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

In rTANDEM: Interfaces the tandem protein identification algorithm in R

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

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

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_05_08_22_25_43.t.xml"

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