R/getChrOrder.R

In karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

#' Get chromosome order from a string of chromosome/contig names
#'
#' `getChrOrder()` takes a string of chromosome or contig names and returns the indices of the string in typical chromosome order, i.e. 1 through 22, X, Y.
#' Contig names that do not match 1:22, X, or Y are sorted numerically and alphabetically (with numbers coming first), and added to the end of the order.
#' The output string can then be used to sort the input string into typical chromosome order.
#'
#' @param chr.vector Character vector of chromosome or contig names.
#'
#' @return A numerical vector of the input vectors indices in chromosome order.
#' @export
#'
#' @concept build experiment
#'
#' @examples
#' chr.order <- getChrOrder(c(1, "virus", 5, "X", 22, "plasmid", "Y"))
#' ordered.vector <- c(1, "virus", 5, "X", 22, "plasmid", "Y")[chr.order]
getChrOrder <- function(chr.vector) {
  chr.df.input <- data.frame(index = seq_along(chr.vector), id = chr.vector)

  chr.df <- chr.df.input[which(chr.df.input$id %in% c(1:22, "X", "Y")), ]

  non.chr.df <- chr.df.input[which(!chr.df.input$id %in% c(1:22, "X", "Y")), ]

  chr.df.ordered <- chr.df[gtools::mixedorder(chr.df$id), ]
  non.chr.df.ordered <- non.chr.df[gtools::mixedorder(non.chr.df$id), ]

  chr.vector.order <- c(chr.df.ordered$index, non.chr.df.ordered$index)

  return(chr.vector.order)
}