra_polarity()`

Method `get_spectra_headers()`

Method `get_spectra_tic()`

Method `get_spectra_bpc()`

Method `get_raw_spectra()`

Method `get_spectra_eic()`

Method `get_spectra_ms1()`

Method `get_spectra_ms2()`

Method `plot_spectra_tic()`

Method `plot_spectra_bpc()`

Method `plot_spectra_eic()`

Method `plot_spectra_xic()`

Method `plot_spectra_ms1()`

Method `plot_spectra_ms2()`

Method `get_chromatograms_number()`

Method `get_chromatograms_headers()`

Method `get_raw_chromatograms()`

Method `has_results_nts()`

Method `has_results_spectra()`

Method `has_results_chromatograms()`

Method `get_chromatograms()`

Method `get_chromatograms_peaks()`

Method `plot_chromatograms()`

Method `plot_chromatograms_baseline()`

Method `plot_chromatograms_peaks()`

Method `get_spectra()`

Method `plot_spectra()`

Method `plot_spectra_3d()`

Method `plot_spectra_charges()`