MSGFplus (version 1.6.2)

runMSGF: Runs MS-GF+ based on the given msgfPar object

Description

This function assembles a system call based on the parameters specified in the object and the arguments given in the function call. By default the function uses the MS-GF+ jar file bundled with this package, but it is possible to specify an alternative location using the msgfPar argument. Version compatibility can not be assured in this case though.

Usage

runMSGF(object, rawfiles, savenames, import, memory, async, msgfPath)

Arguments

object

An msgfPar object

rawfiles

A character vector holding the filepath to the spectrum files to be analysed (currently supported formats: *.mzML, *.mzXML, *.mgf, *.ms2, *.pkl or *_dta.txt)

savenames

An optinal vector of same length as rawfiles. Specifies the name used to save the results. If omitted the results will be saved with the same name as the rawfile, but with an .mzid extension.

import

Logical (default=TRUE). Should the results be imported in to R after the analysis is finished.

memory

An integer (default=10000). How much memory should be allocated to the java virtual machine during execution (in mb)

async

An Logical (default=FALSE). Should MS-GF+ be run asynchronously?

msgfPath

The path to an alternative MSGFPlus.jar file if the bundled one is not desired

Value

If import=TRUE a list of mzID object otherwise NULL

See Also

mzID

Examples

## Not run: 
# parameters <- msgfPar(
#                       database=system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'),
#                       tolerance='20 ppm',
#                       instrument='TOF',
#                       enzyme='Lys-C'
#                      )
# runMSGF(parameters, c('file1.mzML', 'file2.mzML'))
# ## End(Not run)