StringBasedFiltering: Removes lines in the dataset based on a prefix strings...

In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description

This function removes lines in the dataset based on prefix strings (contaminants, reverse or both).

Usage

StringBasedFiltering(
  obj,
  idCont2Delete = NULL,
  prefix_Cont = NULL,
  idRev2Delete = NULL,
  prefix_Rev = NULL
)

Arguments

obj	An object of class MSnSet.
idCont2Delete	The name of the column that correspond to the contaminants to filter
prefix_Cont	A character string that is the prefix for the contaminants to find in the data
idRev2Delete	The name of the column that correspond to the reverse data to filter
prefix_Rev	A character string that is the prefix for the reverse to find in the data

Value

An list of 4 items : obj : an object of class MSnSet in which the lines have been deleted deleted.both : an object of class MSnSet which contains the deleted lines corresponding to both contaminants and reverse, deleted.contaminants : n object of class MSnSet which contains the deleted lines corresponding to contaminants, deleted.reverse : an object of class MSnSet which contains the deleted lines corresponding to reverse,

Author(s)

Samuel Wieczorek

Examples

utils::data(Exp1_R25_pept, package='DAPARdata')
StringBasedFiltering(Exp1_R25_pept, 'Potential_contaminant', '+', 'Reverse', '+')

DAPAR documentation built on April 11, 2021, 6 p.m.