msc.mass.cut {caMassClass} | R Documentation |
Remove low-mass portion of the protein mass spectra (SELDI) data.
msc.mass.cut( X, MinMass=3000)
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 |
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.
Data in the similar format as input variable X
but likely with
fewer features.
Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com
msc.preprocess.run
and
msc.project.run
pipelines.
msc.baseline.subtract
msc.mass.adjust
# 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 )