Load a cytoband annotation table — load

Loads UCSC-style cytoband annotations as a GRanges. With no arguments, returns the built-in cytoband_hg38 dataset. Given a path, reads a TSV cytoband file with columns chrom chromStart chromEnd name gieStain (the standard UCSC cytoBand layout).

Usage

load_cytobands(path = NULL, as_granges = TRUE)

Arguments

path: Optional path to a UCSC-style cytoband TSV. If NULL (default), the bundled cytoband_hg38 table is used.
as_granges: Logical. If TRUE (default), return a GRanges with name and gieStain as mcols — suitable for direct use with seq_ideogram(). If FALSE, return the raw data frame.

Value

A GRanges (default) or data.frame of cytobands.

Examples

cb <- load_cytobands()
head(cb)
#> GRanges object with 6 ranges and 2 metadata columns:
#>       seqnames            ranges strand |        name    gieStain
#>          <Rle>         <IRanges>  <Rle> | <character> <character>
#>   [1]     chr1         1-2300000      * |      p36.33        gneg
#>   [2]     chr1   2300001-5300000      * |      p36.32      gpos25
#>   [3]     chr1   5300001-7100000      * |      p36.31        gneg
#>   [4]     chr1   7100001-9100000      * |      p36.23      gpos25
#>   [5]     chr1  9100001-12500000      * |      p36.22        gneg
#>   [6]     chr1 12500001-15900000      * |      p36.21      gpos50
#>   -------
#>   seqinfo: 711 sequences from an unspecified genome; no seqlengths