filter_proteotypic_peptides: Filter for proteins that are supported by proteotypic...
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

View 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.

1	filter_proteotypic_peptides(data, rm.decoy = TRUE)

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

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

Peter Blattmann

 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)