msc.mass.cut {caMassClass}R Documentation

Remove Low Mass Portion of the Mass Spectra Data.

Description

Remove low-mass portion of the protein mass spectra (SELDI) data.

Usage

msc.mass.cut( X, MinMass=3000) 

Arguments

X Spectrum data either in matrix format [nFeatures x nSamples] or in 3D array format [nFeatures x nSamples x nCopies]. Row names (rownames(X)) store M/Z mass of each row.
MinMass Minimum mass threshold. All data below that mass will be deleted

Details

Low-mass portion of the protein mass spectra is removed since it is not expected to have any biological information, and it has large enough amplitude variations that can skew normalization process. This function also removes all the masses (features) where the values in all the samples are identical. That happens sometimes when the ends of the samples are set to zero.

Value

Data in the similar format as input variable X but likely with fewer features.

Author(s)

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

See Also

Examples

  # load "Data_IMAC.Rdata" file containing raw MS spectra 'X'  
  if (!file.exists("Data_IMAC.Rdata")) example("msc.project.read")
  load("Data_IMAC.Rdata")
  
  # run in 3D input
  Y = msc.mass.cut( X, MinMass=3000)
  cat("Size before: ", dim(X), " and after :", dim(Y), "\n")
  stopifnot( nrow(Y)==9377 )

  # test on data provided in PROcess package (2D input)
  directory  = system.file("Test", package = "PROcess")
  X = msc.rawMS.read.csv(directory) 
  Y = msc.mass.cut( X, MinMass=4000)
  cat("Size before: ", dim(X), " and after :", dim(Y), "\n")
  stopifnot( nrow(Y)==7439 )

[Package caMassClass version 1.6 Index]