Filter for proteins that are supported by proteotypic peptides.

Source: R/filter_proteotypic_peptides.R

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.

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

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)
#> Dimension difference: 931, 0
 data.all <- filter_proteotypic_peptides(data.filtered.decoy)
#> Number of proteins detected: 11
#> Protein identifiers: Protein6, Protein1, iRT_protein, Protein7, Protein4, Protein8
#> Number of proteins detected that are supported by a proteotypic peptide: 9
#> Number of proteotypic peptides detected: 241