R/getGM12878.R

In REMP: Repetitive Element Methylation Prediction

#' @title Get methylation data of HapMap LCL sample GM12878 profiled by
#' Illumina 450k array or EPIC array
#'
#' @description
#' \code{getGM12878} is used to obtain public available methylation profiling
#' data of HapMap LCL sample GM12878.
#'
#' @param arrayType Illumina methylation array type. Currently \code{"450k"}
#' and \code{"EPIC"} are supported. Default = \code{"450k"}.
#' @param mapGenome Logical parameter. If \code{TRUE}, function will return
#' a \code{\link{GenomicRatioSet}} object instead of a \code{link{RatioSet}}
#' object.

#' @details
#' Illumina 450k data were sourced and curated from ENCODE
#' \url{http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12878SitesRep1.bed.gz}.
#' Illumina EPIC data were obtained from data package \code{minfiDataEPIC}.
#'
#' @return A \code{\link{RatioSet}} or \code{\link{GenomicRatioSet}} containing
#' beta value and M value of the methylation data.
#'
#' @examples
#' \dontrun{
#' # Get GM12878 methylation data (450k array)
#' if (!exists("GM12878_450k")) GM12878_450k <- getGM12878("450k")
#' GM12878_450k
#' }
#' 
#' # Get GM12878 methylation data (EPIC array)
#' if (!exists("GM12878_EPIC")) GM12878_EPIC <- getGM12878("EPIC")
#' GM12878_EPIC
#' @export
getGM12878 <- function(arrayType = c("450k", "EPIC"), mapGenome = FALSE) {
  arrayType <- match.arg(arrayType)

  if (toupper(arrayType) == "450K") {
    ### GM12878-450k
    GM12878_450k <- .webDownload(url = remp_options(".default.GM12878.450k.URL"),
                                 tag = "remp.GM12878.450k.file", 
                                 col_types = readr::cols_only(X4 = readr::col_character(),
                                                              X5 = readr::col_integer()))
    GM12878_450k.d <- as.matrix(GM12878_450k$X5 / 1000, ncol = 1)
    colnames(GM12878_450k.d) <- "GM12878"
    rownames(GM12878_450k.d) <- GM12878_450k$X4
    GM12878.RatioSet <- minfi::RatioSet(
      Beta = GM12878_450k.d, M = .toM(GM12878_450k.d),
      annotation = c(
        array = "IlluminaHumanMethylation450k",
        annotation = remp_options(".default.450k.annotation")
      )
    )
    if (mapGenome) {
      GM12878.RatioSet <- minfi::mapToGenome(GM12878.RatioSet)
    }
  }

  if (toupper(arrayType) == "EPIC") {
    ### GM12878-850k
    requireNamespace("minfiDataEPIC", quietly = TRUE)
    GM12878_EPIC.beta <- minfi::getBeta(minfiDataEPIC::MsetEPIC)

    GM12878_EPIC.beta <- rowMeans(GM12878_EPIC.beta, na.rm = TRUE)
    GM12878_EPIC.M <- .toM(GM12878_EPIC.beta)

    GM12878_EPIC.beta.d <- matrix(GM12878_EPIC.beta, ncol = 1)
    GM12878_EPIC.M.d <- matrix(GM12878_EPIC.M, ncol = 1)

    colnames(GM12878_EPIC.beta.d) <- "GM12878"
    colnames(GM12878_EPIC.M.d) <- "GM12878"

    rownames(GM12878_EPIC.beta.d) <- names(GM12878_EPIC.beta)
    rownames(GM12878_EPIC.M.d) <- names(GM12878_EPIC.M)

    GM12878.RatioSet <- minfi::RatioSet(
      Beta = GM12878_EPIC.beta.d,
      M = GM12878_EPIC.M.d,
      annotation = c(
        array = "IlluminaHumanMethylationEPIC",
        annotation = remp_options(".default.epic.annotation")
      )
    )
    if (mapGenome) {
      GM12878.RatioSet <- minfi::mapToGenome(GM12878.RatioSet)
    }
  }

  return(GM12878.RatioSet)
} ## End of getGM12878