mzchannel2pktab: Conversion between peak lists from hyphenated MS (LCMS, GCMS,...
In ptw: Parametric Time Warping

Description Usage Arguments Value Author(s) Examples

Function pktab2mzchannel allows to split a list of peaks into several sublists, for instance on the basis of m/z values. The result can be aligned with stptw. The peak list can be obtained from packages like XCMS. The reverse function, mzchannel2pktab, simply gathers all peak positions in one matrix.

1 2	pktab2mzchannel(pktab, Ivalue = "maxo", masses = NULL, nMasses = 0, massDigits = 2) mzchannel2pktab(mzchannels)

`pktab`	a peak table as generated for example by XCMS. Necessary information: m/z value (column name "mz"), retention time (column name "rt") and intensity.
`Ivalue`	the name of the intensity value to be used. Default is "maxo", one of the columns generated by the XCMS package.
`masses`	a vector of specific masses
`nMasses`	an optional number limiting the number of mass channels. When both `masses` and `nMasses` are defined, the former takes preference
`massDigits`	number of significant mass digits - if no `masses` are supplied this number determines the number of distinct categories in the output
`mzchannels`	a list of peak matrices, e.g. the output of `pktab2mzchannel`

Function pktab2mzchannel returns a list of peak matrices; list elements have the name of the mz value that they represent. Function mzchannel2pktab returns one peak matrix where all masses are in a specific column.

Ron Wehrens

data(lcms)
## first couple of peaks in the first three channels
(smallset <- lapply(lcms.pks[[1]][1:3], head))
## all in one data matrix
allpeaks <- mzchannel2pktab(smallset)
## and back again
pktab2mzchannel(allpeaks, Ivalue = "I")