parseChromaTOF: Parser for ChromaTOF files
In flagme: Analysis of Metabolomics GC/MS Data

Description Usage Arguments Details Value Author(s) References See Also Examples

Reads ASCII ChromaTOF-format files from AMDIS (Automated Mass Spectral Deconvolution and Identification System)

1	parseChromaTOF(fn,min.pc=.01,mz=seq(85,500),rt.cut=.008,rtrange=NULL,skip=1,rtDivide=60)

`fn`	ChromaTOF filename to read.
`min.pc`	minimum percent of maximum intensity.
`mz`	vector of mass-to-charge bins of raw data table.
`rt.cut`	the difference in retention time, below which peaks are merged together.
`rtrange`	retention time range to parse peaks from, can speed up parsing if only interested in a small region (must be `numeric` vector of length 2)
`skip`	number of rows to skip at beginning of the ChromaTOF
`rtDivide`	multiplier to divide the retention times by (default: 60)

parseChromaTOF will typically be called by addChromaTOFPeaks, not called directly.

Peaks that are detected within rt.cut are merged together. This avoids peaks which are essentially overlapping.

Fragments that are less than min.pc of the maximum intensity fragment are discarded.

list with components peaks (table of spectra – rows are mass-to-charge and columns are the different detected peaks) and tab (table of features for each detection), according to what is stored in the ChromaTOF file.

Mark Robinson

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

addAMDISPeaks

require(gcspikelite)

# paths and files
gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/")
tofFiles<-dir(gcmsPath,"tof",full=TRUE)

# parse ChromaTOF file
cTofList<-parseChromaTOF(tofFiles[1])