The GBreaks class is a simple wrapper to the GRanges class.
Details
Aligned sequences of the target genome are represented as the main
ranges of the GRanges object, and their counterparts in the query genome
are represented as a GRanges object sored in the the metadata column
query.
See also
Other Bioconductor API functions:
as(),
getSeq(),
pairwiseAlignment(),
range_GBreaks(),
reverse(),
subsetByOverlaps_GBreaks()
Examples
gb <- load_genomic_breaks(system.file("extdata/SacCer3__SacPar.gff3.gz", package = "GenomicBreaks"))
gb
#> GBreaks object with 505 ranges and 2 metadata columns:
#> seqnames ranges strand | score query
#> <Rle> <IRanges> <Rle> | <numeric> <GRanges>
#> [1] chrI 5860-10010 + | 10609 NC_047487.1:8723-12716
#> [2] chrI 11157-11782 + | 1253 NC_047487.1:13035-13680
#> [3] chrI 25371-26528 + | 3651 NC_047487.1:15380-16537
#> [4] chrI 26849-29699 + | 6130 NC_047487.1:17263-20175
#> [5] chrI 29937-30607 + | 767 NC_047487.1:20203-20866
#> ... ... ... ... . ... ...
#> [501] chrM 67039-67870 + | 1441 NC_018044.1:7758-8439
#> [502] chrM 68205-68580 + | 830 NC_018044.1:8783-9180
#> [503] chrM 69178-76168 + | 14528 NC_018044.1:9650-16261
#> [504] chrM 77356-80022 + | 8066 NC_018044.1:53206-55865
#> [505] chrM 80919-85779 + | 6712 NC_018044.1:57885-61592
#> -------
#> seqinfo: 17 sequences from an unspecified genome; no seqlengths
gb$query
#> GRanges object with 505 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] NC_047487.1 8723-12716 *
#> [2] NC_047487.1 13035-13680 *
#> [3] NC_047487.1 15380-16537 *
#> [4] NC_047487.1 17263-20175 *
#> [5] NC_047487.1 20203-20866 *
#> ... ... ... ...
#> [501] NC_018044.1 7758-8439 *
#> [502] NC_018044.1 8783-9180 *
#> [503] NC_018044.1 9650-16261 *
#> [504] NC_018044.1 53206-55865 *
#> [505] NC_018044.1 57885-61592 *
#> -------
#> seqinfo: 17 sequences from an unspecified genome; no seqlengths