Create a GRanges object from seqlengths

Usage

seqlengths_as_GRanges(x, seqnames = NULL)

Arguments

x: Any object that supports the seqlengths() method.
seqnames: A vector seqnames.

Details

It basically generates a GRanges treating whole chromosomes as genomic intervals.

Examples

require(TxDb.Hsapiens.UCSC.hg19.knownGene)
#> Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
#> Loading required package: GenomicFeatures
#> Loading required package: GenomeInfoDb
#> Loading required package: GenomicRanges
seqlengths_as_GRanges(TxDb.Hsapiens.UCSC.hg19.knownGene)
#> GRanges object with 93 ranges and 0 metadata columns:
#>              seqnames      ranges strand
#>                 <Rle>   <IRanges>  <Rle>
#>    [1]           chr1 1-249250621      *
#>    [2]           chr2 1-243199373      *
#>    [3]           chr3 1-198022430      *
#>    [4]           chr4 1-191154276      *
#>    [5]           chr5 1-180915260      *
#>    ...            ...         ...    ...
#>   [89] chrUn_gl000245     1-36651      *
#>   [90] chrUn_gl000246     1-38154      *
#>   [91] chrUn_gl000247     1-36422      *
#>   [92] chrUn_gl000248     1-39786      *
#>   [93] chrUn_gl000249     1-38502      *
#>   -------
#>   seqinfo: 93 sequences from an unspecified genome; no seqlengths
seqlengths_as_GRanges(TxDb.Hsapiens.UCSC.hg19.knownGene, 
    paste0("chr", c(1:22, "X", "Y")))
#> GRanges object with 24 ranges and 0 metadata columns:
#>        seqnames      ranges strand
#>           <Rle>   <IRanges>  <Rle>
#>    [1]     chr1 1-249250621      *
#>    [2]     chr2 1-243199373      *
#>    [3]     chr3 1-198022430      *
#>    [4]     chr4 1-191154276      *
#>    [5]     chr5 1-180915260      *
#>    ...      ...         ...    ...
#>   [20]    chr20  1-63025520      *
#>   [21]    chr21  1-48129895      *
#>   [22]    chr22  1-51304566      *
#>   [23]     chrX 1-155270560      *
#>   [24]     chrY  1-59373566      *
#>   -------
#>   seqinfo: 24 sequences from an unspecified genome; no seqlengths