filter_proteotypic_peptides: Filter for proteins that are supported by proteotypic...

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Filter for proteins that are supported by proteotypic peptides.

Description

Peptides can match to several proteins. With this function proteotypic peptides, peptides that are only contained in one protein are selected. Additionally the number of proteins are counted and printed.

Usage

filter_proteotypic_peptides(data, rm.decoy = TRUE)

Arguments

data	A data frame containing SWATH data.
rm.decoy	Option to remove the decoys during filtering.

Value

Returns a data frame with only the data supported by proteotypic peptides.

Author(s)

Peter Blattmann

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_proteotypic_peptides(data.filtered.decoy)

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.