GENOME <- "hg17"
ORGANISM <- "Homo sapiens"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:22, "X", "Y", "M"))
CIRC_SEQS <- "chrM"
.hap_sequences <- paste0("chr6_hla_hap", 1:2)
.random_sequences <- paste0("chr", c(1:10, 12:13, 15:19, 22, "X"), "_random")
.order_seqlevels <- function(seqlevels)
{
ordered_seqlevels <- c(ASSEMBLED_MOLECULES,
.hap_sequences,
.random_sequences)
stopifnot(length(seqlevels) == length(ordered_seqlevels))
idx <- match(ordered_seqlevels, seqlevels)
stopifnot(!anyNA(idx))
idx
}
FETCH_ORDERED_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)
}
NCBI_LINKER <- list(
assembly_accession="GCF_000001405.11",
special_mappings=c(chr6_hla_hap1="NG_002392.2",
chr6_hla_hap2="NG_002433.1"),
unmapped_seqs=list(
`assembled-molecule`="chrM",
`pseudo-scaffold`=.random_sequences)
)
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