R/get_chromHMM_annotation.R

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

#' Download ChromHMM annotation file(s)
#'
#' Download ChromHMM annotation file(s) for a given cell-line
#'  (returned as a \link[GenomicRanges]{GRanges} object) 
#'  or a list of cell-lines
#'  (returned as a named list of \link[GenomicRanges]{GRanges} objects).
#'  All annotations are aligned to the hg19 genome build.
#'  All data can be found on the UCSC Genome Browser 
#'  \href{https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/}{
#'  here}. 
#' @param cell_line ChromHMM annotation for user-specified cell-line.
#' Cell-line options are:
#' \itemize{
#'   \item "K562" = K-562 cells
#'   \item "Gm12878" = Cellosaurus cell-line GM12878
#'   \item "H1hesc" = H1 Human Embryonic Stem Cell
#'   \item "Hepg2" = Hep G2 cell
#'   \item "Hmec" = Human Mammary Epithelial Cell
#'   \item "Hsmm" = Human Skeletal Muscle Myoblasts
#'   \item "Huvec" = Human Umbilical Vein Endothelial Cells
#'   \item "Nhek" = Normal Human Epidermal Keratinocytes
#'   \item "Nhlf" = Normal Human Lung Fibroblasts
#' } 
#' @returns Cell-line specific ChromHMM annotation file. Default K562 cell-line.
#' @importFrom genomation readBed
#' @import GenomicRanges
#' @keywords internal
get_chromHMM_annotation <- function(
        cell_line,
        cache=BiocFileCache::BiocFileCache(ask = FALSE)){
  #use bioconductor caching package
  check_dep("BiocFileCache")
  cell_line <- check_cell_lines(cell_lines = cell_line) 
  chromHMM_list_all <- lapply(cell_line, function(x){
      chrHMM_url <- paste0("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/",
                           "encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmm",
                           x,"HMM.bed.gz")
      chrHMM <- genomation::readBed(chrHMM_url)
      chromHMM_list <- split(chrHMM, chrHMM$name, drop = TRUE)
      msg <- paste0("Adding ",x,"'s chrHMM to local cache,",
                    "future invocations will use local image.")
      if (!checkCache(cache,chrHMM_url)) message(msg)
      path <- BiocFileCache::bfcrpath(cache, chrHMM_url)
      # chrHMM <- genomation::readBed(path)
      return(chromHMM_list)
  }) 
  names(chromHMM_list_all) <- cell_line
  if(length(chromHMM_list_all)==1) {
      return(chromHMM_list_all[[1]])
  } else {
      chromHMM_list_all
  } 
}