featureChromatograms {xcms} | R Documentation

## Extract ion chromatograms for each feature

### Description

Extract ion chromatograms for features in an XCMSnExp object. The function returns for each feature its extracted ion chromatogram and all associated peaks with it.

By default only chromatographic peaks associated with a feature are included for an extracted ion chromatogram. Setting `include = "all"` (instead of the default `include = "feature_only"`) will return all chromatographic peaks identified in the m/z - rt data slice of a feature (and eventually also other features within that region).

### Usage

    featureChromatograms(x, expandRt = 0, aggregationFun = "max", features,
      include = c("feature_only", "all"), filled = FALSE, ...)

### 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.
`include` | `character(1)` defining which chromatographic peaks and feature definitions should be included in the returned `XChromatograms()`. See description above for details.
`filled` | `logical(1)` whether filled-in peaks should be included in the result object. The default is `filled = FALSE`, i.e. only detected peaks are reported.
`...` | optional arguments to be passed along to the `chromatogram()` function.

### Value

`XChromatograms()` 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 on a subset of the test data
    od <- filterRt(readMSData(faahko_3_files, mode = "onDisk"), c(250, 3000))
    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 3.9.1 Index]