msc.rawMS.read.mzXML & msc.rawMS.write.mzXML {caMassClass}R Documentation

Read / write raw Mass Spectra to/from mzXML Files

Description

Read / write raw protein mass spectra to/from mzXML Files

Usage

msc.rawMS.write.mzXML(scans, filename, mzXML=NULL, ...)
msc.rawMS.read.mzXML(input, scanIdx=NULL)

Arguments

scans data to be stored in mzXML file, in form of a 2D matrix (nFeatures x nSamples) or 3D array (nFeatures x nSamples x nCopies).
filename character string with name of the file (connection)
mzXML class storing partially parsed mzXML data
input Either mzXML object, or character string with name of the file (connection)
scanIdx List of scans to return. Optional.
... additional parameters to be passed to write.mzXML function

Value

Function read.mzXML returns object of type

scans Data in the matrix format (nFeatures x nSamples) rownames(scan) storing masses (M/Z) of each feature.
mzXML Object of type mzXML. See read.mzXML for details


Functions msc.rawMS.write.mzXML do not return anything.

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")
  
  # save raw MS data as mzXML
  msc.rawMS.write.mzXML(X, "rawMS32.mzXML",  precision="32")
  Y = msc.rawMS.read.mzXML("rawMS32.mzXML")
  y = array(Y$scans, c(nrow(Y$scans), ncol(Y$scans)/2, 2))
  stopifnot(all.equal(X,y, tolerance=1e-5)) # about the same
  
  msc.rawMS.write.mzXML(X, "rawMS64.mzXML",  precision="64")
  Y = msc.rawMS.read.mzXML("rawMS64.mzXML")
  y = array(Y$scans, c(nrow(Y$scans), ncol(Y$scans)/2, 2))
  stopifnot(X==y)                           # exactly the same
  
  # Suggestion: inspect 'rawMS32.mzXML' and 'rawMS64.mzXML' using a text editor
  file.remove("rawMS32.mzXML") # delete temporary files 
  file.remove("rawMS64.mzXML") 

[Package caMassClass version 1.3 Index]