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

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

Removes lines in the dataset based on a prefix strings (contaminants, reverse or both).

Description

Removes lines in the dataset based on a 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

data(Exp1_R25_pept, package="DAPARdata")
StringBasedFiltering(
Exp1_R25_pept[seq_len(100)], "Potential_contaminant", "+", "Reverse", "+")

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.