The MassSpecEngine R6 class is a framework for parsing, processing, inspecting and storing mass spectrometry (MS) data. The MassSpecEngine is using patRoon for assembly of Non-Target Screening 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 .
Kapoulkine A (2022). “pugixml 1.13: Light-weight, simple and fast XML parser for C++ with XPath support.” Copyright (C) 2006-2018. http://pugixml.org.
Super class
StreamFind::CoreEngine
-> MassSpecEngine
Public fields
help
(
list()
)
List of function elements to access specific reference help pages.
Active bindings
analysisInfo
The analysisInfo data.frame with the list of analyses.
features
The features S4 class object from patRoon.
filtered_features
The filtered features as list of data.table objects for each analysis.
feature_list
List of features data.table objects for each analysis.
featureGroups
The featureGroups S4 class object from patRoon.
MSPeakLists
The MSPeakLists S4 class object from patRoon.
formulas
The formulas S4 class object from patRoon.
compounds
The compounds S4 class object from patRoon.
chromatograms
data.table
with processed chromatograms for each analyses.chromatograms_peaks
data.table
with integrated peaks from chromatograms for each analyses.spectra
List of spectra
data.table
objects for each analysis.spectra_charges
data.table
with charges assigned to spectra for each analyses.deconvoluted_spectra
List of deconvoluted spectra for each analysis.
spectra_peaks
data.table
with integrated spectra peaks for each analysis.
Methods
Inherited methods
StreamFind::CoreEngine$add_blank_names()
StreamFind::CoreEngine$add_headers()
StreamFind::CoreEngine$add_metadata()
StreamFind::CoreEngine$add_replicate_names()
StreamFind::CoreEngine$add_settings()
StreamFind::CoreEngine$export()
StreamFind::CoreEngine$export_analyses()
StreamFind::CoreEngine$export_headers()
StreamFind::CoreEngine$export_settings()
StreamFind::CoreEngine$get_analyses()
StreamFind::CoreEngine$get_analysis_names()
StreamFind::CoreEngine$get_blank_names()
StreamFind::CoreEngine$get_files()
StreamFind::CoreEngine$get_formats()
StreamFind::CoreEngine$get_headers()
StreamFind::CoreEngine$get_history()
StreamFind::CoreEngine$get_number_analyses()
StreamFind::CoreEngine$get_replicate_names()
StreamFind::CoreEngine$get_results()
StreamFind::CoreEngine$get_results_names()
StreamFind::CoreEngine$get_settings()
StreamFind::CoreEngine$get_settings_names()
StreamFind::CoreEngine$get_types()
StreamFind::CoreEngine$get_workflow_overview()
StreamFind::CoreEngine$has_analyses()
StreamFind::CoreEngine$has_results()
StreamFind::CoreEngine$has_settings()
StreamFind::CoreEngine$import()
StreamFind::CoreEngine$import_analyses()
StreamFind::CoreEngine$import_headers()
StreamFind::CoreEngine$import_settings()
StreamFind::CoreEngine$load()
StreamFind::CoreEngine$print()
StreamFind::CoreEngine$print_analyses()
StreamFind::CoreEngine$print_headers()
StreamFind::CoreEngine$print_results()
StreamFind::CoreEngine$print_workflow()
StreamFind::CoreEngine$process()
StreamFind::CoreEngine$remove_headers()
StreamFind::CoreEngine$remove_results()
StreamFind::CoreEngine$remove_settings()
StreamFind::CoreEngine$run_app()
StreamFind::CoreEngine$run_workflow()
StreamFind::CoreEngine$save()
Method new()
Creates an R6 MassSpecEngine class object.
Usage
MassSpecEngine$new(
files = NULL,
headers = NULL,
settings = NULL,
analyses = NULL,
results = NULL
)
Arguments
files
A character vector with full file path/s of mzML or mzXML file/s or a data.frame with the columns file, replicate and blank with the full file path of mzML or mzXML file/s (character), the replicate group name (character) and the associated blank replicate group name (character). Note the file paths must have the extension .mzML or .mzXML.
headers
A named list with headers or a ProjectHeaders S3 class object. Each list element must have length one. There is no type restrictions except for name (must be type character length 1), author (must be type character length 1), file (must be type character length 1) and date (must be class POSIXct or class POSIXt length 1). See more information in
?ProjectHeaders
.settings
A named list of ProcessingSettings objects or a single ProcessingSettings object. The list names should match the call name of each ProcessingSettings object. Alternatively, a named list with call name, algorithm and parameters to be transformed and added as ProcessingSettings object.
analyses
A MassSpecAnalysis S3 class object or a list with MassSpecAnalysis S3 class objects as elements. (see
?MassSpecAnalysis
for more information).results
A named list of objects from processing methods.
Method get_spectra_tic()
Gets the total ion chromatogram (TIC) of each analysis.
Usage
MassSpecEngine$get_spectra_tic(analyses = NULL, levels = c(1, 2), rt = NULL)
Method get_spectra_bpc()
Gets the base peak chromatogram (BPC) of each analysis.
Usage
MassSpecEngine$get_spectra_bpc(analyses = NULL, levels = c(1, 2), rt = NULL)
Method get_spectra()
Gets spectra from each analysis.
Usage
MassSpecEngine$get_spectra(
analyses = NULL,
levels = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
allTraces = TRUE,
isolationWindow = 1.3,
minIntensityMS1 = 0,
minIntensityMS2 = 0,
raw_spectra = FALSE,
loaded_spectra = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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. WhenFALSE
and level has 2, only the MS2 traces of MS1 targets are returned, using theisolationWindow
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).
raw_spectra
Logical of length one. Set to
TRUE
for parsing raw spectra not spectra results/processed.loaded_spectra
Logical of length one. Set to
TRUE
for parsing loaded spectra not raw data files.
Method get_spectra_eic()
Gets spectra extract ion chromatograms (EIC) from the analyses based on targets as a data.table.
Usage
MassSpecEngine$get_spectra_eic(
analyses = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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 level 1 spectra from the analyses based on targets as a data.frame.
Usage
MassSpecEngine$get_spectra_ms1(
analyses = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
mzClust = 0.003,
presence = 0.8,
minIntensity = 1000
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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 level 2 spectra from the analyses based on targets as a data.frame.
Usage
MassSpecEngine$get_spectra_ms2(
analyses = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
isolationWindow = 1.3,
mzClust = 0.005,
presence = 0.8,
minIntensity = 0
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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 get_chromatograms()
Gets chromatograms from each analysis.
Usage
MassSpecEngine$get_chromatograms(
analyses = NULL,
chromatograms = NULL,
minIntensity = NULL,
raw_chromatograms = FALSE,
loaded_chromatograms = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
chromatograms
A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
minIntensity
Numeric (length 1) with the minimum intensity.
raw_chromatograms
Logical of length one. Set to
TRUE
for parsing raw chromatograms not chromatograms results/processed.loaded_chromatograms
Logical of length one. Set to
TRUE
for parsing loaded chromatograms not chromatograms from raw data files.
Method get_feature_list()
Gets the list of features for each analysis.
Method get_features()
Gets a data.table with all features in analyses or as selected by the arguments.
Usage
MassSpecEngine$get_features(
analyses = NULL,
features = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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 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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtExpand = 120,
mzExpand = NULL,
filtered = FALSE,
loaded = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.
Method get_features_ms1()
Gets a data.table of averaged MS1 spectrum for features in the analyses or as selected from the arguments.
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
isolationWindow = 1.3,
mzClust = 0.003,
presence = 0.8,
minIntensity = 0,
filtered = FALSE,
loaded = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE,
intensities = TRUE,
average = FALSE,
sdValues = FALSE,
metadata = 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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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).
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtWindow = c(-2, 2),
mzWindow = c(-5, 90),
mzClustFeatures = 0.003,
presenceFeatures = 0.8,
minIntensityFeatures = 1000,
loaded = 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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw 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.
groupBy
String with the way of grouping. Possible values are
groups
andreplicates
to group by feature groups or feature groups and replicates, respectively.filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
isolationWindow = 1.3,
mzClustFeatures = 0.003,
presenceFeatures = 0.8,
minIntensityFeatures = 100,
loaded = 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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw 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.
groupBy
String with the way of grouping. Possible values are
groups
andreplicates
to group by feature groups or feature groups and replicates, respectively.filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.
Method get_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_MSPeakLists(
useLoaded = TRUE,
maxMSRtWindow = 10,
precursorMzWindow = 4,
clusterMzWindow = 0.005,
topMost = 100,
minIntensityPre = 10,
minIntensityPost = 10,
avgFun = mean,
method = "distance",
retainPrecursorMSMS = TRUE
)
Arguments
useLoaded
Logical of length one. When
TRUE
and both MS1 and MS2 are loaded to features, these are used otherwise the native functiongenerateMSPeakLists
from patRoon is used instead.maxMSRtWindow
Maximum chromatographic peak window used for spectrum averaging (in seconds, +/- retention time). If NULL all spectra from a feature will be taken into account. Lower to decrease processing time.
precursorMzWindow
The m/z window (in Da) to find MS/MS spectra of a precursor. This is typically used for Data-Dependent like MS/MS data and should correspond to the isolation m/z window (i.e. +/- the precursor m/z) that was used to collect the data. For Data-Independent MS/MS experiments, where precursor ions are not isolated prior to fragmentation (e.g. bbCID, MSe, all-ion, ...) the value should be NULL.
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.
retainPrecursorMSMS
For MS/MS data only: if TRUE then always retain the precursor mass peak even if is not among the
topMost
peaks. Note that MS precursor mass peaks are always kept. Furthermore, note that precursor peaks in both MS and MS/MS data may still be removed by intensity thresholds (this is unlike the filter method function).pruneMissingPrecursorMS
For MS data only: if TRUE then peak lists without a precursor peak are removed. Note that even when this is set to FALSE, functionality that relies on MS (not MS/MS) peak lists (e.g. formulae calculation) will still skip calculation if a precursor is not found.
Method get_isotopes()
Gets a data.table of feature isotopes (i.e., isotope clusters) in the analyses.
Usage
MassSpecEngine$get_isotopes(
analyses = NULL,
groups = NULL,
features = NULL,
clusters = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
groups
A numeric or character vector with the number or ID of feature groups, respectively.
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 namedanalysis
can be given to specify from which analyses the features matched.clusters
A numeric vector with the number/s of feature cluster/s.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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 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,
drift = NULL,
ppm = 5,
sec = 10,
millisec = 5,
ppmMS2 = 10,
minFragments = 3,
isolationWindow = 1.3,
mzClust = 0.003,
presence = 0.8,
minIntensity = 0,
filtered = FALSE,
onGroups = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
minFragments
Integer (length 1) with the minimum number of fragments.
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.onGroups
Logical (length 1). When
TRUE
results are return based on feature groups not individual features.
Method get_internal_standards()
Gets a data.table with internal standards found by the find_internal_standards
module.
Method add_analyses()
Adds analyses. Note that when adding new analyses, any existing results are removed.
Arguments
analyses
A MassSpecAnalysis S3 class object or a list with MassSpecAnalysis S3 class objects as elements (see
?MassSpecAnalysis
for more information).
Method add_files()
Adds analyses based on mzML/mzXML files. Note that when adding new mzML/mzXML files, any existing grouping or features are removed.
Arguments
files
A character vector with full file path/s of mzML or mzXML file/s or a data.frame with the columns file, replicate and blank with the full file path of mzML or mzXML file/s (character), the replicate group name (character) and the associated blank replicate group name (character). Note the file paths must have the extension .mzML or .mzXML.
Method load_spectra()
Loads all spectra from all analyses.
Usage
MassSpecEngine$load_spectra(
analyses = NULL,
levels = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
allTraces = TRUE,
isolationWindow = 1.3,
minIntensityMS1 = 0,
minIntensityMS2 = 0
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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. WhenFALSE
and level has 2, only the MS2 traces of MS1 targets are returned, using theisolationWindow
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 load_chromatograms()
Loads all chromatograms from all analyses.
Method remove_features()
Removes features. Note that feature groups are also removed when features is set to NULL
Arguments
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 namedanalysis
can be given to specify from which analyses the features matched.filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.
Method remove_features_ms1()
Removes loaded MS1 spectra from features in the analyses. In practice, the column ms1 in the features data.table of each analysis object is removed.
Method remove_features_ms2()
Removes loaded MS2 spectra from features in the analyses. In practice, the column ms2 in the features data.table of each analysis object is removed.
Method remove_groups()
Removes feature groups.
Method subset_features()
Subsets a MassSpecEngine object on features from analyses.
Method subset_groups()
Subsets a MassSpecEngine object on feature groups. Note that when sub-setting groups, features that lose correspondence are removed.
Method has_ion_mobility()
Checks if analyses have have drift time from ion mobility, returning TRUE
or FALSE
for
each analysis.
Method has_loaded_spectra()
Checks for loaded spectra in given analyses names/indices, returning TRUE
or FALSE
for each
analysis.
Method has_loaded_chromatograms()
Checks for loaded chromatograms in given analyses names/indices, returning TRUE
or FALSE
for
each analysis.
Method has_groups()
Checks if there are feature groups from grouping features across analyses, returning TRUE
or FALSE
.
Method has_loaded_features_ms1()
Checks for loaded features MS1 in given analyses names/indices, returning TRUE
or FALSE
.
Method has_loaded_features_ms2()
Checks for loaded features MS2 in given analyses names/indices, returning TRUE
or FALSE
.
Method has_features_eic()
Checks for presence of feature extracted ion chromatograms (EICs) in given analyses names/indices,
returning TRUE
or FALSE
.
Method has_suspects()
Checks for presence of suspects in given analyses names/indices, returning TRUE
or FALSE
.
Method has_formulas()
Checks if there are formulas assigned to feature groups, returning TRUE
or FALSE
.
Method has_compounds()
Checks if there are compounds assigned to feature groups, returning TRUE
or FALSE
.
Method has_chromatograms_peaks()
Checks if there are integrated peaks from chromatograms, returning TRUE
or FALSE
.
Method has_deconvoluted_spectra()
Checks if there are deconvoluted spectra, returning TRUE
or FALSE
.
Method has_spectra_charges()
Checks if there are charges assigned to spectra, returning TRUE
or FALSE
.
Method plot_raw_spectra()
Plots raw spectra in 3D for given MS analyses.
Usage
MassSpecEngine$plot_raw_spectra(
analyses = NULL,
levels = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = 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
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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. WhenFALSE
and level has 2, only the MS2 traces of MS1 targets are returned, using theisolationWindow
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.xVal
Character length one. Possible values are "mz", "rt" or "drift".
yVal
Character length one. Possible values are "mz", "rt" or "drift".
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.
Method plot_spectra()
Plots spectra given MS analyses.
Usage
MassSpecEngine$plot_spectra(
analyses = NULL,
levels = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
allTraces = TRUE,
isolationWindow = 1.3,
minIntensityMS1 = 0,
minIntensityMS2 = 0,
raw_spectra = FALSE,
loaded_spectra = TRUE,
averaged = TRUE,
baseline = FALSE,
legendNames = TRUE,
colorBy = "analyses",
xVal = "mz",
xLab = NULL,
yLab = NULL,
title = NULL,
cex = 0.6,
showLegend = TRUE,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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. WhenFALSE
and level has 2, only the MS2 traces of MS1 targets are returned, using theisolationWindow
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).
raw_spectra
Logical of length one. Set to
TRUE
for plotting the spectra in results not the raw spectra.loaded_spectra
Logical of length one. Set to
TRUE
for parsing loaded spectra not spectra from raw data files.averaged
Logical of length one. Set to
TRUE
for plotting the averaged spectra.baseline
Logical of length one. Set to
TRUE
for plotting the spectra with baseline corrected.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.xVal
Character length one. Possible values are "mz", "rt", "drift" 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.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
showLegend
Logical (length 1). Set to
TRUE
to show legend.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_chromatograms()
Plots chromatograms in the analyses.
Usage
MassSpecEngine$plot_chromatograms(
analyses = NULL,
chromatograms = NULL,
minIntensity = NULL,
raw_chromatograms = FALSE,
loaded_chromatograms = TRUE,
title = NULL,
colorBy = "targets",
legendNames = NULL,
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
chromatograms
A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
minIntensity
Numeric (length 1) with the minimum intensity.
raw_chromatograms
Logical of length one. Set to
TRUE
for parsing raw chromatograms not chromatograms results/processed.loaded_chromatograms
Logical of length one. Set to
TRUE
for parsing loaded chromatograms not chromatograms from raw data files.title
A string with the title.
colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_chromatograms_baseline()
Plots chromatograms corrected baseline for given analyses.
Usage
MassSpecEngine$plot_chromatograms_baseline(
analyses = NULL,
chromatograms = NULL,
xLab = NULL,
yLab = NULL,
title = NULL,
cex = 0.6,
showLegend = TRUE,
colorBy = "analyses",
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
showLegend
Logical (length 1). Set to
TRUE
to show legend.colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
legendNames = NULL,
plotTargetMark = TRUE,
targetsMark = NULL,
ppmMark = 5,
secMark = 10,
numberRows = 1
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
andrt
, 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.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_spectra_tic()
Plots the spectra total ion chromatogram (TIC) of each analysis.
Usage
MassSpecEngine$plot_spectra_tic(
analyses = NULL,
levels = c(1, 2),
rt = NULL,
title = NULL,
colorBy = "analyses",
legendNames = NULL,
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
levels
Integer vector with the levels of MS data.
rt
A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).
title
A string with the title.
colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_spectra_bpc()
Plots the spectra base peak chromatogram (BPC) of each analysis.
Usage
MassSpecEngine$plot_spectra_bpc(
analyses = NULL,
levels = c(1, 2),
rt = NULL,
title = NULL,
colorBy = "analyses",
legendNames = NULL,
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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).
title
A string with the title.
colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
isolationWindow = 1.3,
mzClust = 0.005,
presence = 0.8,
minIntensity = 0,
legendNames = NULL,
title = NULL,
colorBy = "targets",
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
id = NULL,
mzClust = 0.003,
presence = 0.8,
minIntensity = 1000,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showText = FALSE,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
orreplicates
. 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_features()
Plots features from analyses.
Usage
MassSpecEngine$plot_features(
analyses = NULL,
features = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtExpand = 120,
mzExpand = NULL,
loaded = TRUE,
filtered = FALSE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showLegend = TRUE,
xlim = 30,
ylim = 0.05,
cex = 0.6,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = 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,
loaded = TRUE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
isolationWindow = 1.3,
mzClust = 0.005,
presence = 0.8,
minIntensity = 0,
filtered = FALSE,
loaded = TRUE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_groups()
Plots feature groups EIC.
Usage
MassSpecEngine$plot_groups(
groups = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtExpand = 15,
mzExpand = 0.005,
filtered = FALSE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtWindow = c(-2, 2),
mzWindow = c(-5, 90),
mzClustFeatures = 0.005,
presenceFeatures = 0.8,
minIntensityFeatures = 1000,
loaded = TRUE,
mzClust = 0.005,
presence = 0.8,
minIntensity = 1000,
groupBy = "groups",
filtered = FALSE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw 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.
groupBy
String with the way of grouping. Possible values are
groups
andreplicates
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
isolationWindow = 1.3,
mzClustFeatures = 0.003,
presenceFeatures = 0.8,
minIntensityFeatures = 100,
loaded = TRUE,
mzClust = 0.003,
presence = TRUE,
minIntensity = 100,
groupBy = "groups",
filtered = FALSE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw 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.
groupBy
String with the way of grouping. Possible values are
groups
andreplicates
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
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
rtExpand = 120,
mzExpand = 0.005,
loaded = TRUE,
filtered = FALSE,
legendNames = NULL,
title = NULL,
heights = c(0.35, 0.5, 0.15)
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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.
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,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE,
normalized = TRUE,
legendNames = NULL,
title = NULL
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.normalized
Logical (length 1). When
TRUE
the profile intensities are normalized.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.title
A string with the title.
Method plot_suspects()
Plots suspects.
Usage
MassSpecEngine$plot_suspects(
analyses = NULL,
database = NULL,
features = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 4,
sec = 10,
millisec = 5,
ppmMS2 = 10,
minFragments = 3,
isolationWindow = 1.3,
mzClust = 0.003,
presence = 0.8,
minIntensity = 0,
filtered = FALSE,
rtExpand = 120,
mzExpand = 0.005,
loaded = TRUE,
colorBy = "targets"
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
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 namedanalysis
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
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.
minFragments
Integer (length 1) with the minimum number of fragments.
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.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.
loaded
Logical (length 1). When
TRUE
and if available, loaded data will be used instead of raw data.colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.
Method map_isotopes()
Maps isotopic clusters in the analyses.
Usage
MassSpecEngine$map_isotopes(
analyses = NULL,
groups = NULL,
features = NULL,
clusters = NULL,
mass = NULL,
mz = NULL,
rt = NULL,
drift = NULL,
ppm = 20,
sec = 60,
millisec = 5,
filtered = FALSE,
xlim = 30,
ylim = 0.05,
showLegend = TRUE,
legendNames = NULL,
title = NULL,
colorBy = "targets",
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
groups
A numeric or character vector with the number or ID of feature groups, respectively.
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 namedanalysis
can be given to specify from which analyses the features matched.clusters
A numeric vector with the number/s of feature cluster/s.
mass
A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named
min
andmax
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 namedmass
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemin
,max
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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
andmzmax
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 namedmz
andrt
and/ordrift
. Then, the deviations given in theppm
,sec
andmillisec
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 bemzmin
,mzmax
,rtmin
,rtmax
,driftmin
anddriftmax
. Note that when mass/time ranges are given, theppm
,sec
andmillisec
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).
drift
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.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
showLegend
Logical (length 1). Set to
TRUE
to show legend.legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_chromatograms_peaks()
Plots peaks from chromatograms from analyses.
Usage
MassSpecEngine$plot_chromatograms_peaks(
analyses = NULL,
chromatograms = NULL,
legendNames = NULL,
title = NULL,
colorBy = "targets",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
xLab = NULL,
yLab = NULL,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
chromatograms
A character or integer vector with the ID (i.e. name) or the index of the chromatograms.
legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
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.
Method plot_spectra_charges()
Plots charge assignment of deconvoluted spectra from analyses.
Usage
MassSpecEngine$plot_spectra_charges(
analyses = NULL,
legendNames = NULL,
title = NULL,
colorBy = "analyses",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
xLab = NULL,
yLab = NULL,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.title
A string with the title.
colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
xLab
A string with the title for the x axis.
yLab
A string with the title for the y axis.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_deconvoluted_spectra()
Plots deconvoluted spectra in given MS analyses.
Usage
MassSpecEngine$plot_deconvoluted_spectra(
analyses = NULL,
legendNames = NULL,
colorBy = "analyses",
xLab = NULL,
yLab = NULL,
title = NULL,
cex = 0.6,
showLegend = TRUE,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
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
orreplicates
. 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.
title
A string with the title.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
showLegend
Logical (length 1). Set to
TRUE
to show legend.interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method plot_spectra_peaks()
Plots peaks from spectra from analyses.
Usage
MassSpecEngine$plot_spectra_peaks(
analyses = NULL,
legendNames = NULL,
title = NULL,
colorBy = "analyses",
showLegend = TRUE,
xlim = NULL,
ylim = NULL,
cex = 0.6,
xLab = NULL,
yLab = NULL,
interactive = TRUE
)
Arguments
analyses
A numeric/character vector with the number/name of the analyses.
legendNames
A character vector with the same length as the targets or
TRUE
orFALSE
for using the name in the added targets as legend of the plot.title
A string with the title.
colorBy
Character (length 1). One of
analyses
(the default),polarities
,levels
,targets
orreplicates
. Mixed use (e.g.analyses+polarities
) is also possible.showLegend
Logical (length 1). Set to
TRUE
to show legend.xlim
A length one or two numeric vector for setting the x limits of the plot.
ylim
A length one or two numeric vector for setting the y limits of the plot.
cex
Numeric (length 1) defining the scale of the legend for non interactive plotting.
xLab
A string with the title for the x axis.
yLab
A string with the title for the y axis.
interactive
Logical (length 1). When
TRUE
, the data is plotted interactively using plotly.
Method check_correspondence()
Checks the correspondence of features within feature groups, returning TRUE
or FALSE
.
Method report()
Saves the HTML report from the function report from the package patRoon. The interface is exactly the same and the arguments description are taken from the documentation in patRoon. Therefore, for further information, we recommend to consult directly the function report in patRoon.
Usage
MassSpecEngine$report(
path = paste0(getwd(), "/report"),
filtered = FALSE,
settingsFile = system.file("report", "settings.yml", package = "patRoon"),
EICParams = patRoon::getDefEICParams(topMost = 1, topMostByRGroup = TRUE),
specSimParams = patRoon::getDefSpecSimParams(),
clearPath = FALSE,
openReport = TRUE,
parallel = TRUE,
overrideSettings = list()
)
Arguments
path
Character (length 1) with the path to the report destination.
filtered
Logical (length 1). When
TRUE
, filtered features/groups are considered.settingsFile
The path to the report settings file used for report configuration (see Report settings in report).
EICParams
A named list with parameters used for extracted ion chromatogram (EIC) creation. See getDefEICParams.
specSimParams
A named list with parameters that influence the calculation of MS spectra similarities. See getDefSpecSimParams.
clearPath
If TRUE then the report destination path will be (recursively) removed prior to reporting.
openReport
If set to TRUE then the output report file will be opened with the system browser.
parallel
If set to TRUE then code is executed in parallel.
overrideSettings
A list with settings that override those from the report settings file. See report.