#' @title Quantify the repeat space within a genome
#' @description Quantification of the repeat space (= total length of
#' all Repeat Masker annotated repeats) within a given genome of interest.
#' @param file file path to a fasta file storing the Repeat Masker annotation file.
#' @author Hajk-Georg Drost
#' @seealso \code{\link{quant.protein.space}}, \code{\link{quant.cds.space}}
#' @export
quant.repeat.space <- function(file) {
repeat_file <- biomartr::read_rm(file = file)
repeat_space_in_Mbp <-
sum(repeat_file$qry_width, na.rm = TRUE) / 1000000L
nRepeats <- length(repeat_file)
res <-
tibble::tibble(RepeatSpaceMbp = repeat_space_in_Mbp, nRepeats = nRepeats)
return(res)
}
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