lengthRange: Get and set peptide length range in msgfPar objects

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

Get and set peptide length range in msgfPar objects

Description

These functions allow you to retrieve and set the residue length allowed for the peptides search for in MS-GF+

Usage

lengthRange(object)

lengthRange(object) <- value

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

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

## S4 replacement method for signature 'msgfPar,msgfParLengthRange'
lengthRange(object) <- value

Arguments

object	An msgfPar object
value	Either an integer vector or an msgfParLengthRange object

Value

In case of the getter an integer vector of length 2 giving the lower and upper bounds of the length range

Methods (by class)

• msgfPar: Get the lower and upper bounds of peptide lengths

• object = msgfPar,value = numeric: Set the lower and upper bounds of peptide lengths using an integer vector

• object = msgfPar,value = msgfParLengthRange: Set the lower and upper bounds of peptide lengths using an msgfParLengthRange

See Also

Other msgfPar-getter_setter: chargeRange, db, enzyme, fragmentation, instrument, isotopeError, matches, mods, ntt, protocol, tda, tolerance

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
lengthRange(parameters) <- c(6, 40)
lengthRange(parameters)

thomasp85/MSGFplus documentation built on Oct. 2, 2024, 9:26 a.m.