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

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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.

Note that this method will always return profile, not raw data (with profile data being the binned data along M/Z). See details for further information.

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 the group data will be used if mzrange is not provided.
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 (bin) size to use for profile generation. Note that a value of step = 0 is not supported.
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

Details

In contrast to the rawEIC method, that extracts the actual raw values, this method extracts them from the object's profile matrix (or if the provided step argument does not match the profStep of the object the profile matrix is calculated on the fly and the values returned).

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, rawEIC

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.