msgfPar-class: A class to contain parameters used in an MS-GF+ analysis

In thomasp85/MSGFplus-release: An interface between R and MS-GF+

Description

This class collects and stores parameters for an MS-GF+ analysis and is the starting point for peptide identification

Usage

## S4 method for signature 'msgfPar'
show(object)

## S4 method for signature 'msgfPar'
length(x)

## S4 method for signature 'msgfPar'
getMSGFpar(object)

## S4 method for signature 'msgfPar'
runMSGF(object, rawfiles, savenames, import = TRUE,
  memory = 10000, async = FALSE, msgfPath)

Arguments

object	An msgfPar object
x	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

Details

This class contains a range of other classes, each handling a different set of parameters. Often these classes are simple containers that only takes care of errorchecking and generating command line arguments, but in some cases, as with msgfParModificationList, the class is a bit more complex.

Value

length: 1 if a database is defined, 0 otherwise.

getMSGFpar: A stringified version of the parameters compliant with MS-GF+.

runMSGF: If import=TRUE an mzID or mzIDCollection object. If async=TRUE an msgfAsync object. Otherwise NULL

Methods (by generic)

• show: Short summary of msgfPar object

• length: Report the length of an msgfPar object

• getMSGFpar: Get system compliant function call

• runMSGF: Initiate an MS-GF+ analysis using the selected msgfPar object

Slots

database

The location of the database fasta file used for the analysis.

tolerance

An msgfParTolerance object holding the m/z tolerance used in the search.

isotopeError

An msgfParIsotopeError object holding the isotope errors permitted in the search.

tda

An msgfParTda object saying whether FDR should be estimated using the target-decoy approach.

fragmentation

An msgfParFragmentation object holding the type of fragmentation expected from the experiment.

instrument

An msgfParInstrument object holding which type of instrument was used for collecting the data.

enzyme

An msgfParEnzyme object holding which enzyme was used for digestion

protocol

An msgfParProtocol object defining whether a specific protocol should be used in the search.

ntt

An msgfParNtt object defining the number of tolerable termini allowed in the peptides.

modification

An msgfParModificationList object holding the modifications accepted in the search.

lengthRange

An msgfParLengthRange object setting the limits on the peptide length in residues that the search allows.

chargeRange

An msgfParChargeRange object defining which charges should be included in the search.

matches

An msgfParMatches object defining the number of matches per PSM that gets reported in the output.

Objects from the class

Objects can be created using the msgfPar constructor, or with msgfParGUI for a simple graphical user interface

References

http://proteomics.ucsd.edu/Software/MSGFPlus.html

See Also

msgfParGUI

Other msgfParClasses: [[,msgfParModificationList,numeric,missing-method, [[<-,msgfParModificationList,numeric,missing,msgfParModification-method, getMSGFpar,msgfParModificationList-method, length,msgfParModificationList-method, msgfParModificationList, msgfParModificationList-class, show,msgfParModificationList-method; getMSGFpar,msgfParChargeRange-method, length,msgfParChargeRange-method, msgfParChargeRange, msgfParChargeRange-class, show,msgfParChargeRange-method; getMSGFpar,msgfParEnzyme-method, length,msgfParEnzyme-method, msgfParEnzyme, msgfParEnzyme-class, show,msgfParEnzyme-method; getMSGFpar,msgfParFragmentation-method, length,msgfParFragmentation-method, msgfParFragmentation, msgfParFragmentation-class, show,msgfParFragmentation-method; getMSGFpar,msgfParInstrument-method, length,msgfParInstrument-method, msgfParInstrument, msgfParInstrument-class, show,msgfParInstrument-method; getMSGFpar,msgfParIsotopeError-method, length,msgfParIsotopeError-method, msgfParIsotopeError, msgfParIsotopeError-class, show,msgfParIsotopeError-method; getMSGFpar,msgfParLengthRange-method, length,msgfParLengthRange-method, msgfParLengthRange, msgfParLengthRange-class, show,msgfParLengthRange-method; getMSGFpar,msgfParMatches-method, length,msgfParMatches-method, msgfParMatches, msgfParMatches-class, show,msgfParMatches-method; getMSGFpar,msgfParModification-method, msgfParModification, msgfParModification-class, show,msgfParModification-method; getMSGFpar,msgfParNtt-method, length,msgfParNtt-method, msgfParNtt, msgfParNtt-class, show,msgfParNtt-method; getMSGFpar,msgfParProtocol-method, length,msgfParProtocol-method, msgfParProtocol, msgfParProtocol-class, show,msgfParProtocol-method; getMSGFpar,msgfParTda-method, length,msgfParTda-method, msgfParTda, msgfParTda-class, show,msgfParTda-method; getMSGFpar,msgfParTolerance-method, length,msgfParTolerance-method, msgfParTolerance, msgfParTolerance-class, show,msgfParTolerance-method; msgfPar

Examples

parameters <- msgfPar(
                      database=system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'),
                      tolerance='20 ppm',
                      instrument='TOF',
                      enzyme='Lys-C'
                     )
getMSGFpar(parameters)
## 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)

thomasp85/MSGFplus-release documentation built on May 31, 2019, 11:09 a.m.