parseChromaTOF: Parser for ChromaTOF files

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

Parser for ChromaTOF files

Description

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

Usage

parseChromaTOF(
  fn,
  min.pc = 0.01,
  mz = seq(85, 500),
  rt.cut = 0.008,
  rtrange = NULL,
  skip = 1,
  rtDivide = 60
)

Arguments

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)

Details

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.

Value

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.

Author(s)

Mark Robinson

References

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

See Also

addAMDISPeaks

Examples

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])

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.