tandem {rTANDEM} | R Documentation |
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).
tandem(input) rtandem(data.file, taxon, taxonomy, default.parameters, output.path=NA)
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". |
Both tandem(input)
and rtandem(data.file, taxon,
taxonomy, default.parameters)
returns the path of the xml output file
generated.
Authors: Frederic Fournier, Charles Joly Beauparlant, Rene Paradis, Arnaud Droit
Maintainer: Frederic Fournier <frederic.fournier@crchuq.ulaval.ca>, Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>
Robertson Craig and Ronald C. Beavis, TANDEM: matching proteins with mass spectra, Bioinformatics, 2004, 20 1466-7. http://www.thegpm.org/tandem/
# 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