peakTable-methods {xcms} | R 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)

[Package xcms version 3.9.1 Index]