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

Description Arguments Value Methods See Also

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


sneumann/xcms-presvnbridge documentation built on May 30, 2019, 6:02 a.m.