Takes a GBreaks or a GRanges object and if seqlengths are not
available, sets them using the output of the guessSeqLengths function.
Usage
forceSeqLengths(x)
# S4 method for GRanges
forceSeqLengths(x)
# S4 method for GBreaks
forceSeqLengths(x)Value
forceSeqLengths returns the object in which the sequence lengths
have been set to the maximal end coordinates found in the object if if they
did not exist. For GBreaks objects it handles both the target and the
query ranges at the same time.
See also
Other modifier functions:
bridgeRegions(),
coalesce_contigs(),
flipInversions(),
guessSeqLengths(),
keepLongestPair(),
mergeSeqLevels(),
reverse(),
splitSeqLevel(),
swap()
Examples
# Prepare an example object with no seqlengths
gb <- exampleTranslocation
seqlengths(gb) <- seqlengths(gb$query) <- NA
gb
#> GBreaks object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | query
#> <Rle> <IRanges> <Rle> | <GRanges>
#> [1] chrA 100-200 + | chrB:100-200
#> [2] chrA 201-300 + | chrC:201-300
#> [3] chrA 301-400 + | chrB:301-400
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Note that the new seqlengths returned by forceSeqLengths are shorter
# because we can not guess about length of the unaligned ends.
forceSeqLengths(gb) |> seqlengths()
#> chrA
#> 400
exampleTranslocation |> seqlengths()
#> chrA
#> 600
# forceSeqLengths can take whole GBreaks objects as input, or simple GRanges
forceSeqLengths(gb)$query |> seqlengths()
#> chrB chrC
#> 400 300
forceSeqLengths(gb$query) |> seqlengths()
#> chrB chrC
#> 400 300
forceSeqLengths(granges(gb)) |> seqlengths()
#> chrA
#> 400