inst/registered/UCSC_genomes/rn4.R

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

GENOME <- "rn4"
ORGANISM <- "Rattus norvegicus"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:20, "X", "M"))
CIRC_SEQS <- "chrM"

library(GenomeInfoDb)  # for fetch_chrom_sizes_from_UCSC()

.order_seqlevels <- function(seqlevels)
{
    random <- paste0("chr", c(1:20, "X", "Un"), "_random")
    ordered_seqlevels <- c(ASSEMBLED_MOLECULES, random, "chrUn")
    stopifnot(length(seqlevels) == length(ordered_seqlevels))
    idx <- match(ordered_seqlevels, seqlevels)
    stopifnot(!anyNA(idx))
    idx
}

GET_CHROM_SIZES <- function(goldenPath.url=getOption("UCSC.goldenPath.url"))
{
    chrom_sizes <- GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME,
                                              goldenPath.url=goldenPath.url)
    oo <- .order_seqlevels(chrom_sizes[ , "chrom"])
    S4Vectors:::extract_data_frame_rows(chrom_sizes, oo)
}