msc.project.run {caMassClass}R Documentation

Read and Preprocess Protein Mass Spectra

Description

Read and preprocess protein mass spectra (SELDI) files where files could contain multiple copies of spectra taken from the same sample, or spectra from multiple experiments performed on the same sample.

Usage

msc.project.run(ProjectFile, directory.out=NULL, verbose = TRUE, ...)

Arguments

ProjectFile path and name of text file in Excel's CSV format which is used to store information about a batch of Mass Spectra data files. See details.
directory.out Optional character vector with name of directory where output files will be saved. Use "/" slashes in directory name. By default the directory containing ProjectFile and all Mass Spectra files is used, and this argument is provided in case that directory is read-only and user have to choose a different directory.
verbose boolean flag turns debugging printouts on.
... parameters to be passed to msc.preprocess.run

Details

High level processing of protein mass spectra (SELDI) data. msc.project.read supports projects with multiple sets of spectra taken under different experimental condition. Those sets will be called batches. With that in mind, following steps are performed:

Value

X Spectrum data either in matrix format [nFeatures x nSamples]. Row names (rownames(X) store M/Z mass of each row merged with batch name
SampleLabels Class label for each sample as read from msc.project.read
SameSample array of the same length as number of columns in X indicating samples that are multiple copies that came from the same physical sample, and should be the same, if not for noise.
mxXML Experiment information in mzXML file format. Included only if input data was read from mzXML files, and NULL otherwise.

Author(s)

Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com

See Also

msc.project.read, msc.preprocess.run

Examples

  directory  = system.file("Test", package = "caMassClass")
  ProjectFile = file.path(directory,"InputFiles.csv")
  Data = msc.project.run(ProjectFile, '.',  
      baseline.removal=0, mass.drift.adjustment=1, min.mass=3000, 
      peak.extraction=1, merge.copies=7, shiftPar=0.0004)
  stopifnot( dim(Data$X)==c(25,60) )
  strsplit(Data$mzXML$parentFile, '\n')      # show mzXML$parentFile record
  strsplit(Data$mzXML$dataProcessing, '\n')  # show mzXML$dataProcessing record

[Package caMassClass version 1.6 Index]