xcms (version 1.48.0)

getEIC-methods: 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. If not specified, the method for xcmsRaw returns the base peak chromatogram (BPC, i.e. the most intense signal for each RT across all m/z).

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. If not specified, the method returns the chromatogram for the full RT range.

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 xcmsSet and xcmsRaw 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