R/findChr.R

In Timothy-Barry/coproanalysis: Analyze CoPRO and Related Data

#' Find chromosome
#'
#' Find the chromosome and position on that chromosome corresponding to a given ID5.
#'
#' @param pos an ID5
#'
#' @return the chromosome and position on the chromosome corresponding to that ID5
#' @export
#'
#' @examples
findChr = function(pos) {
  hg19chr = paste0( 'chr', c(1:22, 'X', 'Y', 'M') )
  hg19len   = c(  249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747,
                  135006516, 133851895, 115169878, 107349540, 102531392,  90354753,  81195210,  78077248,  59128983,  63025520,
                  48129895,  51304566, 155270560,  59373566,  16571)
  chrOffsets = cumsum(as.numeric(c(0, hg19len)))
  chrOffsets = chrOffsets[1:length(chrOffsets)-1]
  names(chrOffsets) = hg19chr

  m = min(which( chrOffsets > abs(pos) ))-1
  paste0(names(chrOffsets)[m], ":", prettyNum(abs(pos)-chrOffsets[m], big.mark=",", scientific=FALSE))
}