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] chrM 191-813 + | 984 NC_018044.1:61854-62304
#> [2] chrM 6313-9737 - | 9007 NC_018044.1:62854-65728
#> [3] chrM 12828-13986 + | 2733 NC_018044.1:22453-23578
#> [4] chrM 16435-18988 + | 12413 NC_018044.1:23579-26133
#> [5] chrM 20505-20650 + | 774 NC_018044.1:26134-26279
#> ... ... ... ... . ... ...
#> [501] chrXIII 769669-808526 + | 152331 NC_047499.1:762339-801278
#> [502] chrXIII 809285-837102 + | 115538 NC_047499.1:801658-829480
#> [503] chrXIII 837914-912582 + | 303512 NC_047499.1:830467-905221
#> [504] chrXIII 912605-917242 + | 13091 NC_047499.1:905399-910082
#> [505] chrXIII 919705-922192 + | 6580 NC_047501.1:1054871-1057371
#> -------
#> 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_018044.1 61854-62304 *
#> [2] NC_018044.1 62854-65728 *
#> [3] NC_018044.1 22453-23578 *
#> [4] NC_018044.1 23579-26133 *
#> [5] NC_018044.1 26134-26279 *
#> ... ... ... ...
#> [501] NC_047499.1 762339-801278 *
#> [502] NC_047499.1 801658-829480 *
#> [503] NC_047499.1 830467-905221 *
#> [504] NC_047499.1 905399-910082 *
#> [505] NC_047501.1 1054871-1057371 *
#> -------
#> seqinfo: 17 sequences from an unspecified genome; no seqlengths