R: Conversion between peak lists from hyphenated MS (LCMS, GCMS,...

mzchannel2pktab {ptw} | R Documentation

## Conversion between peak lists from hyphenated MS (LCMS, GCMS, ...) data and input for `stptw`.

### Description

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.

### Usage

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

### Arguments

`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`

### Value

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.

### Author(s)

Ron Wehrens

### Examples

    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")

[Package ptw version 1.9-12 Index]