chromPeakArea: Get MS peak area (m/z and rt range) for chromatographic peaks

In EuracBiomedicalResearch/CompMetaboTools: Utility Functions from the Eurac Research Computational Metabolomics Team

Get MS peak area (m/z and rt range) for chromatographic peaks

Description

Extract the peak area (defined by the m/z and retention time range) of chromatographic peaks. The chromatographic peaks can be defined by their ID (i.e. rownames of the chromPeaks matrix) or by m/z and a retention times.

The function identifies first chromatographic peaks in x that match the input parameters mz and rt or peakId and then defines the m/z and rt range based on the "mzmin", "mzmax", "rtmin" and "rtmax" of these. If m/z and rt ranges are provided, by default only chromatographic peaks are considered that have their apex within the region. That can be changed by using a different value for type.

As a result a matrix is returned with columns "mzmin", "mzmax", "rtmin" and "rtmax" defining the lower and upper boundaries of the region of the peaks. Each row in this matrix represent the result for one element in the input parameter specifying the peaks of interest (e.g. mz, rt or peakId).

Usage

chromPeakArea(
  x,
  mz = numeric(),
  rt = numeric(),
  diffRt = 40,
  ppm = 50,
  peakId = character(),
  type = c("apex_within", "any", "within")
)

Arguments

x	XCMSnExp object with identified chromatographic peaks.
mz	numeric or matrix with m/z values to identify chromatographic peaks from which regions should be extracted. If a matrix is provided it is expeted to have 2 columns with the lower and upper m/z boundary. If a numeric is provided parameter ppm is also considered.
rt	numeric or matrix with retention time values to identify chromatographic peaks from which the peak areas are supposed to be defined. If a matrix is provided it is expected to be a two column matrix with the lower and upper rt boundary in which chromatographic peaks should be found. If a numeric is provided, parameter diffRt is considered to define the rt region to search for peaks.
diffRt	numeric(1) to define the rt region in which peaks should be identified if a numeric is provided with parameter rt. The rt region is defined as rt - diffRt to rt + diffRt.
ppm	numeric(1) to define the m/z region in which peaks should be identified if mz is a numeric. The m/z region is defined as mz - ppm(mz, ppm) to mz + ppm(mz, ppm)
peakId	character with the IDs of the chromatographic peaks (i.e. rownames of chromPeaks(object)).
type	character(1) defining which peaks are considered. Defaults to type = "apex_within". See help on chromPeaks for more information.

Value

matrix with columnd "mzmin", "mzmax", "rtmin", "rtmax" with the m/z and retention time ranges calculated on all chromatographic peaks in x matching mz and rt. Each row representing the result for each value in mz and rt.

Author(s)

Johannes Rainer

Examples

library(faahKO)
fls <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
         system.file('cdf/KO/ko16.CDF', package = "faahKO"),
         system.file('cdf/WT/wt19.CDF', package = "faahKO"))

od <- readMSData(fls, mode = "onDisk")
xod <- findChromPeaks(
   od, param = CentWaveParam(noise = 10000, snthresh = 40,
                             prefilter = c(3, 10000)))

chromPeakArea(xod, rt = c(2500, 2700), diffRt = 100,
    mz = cbind(c(400, 300), c(500, 400)))

EuracBiomedicalResearch/CompMetaboTools documentation built on Jan. 31, 2024, 1:14 p.m.