peakTable-methods: Create report of aligned peak intensities

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Create report of aligned peak intensities

Description

Create a report showing all aligned peaks.

Arguments

object	the xcmsSet object
filebase	base file name to save report, .tsv file and _eic will be appended to this name for the tabular report and EIC directory, respectively. if blank nothing will be saved
...	arguments passed down to groupval, which provides the actual intensities.

Details

This method handles creation of summary reports similar to diffreport. It returns a summary report that can optionally be written out to a tab-separated file.

If a base file name is provided, the report (see Value section) will be saved to a tab separated file.

Value

A data frame with the following columns:

mz	median m/z of peaks in the group
mzmin	minimum m/z of peaks in the group
mzmax	maximum m/z of peaks in the group
rt	median retention time of peaks in the group
rtmin	minimum retention time of peaks in the group
rtmax	maximum retention time of peaks in the group
npeaks	number of peaks assigned to the group
Sample Classes	number samples from each sample class represented in the group
...	one column for every sample class
Sample Names	integrated intensity value for every sample
...	one column for every sample

Methods

object = "xcmsSet"

peakTable(object, filebase = character(), ...)

See Also

xcmsSet-class,

Examples

	## Not run: 
	library(faahKO)
	cdfpath <- system.file("cdf", package = "faahKO")
	cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
	xs<-xcmsSet(cdf	files)
	xs<-group(xs)
	peakTable(xs, filebase="peakList")
	
## End(Not run)

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.