combine_spectra: Combine mass spectra of each scan and each file into a single...
In dajofischer/cosmiq: cosmiq - COmbining Single Masses Into Quantities

Description Usage Arguments Details Author(s) Examples

combine_spectra imports each raw file using xcmsRaw and assigns each ion to a previously defined mass vector, which is created using bin size parameter mzbin. This process is repeated for each raw file.

1	combine_spectra(xs, mzbin=0.003, linear=FALSE, continuum=FALSE)

`xs`	xcmsSet object
`mzbin`	Bin size for the generation of mass vector
`linear`	logical. If TRUE, linear vector will be generated with `mzbin` increments. If FALSE, mass vector will be generated using a non-linear function. This option is recommended for TOF-type mass detectors
`continuum`	boolean flag. default value is FALSE.

This processing step calculates a combined mass spectrum. Mass spectra not only from all scans of a single LCMS run alone are combined but from all acquired datasets. As a result, signal to noise ratio increases for each additional LCMS run.

David Fischer 2013

cdfpath <- file.path(find.package("faahKO"), "cdf")

my.input.files <- dir(c(paste(cdfpath, "WT", sep='/'),
    paste(cdfpath, "KO", sep='/')), full.names=TRUE)


# create xcmsSet object
xs <- new("xcmsSet")
xs@filepaths <- my.input.files

x<-combine_spectra(xs=xs, mzbin=0.25,
    linear=TRUE, continuum=FALSE)

plot(x$mz, x$intensity, type='l',
    xlab='m/Z', ylab='ion intensity')