The GBreaks class is a simple wrapper to the GenomicRanges::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:
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