R/import_wiggle.R

In hochwagenlab/hwglabr2: Collection of R functions used in the Hochwagen Lab

#' Import wiggle data generated by the lab's ChIP-seq analysis pipeline
#'
#' Given a path to a collection of 16 tab-separated wiggle data files (one per
#' yeast chromosome), imports data into a \code{GRanges} object.
#' @param path Path to the folder containing the wiggle data. No default.
#' @param local_copy Logical indicating whether to create local copy of target
#' file before importing data. If \code{TRUE} a local copy is automatically
#' created and deleted after use. Use this argument to avoid reading files
#' directly from shared locations (namely \code{LabShare}).
#' Defaults to \code{TRUE}.
#' @return \code{GRanges} object.
#' @examples
#' \dontrun{
#' x <- import_wiggle('wiggle_data/')
#' 
#' dot1 <- import_wiggle('/Volumes/LabShare/HTGenomics/HiSeqOutputs/\
#'                       AveReps_SacCer3_MACS2/Red1-dot1D-195-16-reps-MACS2/',
#'                       local_copy=TRUE)
#' }
#' @export

import_wiggle <- function(path, local_copy=TRUE){
  t0  <- proc.time()[3]
  
  # IO checks
  if (is(path, "character")  & length(list.files(path)) != 0) {
    check_path(path)
  } else stop("'path' argument must be a path to a folder")
  
  check_package("hwglabr")
  check_package("GenomicRanges")
  check_package("IRanges")
  check_package('pbapply')
  
  if (local_copy) path <- make_local_copy(path)
  
  # Import wiggle data
  message('Loading wiggle files...')
  suppressMessages(df <- hwglabr::readall_tab(path, localCopy=F,
                                              asBedGraph=TRUE))
  
  if (local_copy) {
    message('(deleting local copy...)')
    unlink('hwglabr2_imports_temp', recursive = TRUE)
  }
  
  if('strand' %in% colnames(df)){
    df$strand <- gsub(pattern="[^+-]+", replacement = '*', x = df$strand)
  }
  
  message('Converting to "GRanges" object...')
  gr <- with(df, GenomicRanges::GRanges(chr, IRanges::IRanges(start, end),
                                        score=score)) 

  message('---')
  message('Completed in ', hwglabr2::elapsed_time(t0, proc.time()[3]))
  
  return(gr)
}