getEIC-methods {xcms} | R Documentation |
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.
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
|
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.
getEIC(object, mzrange, rtrange = NULL, step = 0.1)
getEIC(object, mzrange, rtrange = 200, groupidx,
sampleidx = sampnames(object), rt = c("corrected", "raw"))
xcmsRaw-class
,
xcmsSet-class
,
xcmsEIC-class