SWATH2stats (version 1.2.3)

filter_all_peptides: Select all proteins that are supported by peptides.

Description

This functions counts all proteins that are supported by peptides (including non proteo-typic peptides). All peptides (incl. non proteotypic peptides are selected. For the proteins supproted by proteotypic peptide the "1/" in front of the identifier is removed to facilitate further data processing.

Usage

filter_all_peptides(data)

Arguments

data

A data frame containing SWATH data.

Value

Examples

data("OpenSWATH_data", package="SWATH2stats")
data("Study_design", package="SWATH2stats")
data <- sample_annotation(OpenSWATH_data, Study_design)
data.filtered.decoy <- filter_mscore(data, 0.01) 
data.all <- filter_all_peptides(data.filtered.decoy)