measureSampleSet: Measure peaks and samples in an RTMS sample set

In rtms: R Toolkit for Mass Spectrometry

Measure peaks and samples in an RTMS sample set

Description

measureSampleSet() extracts one or more measurements for every peak in every sample in an RTMS sample set object (of class rtmsSampleSet).

Usage

measureSampleSet(sampleset, measure = "PeakIntensity")

Arguments

sampleset

An object of class rtmsSampleSet

measure

A character vector of named measurements, or a list of custom measurement functions. Supported measurement names are "PeakIntensity", which takes the total of any local maxima within the peak width, "PeakArea", which takes the area under the intensity curve within the peak width, and "NumPeaks", which counts the local maxima in the peak window. If measure is a list of functions, each function must take an object of class rtmsSubsample, and return a single numeric value. If the functions are named, those names will be returned in the "measure" column of the resulting data frame; otherwise they will be identified as "Measure1", "Measure2", etc.

Value

A data frame with one row for each sample, peak, and measurement. The data.frame will have a character column named "sample", containing either the name of the sample (if the samples in sampleset are named) or the index of the sample if they are not (but it will always be a character column); a column named "peakName" with the name of the relevant peak (if the "peaks" attribute of sampleset is a named list); a column named "peakValue" containing the m/z value at the center of the relevant peak; a column named "measure" containing the name of the relevant measure; and a column named "value" containing the numeric value of the particular measure for that sample and peak.

Examples

peaks <- rtmsPeakList(c(1516.83,1530.84),peakWidth=0.2,windowWidth = c(5,10))
names(peaks) <- c("Product","Substrate")
sample <- getSample(exampleSpectrum,peaks)
sampleSet <- rep(sample,3)
names(sampleSet) <- c("A","B","C")

measures <- measureSampleSet(sampleSet)

rtms documentation built on June 7, 2023, 5:59 p.m.