getEIC-methods: Get extracted ion chromatograms for specified m/z ranges

In benjiec/xcms: LC/MS and GC/MS Data Analysis

Description

Generate multiple extracted ion chromatograms for m/z values of interest. For xcmsSet objects, reread original raw data and apply precomputed retention time correction, if applicable.

Arguments

object	the xcmsRaw or xcmsSet object
mzrange	either a two column matrix with minimum or maximum m/z or a matrix of any dimensions containing columns mzmin and mzmax for xcmsSet objects, if left blank the group data will be used instead
rtrange	a two column matrix the same size as mzrange with minimum and maximum retention times between which to return EIC data points for xcmsSet objects, it may also be a single number specifying the time window around the peak to return EIC data points
step	step size to use for profile generation
groupidx	either character vector with names or integer vector with indicies of peak groups for which to get EICs
sampleidx	either character vector with names or integer vector with indicies of samples for which to get EICs
rt	"corrected" for using corrected retention times, or "raw" for using raw retention times

Value

For xcmsRaw objects, if rtrange is NULL, an intensity matrix with a row for each mzmin, mzmax pair. Columns correspond to individual scans. If rtrange is not NULL, a list of two column (retention time/intensity) matricies, one for each mzmin, mzmax pair.

For xcmsSet objects, an xcmsEIC object.

Methods

object = "xcmsRaw"

getEIC(object, mzrange, rtrange = NULL, step = 0.1)

object = "xcmsSet"

getEIC(object, mzrange, rtrange = 200, groupidx, sampleidx = sampnames(object), rt = c("corrected", "raw"))

See Also

xcmsRaw-class, xcmsSet-class, xcmsEIC-class

benjiec/xcms documentation built on May 12, 2019, 11:57 a.m.