Coerce (and optionally remove) all RaggedExperiments in a curatedTCGAData MAE.

simplifyTCGAData.R

simplifyTCGAData <- function(obj, removeRaggedExperiments=TRUE){
##This function will convert mutations to a genes x samples RangedSummarizedExperiment of 1 for non-silent mutations, 1 for silent or no mutation
##It will convert segmented copy number to copy number per gene, using a weighted average if there are non-disjunct ranges  
  suppressPackageStartupMessages({
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(org.Hs.eg.db)
    library(GenomeInfoDb)
  })
  gn <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
  gn <- keepStandardChromosomes(granges(gn), pruning.mode="coarse")
  seqlevelsStyle(gn) <- "NCBI"
  names(gn) <- mapIds(org.Hs.eg.db, names(gn), keytype = "ENTREZID", column = "SYMBOL")
  ##
  weightedmean <- function(scores, ranges, qranges)
    ## weighted average score per query range
    sum(scores * width(ranges)) / sum(width(ranges))
  ##
  nonsilent <- function(scores, ranges, qranges)
    any(scores != "Silent")
  ##
  isRE <- function(x) vapply(experiments(x), function(y) is(y, "RaggedExperiment"), TRUE)
  ##
  isMut <- function(x) grepl("Mutation", names(x))
  ##
  for (i in which(isMut(obj))){
    mutations <- qreduceAssay(obj[[i]], gn, nonsilent, "Variant_Classification")
    rownames(mutations) <- names(gn)
    mutations[is.na(mutations)] <- 0
    remove.rows <- is.na(rownames(mutations))
    mutations <- SummarizedExperiment(mutations[!remove.rows, ], rowRanges=gn[!remove.rows])
    el <- ExperimentList(x=mutations)
    names(el) <- paste0(names(obj)[i], "_simplified")
    obj <- c(obj, el)
    rm(el, mutations)
  }
  for (i in which(isRE(obj) & !isMut(obj))){
    suppressWarnings(
      cn <- qreduceAssay(obj[[i]], gn, weightedmean, "Segment_Mean")
    )
    rownames(cn) <- names(gn)
    remove.rows <- is.na(rownames(cn))
    cn <- SummarizedExperiment(cn[!remove.rows, ], rowRanges=gn[!remove.rows])
    el <- ExperimentList(x=cn)
    names(el) <- paste0(names(obj)[i], "_simplified")
    obj <- c(obj, el)
  }
  if(removeRaggedExperiments){
    obj <- obj[, , !isRE(obj)]
  }
  return(obj)
}