MSGFplus: mods – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

mods

Get and set the modifications in msgfPar objects

Description

These functions allow you to retrieve and set the specific modifications allowed on peptides during MS-GF+ search, as well as the number allowed on each peptide

Usage

mods(object)

mods(object) <- value

nMod(object)

nMod(object) <- value

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

## S4 replacement method for signature 'msgfPar,msgfParModificationList'
mods(object) <- value

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

## S4 replacement method for signature 'msgfPar,numeric'
nMod(object) <- value

Arguments

`object`	An msgfPar object
`value`	An msgfParModificationList object or in the case of nMod an integer

Value

For the getter an msgfParModificationList object or an integer (in the case of nMod)

Methods (by class)

msgfPar: Get the list of modifications allowed during peptide search
object = msgfPar,value = msgfParModificationList: Set the list of modifications allowed during peptide search
msgfPar: Get the number of peptides allowed per peptide during search
object = msgfPar,value = numeric: Set the number of peptides allowed per peptide during search using an integer

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
nMod(parameters) <- 2
mods(parameters)[[1]] <- msgfParModification(
                                                      name='Carbamidomethyl',
                                                      composition='C2H3N1O1',
                                                      residues='C',
                                                      type='fix',
                                                      position='any'
                                                     )
mods(parameters)

MSGFplus

An interface between R and MS-GF+

v1.24.0

GPL (>= 2)

Authors

Thomas Lin Pedersen

Initial release

2020-09-01