View source: R/DeconvoluteSpectrum.R
DeconvoluteSpectrum | R Documentation |
DeconvoluteSpectrum
will evaluate a list of xcmsRaw objects at a given time (rt) and potential mass (mz1).
The main purpose is to deconvolute the mass spectrum at rt including mz1.
DeconvoluteSpectrum( dat = NULL, rt = NULL, rt_dev = 3, mz1 = NULL, mz_dev = 0.003, use.mz.adjust = FALSE, ionization = c("APCI", "ESI")[1], smooth = 0 )
dat |
A list of xcmsRaws or an xcmsSet object. |
rt |
Retention time to search for maxima. |
rt_dev |
Allowed retention time window. |
mz1 |
If specified, ensure that this mass is included in the spectrum (assumed base peak). NULL otherwise. |
mz_dev |
Allowed mz deviation [Da]. |
use.mz.adjust |
Will adjust mz on an experiment wide basis. |
ionization |
Either APCI or ESI. Choice will modify some internal parameters and checks performed. |
smooth |
Smoothing parameter passed on to getMultipleBPC. |
Will test all mz at spectrum of base peak within range for co-apex, rt diff and ratio consistency/correlation over a set of samples.
A pseudo spectrum at rt (containing mz1 if specified). Effectively a 2-column matrix (mz, int) with rt as attribute
# Please use examples from previous versions as xcms (and xcms objects) # are no longer supported during CRAN checks leading to package rejection # if included (and I do not know a work around). :(
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