rTANDEM (version 1.12.0)

rTANDEM-package: An R encapsulation of X!TANDEM ('Jackhammer' release, 2013.06.15)

Description

X!Tandem is an open source software for protein identification by tandem mass spectrometry, and rTANDEM encapsultates this software in R. rTANDEM provides a 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 functions to transform parameters or results files into R objects and vice versa. Some functions are also available to examine the results within R. An associated package, shinyTANDEM, provides a graphical interface to visualize results objects.

Details

Package:

rTANDEM

Type:

Package

Version:

1.2.3

Date:

2013-11-07

License:

Artistic License 1.0

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