Concept examples of structural variants for test and demonstration purpose
Format
GBreaks objects described in more details in the
Structural Variants vignette, available with the command
vignette("StructuralVariants", package = "GenomicBreaks").
Details
The variants represented here are the ones that can be represented
in a GBreaks object. Short ones that are entirely contained in an
aligned region, for instance as a gap, are not covered
See also
Other Structural variants:
flagDoubleInversions(),
flagInversions(),
flagPairs(),
flagTranslocations(),
plotApairOfChrs()
Examples
exampleColinear
#> GBreaks object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-150 + | chrB:100-150
#> [2] chrA 251-300 + | chrB:251-300
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleNotColinear
#> GBreaks object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-150 + | chrB:201-251
#> [2] chrA 251-300 + | chrB:50-100
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleColinear3
#> GBreaks object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-200 + | chrB:100-200
#> [2] chrA 201-300 + | chrB:201-300
#> [3] chrA 301-400 + | chrB:301-400
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleColinear5
#> GBreaks object with 5 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-190 + | chrB:100-190
#> [2] chrA 200-290 + | chrB:200-290
#> [3] chrA 300-390 + | chrB:300-390
#> [4] chrA 400-490 + | chrB:400-490
#> [5] chrA 500-590 + | chrB:500-590
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleInversion
#> GBreaks object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-190 + | chrB:100-190
#> [2] chrA 210-291 - | chrB:210-291
#> [3] chrA 301-400 + | chrB:301-400
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleInversion5uncollapsed
#> GBreaks object with 5 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-190 + | chrB:100-190
#> [2] chrA 200-290 - | chrB:300-390
#> [3] chrA 300-390 - | chrB:200-290
#> [4] chrA 400-490 + | chrB:400-490
#> [5] chrA 500-590 + | chrB:500-590
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleNestedInversions
#> GBreaks object with 5 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-190 + | chrA:100-190
#> [2] chrA 200-290 - | chrA:400-490
#> [3] chrA 300-390 + | chrA:300-390
#> [4] chrA 400-490 - | chrA:200-290
#> [5] chrA 500-590 + | chrA:500-590
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleDoubleInversion1
#> GBreaks object with 5 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-190 + | chrB:100-190
#> [2] chrA 200-290 + | chrB:400-490
#> [3] chrA 300-390 - | chrB:200-290
#> [4] chrA 400-490 - | chrB:300-390
#> [5] chrA 500-590 + | chrB:500-590
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleTranslocation
#> GBreaks object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-200 + | chrB:100-200
#> [2] chrA 201-300 + | chrC:201-300
#> [3] chrA 301-400 + | chrB:301-400
#> -------
#> seqinfo: 1 sequence from an unspecified genome
exampleTranslocation2
#> GBreaks object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-200 + | chrB:100-200
#> [2] chrA 201-300 - | chrC:201-300
#> [3] chrA 301-400 + | chrB:301-400
#> -------
#> seqinfo: 1 sequence from an unspecified genome