rTANDEM-package: An R encapsulation of X!TANDEM ('Jackhammer' release,...

In CharlesJB/rTANDEM: Encapsulate X!Tandem in R.

Description

X!Tandem is an open source software for protein identification from tandem mass spectrometry experiments, and rTANDEM is an R encapsulation of this software. As of now, rTANDEM provides a very basic encapsulation of X!Tandem: it has a function that takes as an argument the path to an X!Tandem style parameter file and return the path to an X!tandem style output file. The package also presents some function to transform parameters or results files into R objects and vice versa. We are planning to add functions for visualisation, data manipulation and conversion in a near future.

Details

Package:	rTANDEM
Type:	Package
Version:	0.99.4
Date:	2012-10-22
License:	Artistic License 1.0

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 and from X!Tandem xml files
# 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

CharlesJB/rTANDEM documentation built on May 6, 2019, 9:58 a.m.