Get gap regions from UCSC

Get gap regions from UCSC

getGapFromUCSC(genome, seqnames = NULL)

Arguments

genome

UCSC genome, such as "hg19".

seqnames

A vector of chromosome names.

Value

A GRanges object.

Examples

getGapFromUCSC("hg19")
#> GRanges object with 497 ranges and 0 metadata columns:
#>         seqnames            ranges strand
#>            <Rle>         <IRanges>  <Rle>
#>     [1]     chr1           1-10000      *
#>     [2]     chr1     177418-227417      *
#>     [3]     chr1     267720-317719      *
#>     [4]     chr1     471369-521368      *
#>     [5]     chr1   2634221-2684220      *
#>     ...      ...               ...    ...
#>   [493]     chrY 22369680-22419679      *
#>   [494]     chrY 23901429-23951428      *
#>   [495]     chrY 28819362-58819361      *
#>   [496]     chrY 58917657-58967656      *
#>   [497]     chrY 59363567-59373566      *
#>   -------
#>   seqinfo: 49 sequences from an unspecified genome; no seqlengths