tandem: Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R...

In rTANDEM: Interfaces the tandem protein identification algorithm in R

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.

Author(s)

Authors: Frederic Fournier, Charles Joly Beauparlant, Rene Paradis, Arnaud Droit

Maintainer: Frederic Fournier <[e-mail]>, Charles Joly Beauparlant <[e-mail]>

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

Example output

Loading required package: XML
Loading required package: Rcpp
Loading required package: data.table
Loading spectra
 (mgf). loaded.
Spectra matching criteria = 242
Starting threads . started.
Computing models:
	testin
		sequences modelled = 5 ks
Model refinement:
	partial cleavage ..... done.
	unanticipated cleavage ..... done.
	modified N-terminus ..... done.
	finishing refinement ... done.
Creating report:
	initial calculations  ..... done.
	sorting  ..... done.
	finding repeats ..... done.
	evaluating results ..... done.
	calculating expectations ..... done.
	writing results ..... done.

Valid models = 40
Unique models = 41
Estimated false positives = 1 +/- 1


[1] "/work/tmp/output.2019_06_02_21_21_52.t.xml"

rTANDEM documentation built on April 28, 2020, 7:04 p.m.