chromatogram-MSnExp-method: Extract chromatogram object(s)

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Extract chromatogram object(s)

Description

The chromatogram method extracts chromatogram(s) from an MSnExp or OnDiskMSnExp object. Depending on the provided parameters this can be a total ion chromatogram (TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram (XIC) extracted from each sample/file.

Usage

## S4 method for signature 'MSnExp'
chromatogram(
  object,
  rt,
  mz,
  aggregationFun = "sum",
  missing = NA_real_,
  msLevel = 1L,
  BPPARAM = bpparam()
)

Arguments

object	For chromatogram: a MSnExp or OnDiskMSnExp object from which the chromatogram should be extracted.
rt	A numeric(2) or two-column matrix defining the lower and upper boundary for the retention time range/window(s) for the chromatogram(s). If a matrix is provided, a chromatogram is extracted for each row. If not specified, a chromatogram representing the full retention time range is extracted. See examples below for details.
mz	A numeric(2) or two-column matrix defining the mass-to-charge (mz) range(s) for the chromatogram(s). For each spectrum/retention time, all intensity values within this mz range are aggregated to result in the intensity value for the spectrum/retention time. If not specified, the full mz range is considered. See examples below for details.
aggregationFun	character defining the function to be used for intensity value aggregation along the mz dimension. Allowed values are "sum" (TIC), "max" (BPC), "min" and "mean".
missing	numeric(1) allowing to specify the intensity value for if for a given retention time (spectrum) no signal was measured within the mz range. Defaults to NA_real_.
msLevel	integer specifying the MS level from which the chromatogram should be extracted. Defaults to msLevel = 1L.
BPPARAM	Parallelisation backend to be used, which will depend on the architecture. Default is BiocParallel::bpparam().

Details

Arguments rt and mz allow to specify the MS data slice from which the chromatogram should be extracted. The parameter aggregationSum allows to specify the function to be used to aggregate the intensities across the mz range for the same retention time. Setting aggregationFun = "sum" would e.g. allow to calculate the total ion chromatogram (TIC), aggregationFun = "max" the base peak chromatogram (BPC). The length of the extracted Chromatogram object, i.e. the number of available data points, corresponds to the number of scans/spectra measured in the specified retention time range. If in a specific scan (for a give retention time) no signal was measured in the specified mz range, a NA_real_ is reported as intensity for the retention time (see Notes for more information). This can be changed using the missing parameter.

By default or if \code{mz} and/or \code{rt} are numeric vectors, the
function extracts one \code{\link{Chromatogram}} object for each file
in the \code{\linkS4class{MSnExp}} or \code{\linkS4class{OnDiskMSnExp}}
object. Providing a numeric matrix with argument \code{mz} or \code{rt}
enables to extract multiple chromatograms per file, one for each row in
the matrix. If the number of columns of \code{mz} or \code{rt} are not
equal to 2, \code{range} is called on each row of the matrix.

Value

chromatogram returns a MChromatograms object with the number of columns corresponding to the number of files in object and number of rows the number of specified ranges (i.e. number of rows of matrices provided with arguments mz and/or rt). The featureData of the returned object contains columns "mzmin" and "mzmax" with the values from input argument mz (if used) and "rtmin" and "rtmax" if the input argument rt was used.

Author(s)

Johannes Rainer

See Also

Chromatogram and MChromatograms for the classes that represent single and multiple chromatograms.

Examples

## Read a test data file.
library(BiocParallel)
register(SerialParam())
library(msdata)
f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
     system.file("microtofq/MM8.mzML", package = "msdata"))

## Read the data as an MSnExp
msd <- readMSData(f, msLevel = 1)

## Extract the total ion chromatogram for each file:
tic <- chromatogram(msd)

tic

## Extract the TIC for the second file:
tic[1, 2]

## Plot the TIC for the first file
plot(rtime(tic[1, 1]), intensity(tic[1, 1]), type = "l",
    xlab = "rtime", ylab = "intensity", main = "TIC")

## Extract chromatograms for a MS data slices defined by retention time
## and mz ranges.
rtr <- rbind(c(10, 60), c(280, 300))
mzr <- rbind(c(140, 160), c(300, 320))
chrs <- chromatogram(msd, rt = rtr, mz = mzr)

## Each row of the returned MChromatograms object corresponds to one mz-rt
## range. The Chromatogram for the first range in the first file is empty,
## because the retention time range is outside of the file's rt range:
chrs[1, 1]

## The mz and/or rt ranges used are provided as featureData of the object
fData(chrs)

## The mz method can be used to extract the m/z ranges directly
mz(chrs)

## Also the Chromatogram for the second range in the second file is empty
chrs[2, 2]

## Get the extracted chromatogram for the first range in the second file
chr <- chrs[1, 2]
chr

plot(rtime(chr), intensity(chr), xlab = "rtime", ylab = "intensity")

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.