getMSGFpar: Get a string representation of an msgfPar-related object
In thomasp85/MSGFplus: An interface between R and MS-GF+

getMSGFpar

R Documentation

Get a string representation of an msgfPar-related object

Description

The string representation is defined as the arguments that should get appended to the call when running MSGF+ in the terminal/command prompt

Usage

getMSGFpar(object)

Arguments

object

An msgfPar object or a related object

Value

A string that can be appended to a system() call to specify the parameters for the MSGF+ analysis

Examples

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

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