filter_all_peptides {SWATH2stats} | R Documentation |
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)
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) }