tandem {rTANDEM} | R Documentation

## Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R objects or xml files

### 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 <frederic.fournier@crchuq.ulaval.ca>, Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>

### 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

[Package rTANDEM version 1.27.0 Index]