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, wipe=TRUE)

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. By default all will be returned, but one can choose only a subset using this argument.
wipe Should all scans that were returned be also deleted (wiped) from mzXML record? Set to TRUE by default to minimize memory use.
... additional parameters to be passed to write.mzXML function

Value

Function msc.rawMS.read.mzXML returns data in the matrix format (nFeatures x nSamples) rownames(scan) storing masses (M/Z) of each feature. In addition, object of type mzXML is attached as "mzXML" attribute. 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 using 32-bit precision
  msc.rawMS.write.mzXML(X, "rawMS32.mzXML",  precision="32")
  Y = msc.rawMS.read.mzXML("rawMS32.mzXML")
  dim(Y) = c(nrow(Y), ncol(Y)/2, 2)
  stopifnot(all.equal(X,Y, tolerance=1e-5, check.attributes = FALSE)) # about the same
  
  # save raw MS data as mzXML using 64-bit precision
  msc.rawMS.write.mzXML(X, "rawMS64.mzXML",  precision="64")
  Y = msc.rawMS.read.mzXML("rawMS64.mzXML")
  dim(Y) = c(nrow(Y), ncol(Y)/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 1.6 Index]