Define the Pseudo-Autosomal Regions from a Seqinfo Object
Usage
parY(x, ...)
# S4 method for class 'Seqinfo'
parY(x, ...)
# S4 method for class 'character'
parY(x, prefix = NULL, ...)Arguments
- x
A Seqinfo object or any of named build. If passing a character vector,
match.arg()will be used to match the build.- ...
Not used
- prefix
Optional prefix to place before chromosome names. Can only be NULL, "" or "chr"
Details
Using a seqinfo object based on either hg38, hg19, CHM13.v2 or their variations, create a GRanges object with the Pseudo-Autosomal Regions from the Y chromosome for that build. The length of the Y chromosome on the seqinfo object is used to determine the correct genome build when passing a Seqinfo object. Otherwise
An additional mcols column called PAR will indicate PAR1 and PAR2
Examples
library(GenomeInfoDb)
sq <- Seqinfo(
seqnames = "chrY", seqlengths = 59373566, genome = "hg19_only_chrY"
)
parY(sq)
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | PAR
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chrY 10001-2649520 * | PAR1
#> [2] chrY 59034050-59363566 * | PAR2
#> -------
#> seqinfo: 1 sequence from hg19_only_chrY genome
## PAR regions for CHM13 are also available
sq <- Seqinfo(
seqnames = "chrY", seqlengths = 62460029, genome = "CHM13"
)
parY(sq)
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | PAR
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chrY 1-2458320 * | PAR1
#> [2] chrY 62122809-62460029 * | PAR2
#> -------
#> seqinfo: 1 sequence from CHM13 genome
## Or just call by name
parY("GRCh38", prefix = "chr")
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | PAR
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chrY 10001-2781479 * | PAR1
#> [2] chrY 56887903-57217415 * | PAR2
#> -------
#> seqinfo: 1 sequence from GRCh38 genome; no seqlengths