R/unifyProteinGroupLabels.R

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

#' Unify the protein group labels.
#'
#' Unify the protein group labels (2/ProteinA/ProteinB and 2/ProteinB/ProteinA)
#' to one common label (e.g. 2/ProteinA/ProteinB)
#'
#' @param data  A data frame containing SWATH data.
#' @param column Which column to use for unifying the protein group identifiers.
#' @return Returns a data frame with the unififed protein labels.
#' @author Moritz Heusel
#' @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.unified <- unifyProteinGroupLabels(data.filtered.decoy)
#' @export
unifyProteinGroupLabels <- function(data,
                                    column = "ProteinName"){
    data[,column] <- as.character(data[,column])
    ids <- grep("^([2-9])|([1-9][0-9][0-9]*)/", data[,column])
    identifiers <- data[ids, column]
    identifiers_split <- strsplit(as.character(identifiers), "/")
    identifiers_split_sorted <- lapply(identifiers_split, function(x) {
        sort(x)
    })
    identifiers_sorted <- vapply(identifiers_split_sorted, function(x) {
        paste(x, collapse = "/")
    }, "a")
    data[ids, column] <- identifiers_sorted
    return(data)
}