R: Extract ion chromatograms for each feature

featureChromatograms {xcms}

R Documentation

Extract ion chromatograms for each feature

Description

Extract ion chromatograms for each feature in an XCMSnExp object.

Usage

featureChromatograms(x, expandRt = 0, aggregationFun = "max", features,
  ...)

Arguments

`x`	`XCMSnExp` object with grouped chromatographic peaks.
`expandRt`	`numeric(1)` to expand the retention time range for each chromatographic peak by a constant value on each side.
`aggregationFun`	`character(1)` specifying the name that should be used to aggregate intensity values across the m/z value range for the same retention time. The default `"sum"` returns a base peak chromatogram.
`features`	`integer`, `character` or `logical` defining a subset of features for which chromatograms should be returned. Can be the index of the features in `featureDefinitions`, feature IDs (row names of `featureDefinitions`) or a logical vector.
`...`	optional arguments to be passed along to the `chromatogram()` function.

Value

Chromatograms object.

Author(s)

Johannes Rainer

Examples


library(xcms)
library(faahKO)
faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
                    system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                    system.file('cdf/KO/ko18.CDF', package = "faahKO"))

## Do a simple and fast preprocessing of the test data
od <- readMSData(faahko_3_files, mode = "onDisk")
od <- findChromPeaks(od, param = CentWaveParam(peakwidth = c(30, 80),
    noise = 1000))
od <- adjustRtime(od, param = ObiwarpParam(binSize = 0.6))
od <- groupChromPeaks(od,
    param = PeakDensityParam(minFraction = 0.8, sampleGroups = rep(1, 3)))

## Extract ion chromatograms for each feature
chrs <- featureChromatograms(od)

## Plot the XIC for the first feature using different colors for each file
par(mfrow = c(1, 2))
plot(chrs[1, ], col = c("red", "green", "blue"))

[Package xcms version 3.4.4 Index]