rTANDEM (version 1.12.0)

tandem: Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R objects or xml files

Description

The function tandem(input) takes a rTParam object or the path of a parameter file as argument and calls X!Tandem on it. The function rtandem(data.file, taxon, taxonomy, default.parameters) is a wrapper that can be used to circumvent the need for a rTParam input object (or of an xml input file).

Usage

tandem(input)
rtandem(data.file, taxon, taxonomy, default.parameters, output.path=NA)

Arguments

input

A path to a X!Tandem style parameter file or a rTParam object.

data.file

The path to the file containing the raw data to be analysed (in 'DTA', 'PKL' or 'MGF' format).

taxon

A string containing the taxon to be used for the analysis (e.g. "yeast" or "Homo sapiens").

taxonomy

Either a rTTaxo object or the path to a X!Tandem style taxonomy xml file.

default.parameters

Either a rTParam object containing the default parameters to be used, or the path to a X!Tandem style default-parameters xml file.

output.path

The path and name of the output file. If this name ends by ".xml" and the option 'path hashing' is enabled, a timestamp will be inserted just before the ".xml".

Value

Both tandem(input) and rtandem(data.file, taxon, taxonomy, default.parameters) returns the path of the xml output file generated.

References

Robertson Craig and Ronald C. Beavis, TANDEM: matching proteins with mass spectra, Bioinformatics, 2004, 20 1466-7. http://www.thegpm.org/tandem/

Examples

# X!Tandem call style: we call tandem(input) on a single
# rTParam object.

# We create rTParam from an X!Tandem xml file
# located in the installation folder: 
param <- GetParamFromXML(system.file("extdata/input.xml", package="rTANDEM"))

# We create a rTTaxo object and identify a database for yeast
taxonomy <- rTTaxo( 
  taxon="yeast",
  format="peptide",
  URL= system.file("extdata/fasta/scd.fasta.pro", package="rTANDEM")
  )

# We will adjust those two objects to use one another and to use
# the path of some data and configuration files located
# in the installation folder:
param <- setParamValue(param, 'list path', 'taxonomy information', taxonomy)
param <- setParamValue(param, 'list path', 'default parameters',
  value=system.file("extdata/default_input.xml", package="rTANDEM"))
param <- setParamValue(param, 'spectrum', 'path',
  value=system.file("extdata/test_spectra.mgf", package="rTANDEM"))
param <- setParamValue(param, 'output', 'xsl path',
  value=system.file("extdata/tandem-input-style.xsl", package="rTANDEM"))
param <- setParamValue(param, 'output', 'path',
  value=paste(getwd(), "output.xml", sep="/"))

# This is the main command to run rTANDEM. The output will be
# written to a file in the working directory and the function
# returns the path to this file.
output.file <- tandem(param)
output.file