peakTable-methods: 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.

Value

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(), ...)

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.

Examples

Run this code

	## 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)