To construct annotations by supplying annotation information
use genome_info. 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)A character vector of length one indicating the genome build.
A character vector containing the name of sequences.
An optional integer vector containg the lengths of sequences.
An optional logical vector indicating whether a sequence is ciruclar.
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.
x <- genome_info(genome = "toy",
seqnames = letters[1:4],
seqlengths = c(100, 300, 15, 600),
is_circular = c(NA, FALSE, FALSE, TRUE))
x
#> GRanges object with 4 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> a a 1-100 *
#> b b 1-300 *
#> c c 1-15 *
#> d d 1-600 *
#> -------
#> seqinfo: 4 sequences (1 circular) from toy genome
rng <- as_granges(data.frame(seqnames = "a", start = 30:50, width = 10))
rng
#> GRanges object with 21 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] a 30-39 *
#> [2] a 31-40 *
#> [3] a 32-41 *
#> [4] a 33-42 *
#> [5] a 34-43 *
#> ... ... ... ...
#> [17] a 46-55 *
#> [18] a 47-56 *
#> [19] a 48-57 *
#> [20] a 49-58 *
#> [21] a 50-59 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
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)
#> GRanges object with 4 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> a a 1-100 *
#> b b 1-300 *
#> c c 1-15 *
#> d d 1-600 *
#> -------
#> seqinfo: 4 sequences (1 circular) from toy genome
if (FALSE) {
if (interactive()) {
# requires internet connection
genome_info(genome = "hg38")
}
}