Maps unaligned regions of the target to the query genome when they are flanked by colinear regions.
Arguments
- gb
A
GBreaksobject.
Value
Returns a new GBreaks object of shorter length. Its length will
be zero if no bridge regions were found.
Note
Because some aligned regions can be directly adjacent (no gaps), the
returned GBreaks object may contain ranges of width zero, where the start
coordinate is 1 nucleotide higher than the end coordinate.
References
Bridge regions have also been called “simultaneous gaps” in the comparison of the mouse and human genomes by Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. (Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003;100(20):11484-11489. doi:10.1073/pnas.1932072100)
See also
Other Colinearity functions:
GOC(),
chain_contigs(),
coalesce_contigs(),
dist2next(),
filterColinearRegions(),
flagColinearAlignments(),
flagPairs()
Other modifier functions:
coalesce_contigs(),
flipInversions(),
forceSeqLengths(),
guessSeqLengths(),
keepLongestPair(),
mergeSeqLevels(),
reverse(),
splitSeqLevel(),
swap()
Examples
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
bridgeRegions(exampleColinear5)
#> GBreaks object with 4 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 191-199 * | chrB:191-199
#> [2] chrA 291-299 * | chrB:291-299
#> [3] chrA 391-399 * | chrB:391-399
#> [4] chrA 491-499 * | chrB:491-499
#> -------
#> seqinfo: 1 sequence from an unspecified genome
# Note the zero-width ranges when aligned regions are directly adjacent.
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
bridgeRegions(exampleColinear3)
#> GBreaks object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 201-200 * | chrB:201-200
#> [2] chrA 301-300 * | chrB:301-300
#> -------
#> seqinfo: 1 sequence from an unspecified genome