Guided scaffolding
Arguments
- gr
A GenomicRanges::GRanges object.
- guide
A named list of data frames of contig names and orientations.
- drop
Drop the contigs that were not included in the guide. The new sequence levels will be in the same order as in the
guide.
See also
Other scaffolding functions:
flipStrandNames(),
longestMatchesInTarget(),
mergeSeqLevels(),
splitSeqLevel(),
strandNames()
Examples
(gr <- GRanges(c("chrB:100-200:+", "chrC:201-300:+",
"chrB:301-400:+", "chrD:100-200:+")) |> forceSeqLengths())
#> GRanges object with 4 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chrB 100-200 +
#> [2] chrC 201-300 +
#> [3] chrB 301-400 +
#> [4] chrD 100-200 +
#> -------
#> seqinfo: 3 sequences from an unspecified genome
(g <- list(
chrD = data.frame(contig = "chrD", orientation = 1),
chrBC = data.frame(contig = c("chrB", "chrC"), orientation = c(1,-1))))
#> $chrD
#> contig orientation
#> 1 chrD 1
#>
#> $chrBC
#> contig orientation
#> 1 chrB 1
#> 2 chrC -1
#>
scaffoldByFlipAndMerge(gr, g, drop = TRUE)
#> GRanges object with 4 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chrD 100-200 +
#> [2] chrBC 100-200 +
#> [3] chrBC 301-400 +
#> [4] chrBC 401-500 -
#> -------
#> seqinfo: 2 sequences from an unspecified genome