#' Download GISTIC2 peak-level data from the Firehose pipeline #' #' @description Access GISTIC2 level 4 copy number data through #' `gdac.broadinstitute.org` #' #' @param object A FirehoseData GISTIC type object #' #' @param peak The peak type, select from "wide", "narrow", "full". #' #' @param rm.chrX (logical default TRUE) Whether to remove observations in the #' X chromosome #' #' @return A `data.frame` of peak values #' #' @importFrom GenomicRanges seqnames order #' @importFrom GenomeInfoDb orderSeqlevels seqlevels seqlevels<- #' @importFrom methods as #' #' @author Ludwig Geistlinger #' #' @examples #' #' co <- getFirehoseData("COAD", clinical = FALSE, GISTIC = TRUE) #' peaks <- getGISTICPeaks(co, "wide") #' class(peaks) #' head(peaks)[1:6] #' #' @export getGISTICPeaks <- function( object, peak = c("wide", "narrow", "full"), rm.chrX = TRUE ) { stopifnot(is(object, "FirehoseData") || is(object, "FirehoseGISTIC")) gistic <- getData(object, "GISTIC", "Peaks") validCols <- vapply(gistic, function(x) !all(is.na(x)), logical(1L)) rel.rows <- grepl("Peak +[0-9]+$", gistic[["Unique.Name"]]) gistic <- gistic[rel.rows, validCols] isBCodes <- grepl("^TCGA", names(gistic)) names(gistic)[isBCodes] <- .stdIDs(names(gistic)[isBCodes]) # (a) get the ranges from chosen peaks peak <- match.arg(peak, c("wide", "narrow", "full")) peak.col <- switch (peak, wide = "Wide.Peak.Limits", narrow = "Peak.Limits", full = "Region.Limits" ) ranges <- gistic[, peak.col] ranges <- sub("\\(probes [0-9]+:[0-9]+\\) *$", "", ranges) grs <- as(ranges, "GRanges") if (rm.chrX) { chrx_ind <- seqnames(grs) != "chrX" grs <- grs[chrx_ind] gistic <- gistic[as.logical(chrx_ind),] ranges <- ranges[as.logical(chrx_ind)] } gistic <- cbind.data.frame(rowRanges = ranges, gistic, stringsAsFactors = FALSE) seq_ind <- orderSeqlevels(seqlevels(grs)) seqlevels(grs) <- seqlevels(grs)[seq_ind] range_ind <- order(grs) gistic[range_ind, ] }