getEIC-methods {xcms}R Documentation

Get extracted ion chromatograms for specified m/z ranges

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, a matrix with a column for each mzmin, mzmax pair. Rows correspond to individual scans. Otherwise, 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


[Package xcms version 1.4.0 Index]