R/filter_proteotypic_peptides.R

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

#' Filter for proteins that are supported by proteotypic peptides.
#'
#' 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.
#'
#' @param data  A data frame containing SWATH data.
#' @param rm.decoy  Option to remove the decoys during filtering.
#' @return  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)
#'  data.all <- filter_proteotypic_peptides(data.filtered.decoy)
#' @export
filter_proteotypic_peptides <- function(data, 
                                        rm.decoy = TRUE) {
    data <- unifyProteinGroupLabels(data)
    if (isTRUE(rm.decoy)) {
        data <- removeDecoyProteins(data)
    }

    data.proteins <- gsub("^[[:digit:]]\\/", "", data$ProteinName)
    data.proteins <- unlist(strsplit(as.character(data.proteins), "\\/"))
    data.proteins <- unique(data.proteins)

    message("Number of proteins detected: ", length(data.proteins), "\n",
            "Protein identifiers: ", paste(head(data.proteins), collapse = ", "))
    
    ## Delete non-unique features (unique features have '1/' in front of protein name)
    data.unique <- data[grep("^1/", data$ProteinName), ]
    data.unique$ProteinName <- gsub("^1\\/", "", data.unique$ProteinName)
    
    message("Number of proteins detected that are supported by a proteotypic peptide: ",
            length(unique(data.unique$ProteinName)),
            "\n", "Number of proteotypic peptides detected: ",
            length(unique(data.unique$FullPeptideName)))
    
    return(data.unique)
}