MSGFplus: getMSGFpar – R documentation

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getMSGFpar

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)

MSGFplus

An interface between R and MS-GF+

v1.24.0

GPL (>= 2)

Authors

Thomas Lin Pedersen

Initial release

2020-09-01