addChromaTOFPeaks: Add ChromaTOF peak detection results

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

Add ChromaTOF peak detection results

Description

Reads ASCII tab-delimited format files (output from ChromaTOF) and attaches them to an already created peaksDataset object

Usage

addChromaTOFPeaks(
  object,
  fns = dir(, "[Tt][Xx][Tx]"),
  rtDivide = 60,
  verbose = TRUE,
  ...
)

Arguments

object	a peaksDataset object.
fns	character vector of same length as object@rawdata (user ensures the order matches)
rtDivide	number giving the amount to divide the retention times by.
verbose	whether to give verbose output, default TRUE
...	arguments passed on to parseChromaTOF

Details

Repeated calls to parseChromaTOF to add peak detection results to the original peaksDataset object.

Value

peaksDataset object

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

parseChromaTOF, peaksDataset

Examples

# need access to CDF (raw data) and ChromaTOF files 
require(gcspikelite)
gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/")

# full paths to file names
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
# [not run] cTofFiles<-dir(gcmsPath,"txt",full=TRUE)

# create a 'peaksDataset' object and add ChromaTOF peaks to it
pd<-peaksDataset(cdfFiles[1],mz=seq(50,550),rtrange=c(7.5,8.5))
# [not run] pd<-addChromTOFPeaks(pd,...)

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