msgfPar: Constructor for the msgfPar class
In MSGFplus: An interface between R and MS-GF+

Description Usage Arguments Details Value References See Also Examples

This function creates an msgfPar object with the specified parameters. If some parameters have not been specified they will not be part of the MS-GF+ call and MS-GF+'s own defaults kicks in; Consult the MS-GF+ documentation for these. Note however that at least a database file is required to run an analysis.

1 2	msgfPar(database, tolerance, isotopeError, tda, fragmentation, instrument, enzyme, protocol, ntt, modification, lengthRange, chargeRange, matches)

`database`	The location of the fasta file to use as search database
`tolerance`	The parent ion tolerance to use. In simple cases a string in the form '20 ppm' or '1 Da' or an msgfParTolerance object if asymmetric tolerance is desired
`isotopeError`	The range of isotope errors used to correct for non-monoisotopic peaks. Either a numeric vector of length 2 specifying the lower and upper bounds of the range, or an msgfParIsotopeError object
`tda`	`Logical` Should Target-Decoy approach be used to calculate FDR values.
`fragmentation`	An integer specifying which fragmentation has been used during data acquisition. See details.
`instrument`	An integer specifying the type of instrument used during data acquisition. See details.
`enzyme`	An integer or name specifying the enzyme that has been used for protein digestion. See details.
`protocol`	An integer or name specifying the type of preparation that has been done for the samples. See details.
`ntt`	An integer specifying the cleavage specificity (Number of Tolerable Termini). 2 only allows fully tryptic peptide (if trypsin is used), 1 allows semitryptic peptides and 0 allows unspecific peptides
`modification`	An msgfParModificationList object or a list containing the named elements nMod and modifications containing respectively an integer with the number of allowed modifications per petide and the modifications to search for as msgfParModification
`lengthRange`	A two element vector containing the lower and upper bounds of the residue length to search for
`chargeRange`	A two element vector containing the lower and upper bounds of the charge range to search for
`matches`	The number of matches to report per spectrum

Please consult the MS-GF+ documentation for full description of the parameters

Fragmentation is usually specified as an integer according to the following lookup

0: As written in the spectrum or CID if no info
1: CID
2: ETD
3: HCD
4: Merge spectra from the same precursor

It is possible to use the full name of the description for a more litteral function call

Instrument can likewise be specified as an integer or as a name according to this list

0: LowRes
1: HighRes
2: TOF
3: QExactive

Enymes are specified in the same manner using the following list

0: Unspecific cleavage
1: Trypsin
2: Chymotrypsin
3: Lys-C
4: Lys-N
5: glutamyl endopeptidase (Glu-C)
6: Arg-C
7: Asp-N
8: alphaLP
9: No cleavage

The protocol informs MS-GF+ whether a special sample treatment has been performed as part of the analysis. The protocol is specified according to the following list

0: No protocol
1: Phosphorylation
2: iTRAQ
3: iTRAQPhospho

An msgfPar object

MS-GF+

Other msgfParClasses: msgfPar-class, msgfParChargeRange-class, msgfParEnzyme-class, msgfParFragmentation-class, msgfParInstrument-class, msgfParIsotopeError-class, msgfParLengthRange-class, msgfParMatches-class, msgfParModification-class, msgfParModificationList-class, msgfParNtt-class, msgfParProtocol-class, msgfParTda-class, msgfParTolerance-class

# Example of specifying all parameters - usually not necessary
parameters <- msgfPar(
                      database=system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'),
                      tolerance='20 ppm',
                      isotopeError=c(0, 2),
                      tda=TRUE,
                      fragmentation='CID',
                      instrument='TOF',
                      enzyme='Lys-C',
                      protocol='No protocol',
                      ntt=2,
                      modification=list(
                          nMod=2,
                          modifications=list(
                              list(name='Carbamidomethyl',
                                   composition='C2H3N1O1',
                                   residues='C',
                                   type='fix',
                                   position='any'
                              ),
                              list(name='Oxidation',
                                   mass=15.994915,
                                   residues='M',
                                   type='opt',
                                   position='any'
                              )
                          )
                      ),
                      lengthRange=c(6,40),
                      chargeRange=c(2,7),
                      matches=1
                     )
parameters