When no GenomeInfoDb::seqlengths
are available, one can resort to set
them as to the maximal end coordinate found in the object.
Arguments
- gr
A
GenomicRanges::GRanges
object
Value
Returns sequence lengths that have been guessed as the maximal end
coordinates found in the gr
, or the gr
's seqlengths
if if they did
already exist.
See also
Other modifier functions:
bridgeRegions()
,
coalesce_contigs()
,
flipInversions()
,
forceSeqLengths()
,
keepLongestPair()
,
mergeSeqLevels()
,
reverse()
,
splitSeqLevel()
,
swap()
Examples
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
seqlengths(exampleTranslocation$query)
#> chrB chrC
#> 600 600
guessSeqLengths(exampleTranslocation$query)
#> chrB chrC
#> 600 600
gb2 <- exampleTranslocation
seqlengths(gb2$query) <- NA
guessSeqLengths(gb2$query)
#> chrB chrC
#> 400 300