ranges-info {plyranges} | R Documentation |
To construct annotations by supplying annotation information
use genome_info
. This function allows you to get UCSC build information
via GenomeInfoDb::fetchExtendedChromInfoFromUCSC()
. To add
annotations to an existing Ranges object use set_genome_info
. To retrieve
an annotation as a Ranges object use get_genome_info
.
genome_info( genome = NULL, seqnames = NULL, seqlengths = NULL, is_circular = NULL ) set_genome_info( .data, genome = NULL, seqnames = NULL, seqlengths = NULL, is_circular = NULL ) get_genome_info(.data)
genome |
A character vector of length one indicating the genome build. If this is the only argument supplied, the build information will be retrieved from UCSC database. |
seqnames |
A character vector containing the name of sequences. |
seqlengths |
An optional integer vector containg the lengths of sequences. |
is_circular |
An optional logical vector indicating whether a sequence is ciruclar. |
.data |
A Ranges object to annotate or retrieve an annotation for. |
a GRanges object containing annotations. To retrieve the annotations
as a Ranges object use get_genome_info
.
GenomeInfoDb::Seqinfo()
, GenomeInfoDb::fetchExtendedChromInfoFromUCSC()
x <- genome_info(genome = "toy", seqnames = letters[1:4], seqlengths = c(100, 300, 15, 600), is_circular = c(NA, FALSE, FALSE, TRUE)) x rng <- as_granges(data.frame(seqnames = "a", start = 30:50, width = 10)) rng rng <- set_genome_info(rng, genome = "toy", seqnames = letters[1:4], seqlengths = c(100, 300, 15, 600), is_circular = c(NA, FALSE, FALSE, TRUE)) get_genome_info(rng) ## Not run: if (interactive()) { # requires internet connection genome_info(genome = "hg38") } ## End(Not run)