msc.biomarkers.read.csv & msc.biomarkers.write.csv {caMassClass}R Documentation

Read and Write biomarker matrix in CSV format

Description

Functions to read and write CSV (comma separated values) text files containing biomarkers (aligned peaks) in the format used by Ciphergen's biomarker file, with spectra (samples) as rows, and biomarkers as columns (features).

Usage

  X = msc.biomarkers.read.csv(fname, mzXML.record=FALSE)
  msc.biomarkers.write.csv(X, fname)

Arguments

fname either a character string naming a file or a connection.
X biomarker data in form of a 2D matrix (nFeatures x nSamples) or 3D array (nFeatures x nSamples x nCopies. Notice that this data is in format which is a transpose of data in CSV file.
mzXML.record should mzXML record be created to store mata-data (input file names)?

Value

Function msc.biomarkers.read.csv returns peak information data frame. See argument X above. If mzXML.record was set to true than mzXML record with input file names will be attached to X as "mzXML" attribute.
Function msc.biomarkers.write.csv does not return anything.

Author(s)

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

See Also

msc.biomarkers.fill, msc.rawMS.read.csv

Examples

  example("msc.peaks.align", verbose=FALSE) # create biomarkers data
  X = Y$Bmrks   #  biomarkers data is stored in variable 'Y$Bmrks'
  msc.biomarkers.write.csv(X, "biomarkers.csv")
  Y = msc.biomarkers.read.csv("biomarkers.csv", mzXML.record=TRUE)
  stopifnot( all(X==Y, na.rm=TRUE) )
  mzXML = attr(Y,"mzXML")
  strsplit(mzXML$parentFile, '\n')      # show mzXML$parentFile record
  file.remove("biomarkers.csv")

[Package caMassClass version 1.6 Index]