peaksDataset: Data Structure for raw GCMS data and peak detection results

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

Data Structure for raw GCMS data and peak detection results

Description

Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs

Usage

peaksDataset(
  fns = dir(, "[Cc][Dd][Ff]"),
  verbose = TRUE,
  mz = seq(50, 550),
  rtDivide = 60,
  rtrange = NULL
)

Arguments

fns	character vector, filenames of raw data in CDF format.
verbose	logical, if TRUE then iteration progress information is output.
mz	vector giving bins of raw data table.
rtDivide	number giving the amount to divide the retention times by.
rtrange	retention time range to limit data to (must be numeric vector of length 2)

Details

peaksDataset is a hold-all data structure of the raw and peak detection data.

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.

Examples

require(gcspikelite)

# paths and files
gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/")
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
eluFiles<-dir(gcmsPath,"ELU",full=TRUE)

# read data
pd<-peaksDataset(cdfFiles[1:2],mz=seq(50,550),rtrange=c(7.5,8.5))
show(pd)

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