R/zzz.R

In TransBioInfoLab/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

#' @title Cache sesameData at Package Load
#' 
#' @description Check if the user has both the HM540 and EPIC manifests in their
#'   cache. The contents of the cache are checked via a call to the
#'   \code{ExperimentHub} function. If not all data components are available in
#'   the cache for these two platforms, we \code{\link[AnnotationHub]{query}} 
#'   the necessary data to save them to the cache for later use.
#'
#' @param libname path to package library
#' @param pkgname package name
#' 
#' 
#' @importFrom ExperimentHub ExperimentHub
#' @importFrom AnnotationHub query
#' @importFrom utils tail
#'
#' @details arguments are unused
#' 
#' @keywords internal
#' @name coMethDMR_setup
#'
NULL

.onLoad <- function(libname, pkgname){
  
  manifestsNeeded_char <- c(
    "HM450.hg19.manifest", "EPIC.hg19.manifest",
    "HM450.hg38.manifest", "EPIC.hg38.manifest"
  )
  
  
  ###  Check if data has been cached  ###
  packageStartupMessage("Checking for cached SeSAMe data.")
  ehub <- ExperimentHub::ExperimentHub(localHub = FALSE)
  cachedDataNames_char <- names(ehub)
  # platformInfo_df <- sesameData::sesameDataList()
  
  ahID_char <- vapply(
    X = manifestsNeeded_char,
    FUN = function(char) {
      res <- AnnotationHub::query(ehub, c("sesameData", char))
      tail(names(res[res$title == char,]),n = 1)
    },
    FUN.VALUE = character(1)
  )
  
  # # 450k
  # hmTitles_char <- c("HM450.hg19.manifest", "HM450.hg38.manifest")
  # ehNames450k_char <- platformInfo_df[
  #   platformInfo_df$"Title" %in% hmTitles_char, "EHID", drop = TRUE
  # ]
  # all450k_lgl <- all(ehNames450k_char %in% cachedDataNames_char)
  # 
  # # EPIC
  # epicTitles_char <- c("EPIC.hg19.manifest", "EPIC.hg38.manifest")
  # ehNamesEPIC_char <- platformInfo_df[
  #   platformInfo_df$"Title" %in% epicTitles_char, "EHID", drop = TRUE
  # ]
  # allEPIC_lgl <- all(ehNamesEPIC_char %in% cachedDataNames_char)
  
  
  ###  Download manifests as necessary  ###
  whichCached_lgl <- ahID_char %in% cachedDataNames_char
  if(any(!whichCached_lgl)) {
    packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")
  }
  for (ID in ahID_char[!whichCached_lgl]) {
    ehub[[ID, verbose = FALSE]]
  }
  
  # if(!all450k_lgl) {
  #   packageStartupMessage("Caching SeSAMe data for 450k arrays.")
  #   sesameDataCache("HM450")
  # }
  # if(!allEPIC_lgl) {
  #   packageStartupMessage("Caching SeSAMe data for EPIC arrays.")
  #   sesameDataCache("EPIC")
  # }
  
  invisible()
}