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Constructor and methods to handle mass spectrometry spectra results

Source: R/class_MassSpecResults_Spectra.R
MassSpecResults_Spectra.Rd

The MassSpecResults_Spectra class is a child of Results and is used to store mass spectrometry spectra results.

Usage

MassSpecResults_Spectra(
  spectra = list(),
  replicates = character(),
  is_averaged = FALSE,
  is_neutralized = FALSE,
  peaks = list(),
  charges = list()
)

# S3 method for class 'MassSpecResults_Spectra'
validate_object(x)

# S3 method for class 'MassSpecResults_Spectra'
show(x)

# S3 method for class 'MassSpecResults_Spectra'
x[i]

# S3 method for class 'MassSpecResults_Spectra'
get_spectra(
  x,
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0
)

# S3 method for class 'MassSpecResults_Spectra'
plot_spectra(
  x,
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "mz",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

# S3 method for class 'MassSpecResults_Spectra'
plot_spectra_3d(
  x,
  analyses = NULL,
  levels = NULL,
  mass = NULL,
  mz = NULL,
  rt = NULL,
  mobility = NULL,
  ppm = 20,
  sec = 60,
  millisec = 5,
  id = NULL,
  allTraces = TRUE,
  isolationWindow = 1.3,
  minIntensityMS1 = 0,
  minIntensityMS2 = 0,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "rt",
  yVal = "mz",
  xLab = NULL,
  yLab = NULL,
  zLab = NULL,
  renderEngine = "webgl"
)

# S3 method for class 'MassSpecResults_Spectra'
plot_spectra_charges(
  x,
  analyses = NULL,
  legendNames = NULL,
  title = NULL,
  colorBy = "analyses",
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

# S3 method for class 'MassSpecResults_Spectra'
get_spectra_matrix(x, analyses = NULL)

# S3 method for class 'MassSpecResults_Spectra'
get_spectra_peaks(x, analyses = NULL)

# S3 method for class 'MassSpecResults_Spectra'
plot_spectra_peaks(
  x,
  analyses = NULL,
  legendNames = TRUE,
  colorBy = "analyses",
  xVal = "mz",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

spectra

A list of spectra data.table objects.

replicates

A character vector of replicate names.

is_averaged

Logical indicating if the spectra are averaged.

is_neutralized

Logical indicating if the spectra are neutralized.

peaks

A list of data.table objects containing peak information for each spectrum.

charges

A list of data.table objects containing charge information for each spectrum

x

A MassSpecResults_Spectra object.

analyses

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

levels

Integer vector with the levels of MS data.

mass

A vector with target neutral mass value/s (in Da) or a two columns data.table or data.frame named min and max with minimum and maximum neutral mass values (in Da), respectively. Alternatively, neutral mass (in Da) and retention time (in seconds) and/or drift time values (in milliseconds) can be given as one data.table or data.frame with columns named mass and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of neutral mass, retention time and drift time targets. In this case, the column names must be min, max, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.

mz

A vector with target m/z value/s (in Da) or a two columns data.table or data.frame named mzmin and mzmax with minimum and maximum m/z values (in Da), respectively. Alternatively, m/z (in Da) and retention time values (in seconds) can be given as one data.table or data.frame with columns named mz and rt and/or drift. Then, the deviations given in the ppm, sec and millisec arguments are used to calculate the ranges. Also works with a data.table or data.frame with minimum and maximum values of m/z, retention time and drift time targets. In this case, the column names must be mzmin, mzmax, rtmin, rtmax, driftmin and driftmax. Note that when mass/time ranges are given, the ppm, sec and millisec arguments are not used.

rt

A vector with target retention time values (in seconds) or a two columns data.table or data.frame with minimum and maximum retention time values (in seconds).

mobility

A vector with target drift time values (in milliseconds) or a two columns data.table or data.frame with minimum and maximum drift time values (in milliseconds).

ppm

Numeric of length one with the mass deviation, in ppm.

sec

Numeric of length one with the time deviation, in seconds.

millisec

Numeric of length one with the drift time deviation, in milliseconds.

id

Character with the same length as m/z and retention time targets to be used as identifier/s. When not given, the id is built as a combination of the m/z and retention time ranges or values.

allTraces

Logical, when TRUE all level 2 data is returned. When FALSE and level has 2, only the MS2 traces of MS1 targets are returned, using the isolationWindow to calculate the mass window.

isolationWindow

Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).

minIntensityMS1

Numeric value with the minimum intensity of level 1 data (i.e., MS1 data).

minIntensityMS2

Numeric value with the minimum intensity of level 2 data (i.e., MS2 data).

legendNames

A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.

colorBy

A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.

xVal

A character string indicating the x-axis variable. Options are "mz", "mass", or "mobility".

xLab

A string with the title for the x axis.

yLab

A string with the title for the y axis.

title

A string with the title.

interactive

Logical (length 1). When TRUE, the data is plotted interactively using plotly.

renderEngine

The engine to render the data. The default is "webgl".

yVal

A character string indicating the y-axis variable. Options are "rt", "mz", "mass", or "mobility".

zLab

A character string indicating the z-axis label. Default is "Intensity / counts".

Methods (by generic)

  • validate_object(MassSpecResults_Spectra): Validate the MassSpecResults_Spectra object, returning NULL if valid.

  • show(MassSpecResults_Spectra): Show the MassSpecResults_Spectra object.

  • [: Subset the MassSpecResults_Spectra object.

  • get_spectra(MassSpecResults_Spectra): Get spectra from the MassSpecResults_Spectra object, returning a list of data.table objects.

  • plot_spectra(MassSpecResults_Spectra): Plot spectra from the MassSpecResults_Spectra object.

  • plot_spectra_3d(MassSpecResults_Spectra): Plot 3D spectra from the MassSpecResults_Spectra object.

  • plot_spectra_charges(MassSpecResults_Spectra): Plot spectra charges from the MassSpecResults_Spectra object.

  • get_spectra_matrix(MassSpecResults_Spectra): Get spectra matrix from the MassSpecResults_Spectra object.

  • get_spectra_peaks(MassSpecResults_Spectra): Get spectra peaks from the MassSpecResults_Spectra object.

  • plot_spectra_peaks(MassSpecResults_Spectra): Plot spectra peaks from the MassSpecResults_Spectra object.

See also

Results