refineChromPeaks-clean: Remove chromatographic peaks with too large rt width

In xcms: LC-MS and GC-MS Data Analysis

Description

Remove chromatographic peaks with a retention time range larger than the provided maximal acceptable width (maxPeakwidth).

Usage

CleanPeaksParam(maxPeakwidth = 10)

## S4 method for signature 'XCMSnExp,CleanPeaksParam'
refineChromPeaks(object, param = CleanPeaksParam(), msLevel = 1L)

Arguments

maxPeakwidth	for CleanPeaksParam: numeric(1) defining the maximal allowed peak width (in retention time).
object	XCMSnExp object with identified chromatographic peaks.
param	CleanPeaksParam object defining the settings for the method.
msLevel	integer defining for which MS level(s) the chromatographic peaks should be cleaned.

Value

XCMSnExp object with chromatographic peaks exceeding the specified maximal retention time width being removed.

Note

refineChromPeaks methods will always remove feature definitions, because a call to this method can change or remove identified chromatographic peaks, which may be part of features.

Author(s)

Johannes Rainer

See Also

Other chromatographic peak refinement methods: FilterIntensityParam, MergeNeighboringPeaksParam

Examples

## Load a test data set with detected peaks
data(faahko_sub)
## Update the path to the files for the local system
dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

## Disable parallel processing for this example
register(SerialParam())

## Distribution of chromatographic peak widths
quantile(chromPeaks(faahko_sub)[, "rtmax"] - chromPeaks(faahko_sub)[, "rtmin"])

## Remove all chromatographic peaks with a width larger 60 seconds
data <- refineChromPeaks(faahko_sub, param = CleanPeaksParam(60))

quantile(chromPeaks(data)[, "rtmax"] - chromPeaks(data)[, "rtmin"])

xcms documentation built on Nov. 8, 2020, 5:13 p.m.