msc.baseline.subtract {caMassClass}R Documentation

Baseline Subtraction for Mass Spectra Data

Description

Perform baseline subtraction on batch of mass spectra data

Usage

msc.baseline.subtract(X, ...) 

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/feature.
... Parameters to be passed to bslnoff function from PROcess library. See details for explanation of breaks, qntl, and bw. Boolean parameter plot can be used to plot results.

Details

Perform baseline subtraction for every sample in a batch of data, using bslnoff function from PROcess library. The bslnoff function splits spectrum into breaks number of exponentially growing regions. Baseline is calculated by applying quantile(...,probs=qntl) to each region and smoothing the results using loess(..., span=bw, degree=1) function.

Value

Data in the same format and size as input variable X but with the subtracted baseline.

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 msc.baseline.subtract using 3D input
  # this data had baseline removed already so little change is expected
  Y = msc.baseline.subtract(X)
  avr = mean(abs(X-Y))
  cat("Data Size: ", dim(X), " average change :", avr, "\n")
  stopifnot(avr<0.3)

  # test on data provided in PROcess package (2D input)
  # this is "raw" data, so large changes are expected
  directory  = system.file("Test", package = "PROcess")
  X = msc.rawMS.read.csv(directory) 
  Y = msc.baseline.subtract(X, plot=TRUE)
  avr = mean(abs(X-Y))
  cat("Data Size: ", dim(X), " average change :", avr, "\n")
  stopifnot(avr>7.5)

[Package caMassClass version 1.6 Index]