Coalesce Pairwise Alignments
Arguments
- gb
GBreaksobject of the pairwise alignment.- tol
Unaligned region of width lesser than or equal to
tolin both the reference and query case will be bridged in coalescing.- minwidth
Remove the intervals whose width smaller than this value.
Value
Returns a new GBreaks object with a reduced number of alignments
fragments due to coalescion. The returned object is sorted ignoring strand.
For convenience during analysis sessions, its score is set to the width of
the ranges on the target genome.
Note
Fragmented alignments arising from incorrect basecalls, misassembly or misalignments can cause us to infer artificial breakpoints
Internally, coalesce_contigs uses flagColinearAlignments() See the
examples for details.
See also
Other Colinearity functions:
GOC(),
bridgeRegions(),
chain_contigs(),
dist2next(),
filterColinearRegions(),
flagColinearAlignments(),
flagPairs()
Other modifier functions:
bridgeRegions(),
flipInversions(),
forceSeqLengths(),
guessSeqLengths(),
keepLongestPair(),
mergeSeqLevels(),
reverse(),
splitSeqLevel(),
swap()
Examples
flagColinearAlignments(exampleColinear3, details = TRUE)
#> GBreaks object with 3 ranges and 10 metadata columns:
#> seqnames ranges strand | query tfoll qfoll tprev
#> <Rle> <IRanges> <Rle> | <GRanges> <integer> <integer> <integer>
#> [1] chrA 100-200 + | chrB:100-200 1 1 <NA>
#> [2] chrA 201-300 + | chrB:201-300 1 1 -1
#> [3] chrA 301-400 + | chrB:301-400 <NA> <NA> -1
#> qprev t_col q_col tdist qdist colinear
#> <integer> <logical> <logical> <numeric> <numeric> <logical>
#> [1] <NA> TRUE TRUE 1 1 TRUE
#> [2] -1 TRUE TRUE 1 1 TRUE
#> [3] -1 <NA> <NA> Inf Inf FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome
coalesce_contigs(exampleColinear3)
#> GBreaks object with 1 range and 2 metadata columns:
#> seqnames ranges strand | query score
#> <Rle> <IRanges> <Rle> | <GRanges> <integer>
#> [1] chrA 100-400 + | chrB:100-400 301
#> -------
#> seqinfo: 1 sequence from an unspecified genome
# Target range [1] precedes target range [2]
precede(exampleColinear3)
#> [1] 2 3 NA
# Query range [1] precedes query range [2]
precede(exampleColinear3$query)
#> [1] 2 3 NA
# Ranges on the minus strand
gb2 <- exampleColinear3 |> reverse() |> sort(ignore.strand = TRUE)
flagColinearAlignments(gb2, details = TRUE)
#> GBreaks object with 3 ranges and 10 metadata columns:
#> seqnames ranges strand | query tfoll qfoll tprev
#> <Rle> <IRanges> <Rle> | <GRanges> <integer> <integer> <integer>
#> [1] chrA 201-300 - | chrB:301-400 <NA> <NA> 1
#> [2] chrA 301-400 - | chrB:201-300 -1 -1 1
#> [3] chrA 401-501 - | chrB:100-200 -1 -1 <NA>
#> qprev t_col q_col tdist qdist colinear
#> <integer> <logical> <logical> <numeric> <numeric> <logical>
#> [1] 1 TRUE TRUE 1 1 TRUE
#> [2] 1 TRUE TRUE 1 1 TRUE
#> [3] <NA> <NA> <NA> Inf Inf FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome
coalesce_contigs(gb2)
#> GBreaks object with 1 range and 2 metadata columns:
#> seqnames ranges strand | query score
#> <Rle> <IRanges> <Rle> | <GRanges> <integer>
#> [1] chrA 201-501 - | chrB:100-400 301
#> -------
#> seqinfo: 1 sequence from an unspecified genome
# Target range [1] follows target range [2]
follow(gb2)
#> [1] 2 3 NA
# Or, ignoring strand, target range [1] precedes target range [2]
precede(gb2, ignore.strand = TRUE)
#> [1] 2 3 NA
# Query range [1] follows query range [2]
follow(gb2$query)
#> [1] 2 3 NA
# Coalescing strandless objects
gb3 <- exampleColinear3
gb4 <- gb2
strand(gb4) <- strand(gb3) <- "*"
coalesce_contigs(gb3)
#> GBreaks object with 1 range and 2 metadata columns:
#> seqnames ranges strand | query score
#> <Rle> <IRanges> <Rle> | <GRanges> <integer>
#> [1] chrA 100-400 * | chrB:100-400 301
#> -------
#> seqinfo: 1 sequence from an unspecified genome
coalesce_contigs(gb4)
#> GBreaks object with 1 range and 2 metadata columns:
#> seqnames ranges strand | query score
#> <Rle> <IRanges> <Rle> | <GRanges> <integer>
#> [1] chrA 201-501 * | chrB:100-400 301
#> -------
#> seqinfo: 1 sequence from an unspecified genome