filter_all_peptides: Select all proteins that are supported by peptides.
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

This function can be used as opposed to the function "filter_proteotypic_peptides()". This function counts all proteins (including proteins supported by non proteo-typic (i.e. shared) peptides). All peptides (incl. non proteotypic peptides are selected. For the proteins supported by proteotypic peptide the "1/" in front of the identifier is removed to facilitate further data processing. The protein identifier of shared peptides needs to be separated by a slash "/".

1	filter_all_peptides(data)

data

A data frame containing SWATH data.

Returns a data frame with the data from both proteotypic and non-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_all_peptides(data.filtered.decoy)
 }