Get extracted ion chromatograms for specified m/z ranges
getEIC-methods.RdGenerate 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.
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"))
Arguments
- object
the
xcmsRaworxcmsSetobject- mzrange
Either a two column matrix with minimum or maximum m/z or a matrix of any dimensions containing columns
mzminandmzmax. If not specified, the method forxcmsRawreturns the base peak chromatogram (BPC, i.e. the most intense signal for each RT across all m/z).For
xcmsSetobjects the group data will be used ifmzrangeis not provided.- rtrange
A two column matrix the same size as
mzrangewith 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
xcmsSetobjects, 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 = 0is 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).