msc.project.read {caMassClass}R Documentation

Read and Manage a Batch of Protein Mass Spectra

Description

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

Usage

msc.project.read(ProjectFile, directory.out=NULL) 

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.

Details

Function msc.project.read allows to user to manage large batches of Mass Spectra files, especially when multiple copies of each sample are present. The ProjectFile contains all the information about the project. An example format might be:

Name, Class, IMAC1, IMAC2, WCX1, WCX2
r0008, 1, Nr/imac_r0008.csv, Nr/imac_r0008(2).csv, Nr/wcx_r0008.csv, Nr/wcx_r0008(2).csv
r0012, 1, Nr/imac_r0012.csv, Nr/imac_r0012(2).csv, Nr/wcx_r0012.csv, Nr/wcx_r0012(2).csv
r0014, 1, Nr/imac_r0014.csv, Nr/imac_r0014(2).csv, Nr/wcx_r0014.csv, Nr/wcx_r0014(2).csv
r0021, 2, Ca/imac_r0021.csv, Ca/imac_r0021(2).csv, Ca/wcx_r0021.csv, Ca/wcx_r0021(2).csv
r0022, 2, Ca/imac_r0022.csv, Ca/imac_r0022(2).csv, Ca/wcx_r0022.csv, Ca/wcx_r0022(2).csv
r0024, 2, Ca/imac_r0024.csv, Ca/imac_r0024(2).csv, Ca/wcx_r0024.csv, Ca/wcx_r0024(2).csv
r0027, 2, Ca/imac_r0027.csv, Ca/imac_r0027(2).csv, Ca/wcx_r0027.csv, Ca/wcx_r0027(2).csv

ProjectFile always has the following format:

File names in ProjectFile could be compressed uzing zip and gzip file compression. For example if individual file name is in the format:

Value

List of .Rdata files storing data that was just read. Each file contains either 2D data (if only one copy of the the data existed) or 3D data (if multiple copies of the data existed). Multiple files are produced if multiple experiments were performed under different conditions. In above example two files will be produced: Data_IMAC.Rdata and Data_WCX.Rdata.

Author(s)

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

See Also

Examples

  directory = system.file("Test", package = "caMassClass")
  ProjectFile = file.path(directory,"InputFiles.csv")
  FileNames = msc.project.read(ProjectFile, '.')
  cat("File ",FileNames," was created\n")

[Package caMassClass version 1.1 Index]