R/loadFilteredResultsAsGRanges.R

In AdrijaK/omicsWrappers: wrapper functions for integrating and visualising ChIPseq, ATACseq, Hi-C, pcHi-C and RNAseq data

#' load snakePipes Filtered.results.*.bed file as GRanges object with appropriate column names
#'
#' loads snakePipes Filtered.results.*.bed file as GRanges object, giving appropriate column names
#' @param pathToFile (string) an absolute or relative path to a file
#' @export

loadFilteredResultsAsGRanges = function(pathToFile){

  columnNames =
    c("chr", "start", "end", "width", "strand", "score", "nWindows", "logFC.up", "logFC.down", "PValue", "FDR", "direction", "best.logFC" , "best.start", "name")

  output =
    data.table::fread(pathToFile, col.names = columnNames) %>%
    dplyr::mutate(start = start+1) %>%
    as("GRanges")

  return(output)

}