Select all proteins that are supported by peptides. — filter_all

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 "/".

filter_all_peptides(data)

Arguments

data: A data frame containing SWATH data.

Value

Returns a data frame with the data from both proteotypic and non-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)
 data.all <- filter_all_peptides(data.filtered.decoy)
 }
#> Dimension difference: 931, 0
#> Number of proteins detected: 11
#> Protein identifiers: Protein6, Protein1, iRT_protein, Protein7, Protein4, Protein8