Guesstimate seqlevel lengths

When no GenomeInfoDb::seqlengths are available, one can resort to set them as to the maximal end coordinate found in the object.

Usage

guessSeqLengths(gr)

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()

Author

Charles Plessy

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