peakTable-methods: Create report of aligned peak intensities

peakTable-methodsR Documentation

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.