Whole-genome classification object

Classifies aligned genomic regions as isolated or collinear, and unaligned regions as breakpoint or bridge regions. The bridge regions are always flanked by collinear alignments and the isolated alignments are always flanked by breakpoint regions.

Usage

wholeGenomeClassification(gb, coa = coalesce_contigs(gb), ends = FALSE)

Arguments

gb

A GBreaks object representing a one-to-one whole genome alignment.

coa

The coalesced one-to-one alignment. If not provided, it will be\ computed on-the-fly with the coalesce_contigs function.

ends

Add a a end region type for the extremities of the sequence features not covered by the original alignment.

Value

A GenomicRanges::GRanges object representing the target genome, inheriting its sequence information (GenomeInfoDb::Seqinfo). The class of each region is indicated by a factor in the type metadata column.

Details

The strand of bridge regions is the one of their flanking collinear alignment regions. Breakpoint and end regions are unstranded.

See also

Other Reducing functions: cleanGaps(), get_bps()

Author

Charles Plessy

Michael Mansfield

Examples

exampleColinear5 |> wholeGenomeClassification(ends = TRUE)
#> GRanges object with 11 ranges and 1 metadata column:
#>        seqnames    ranges strand |                type
#>           <Rle> <IRanges>  <Rle> |            <factor>
#>    [1]     chrA      1-99      * | end region         
#>    [2]     chrA   100-190      + | collinear alignment
#>    [3]     chrA   191-199      + | bridge region      
#>    [4]     chrA   200-290      + | collinear alignment
#>    [5]     chrA   291-299      + | bridge region      
#>    [6]     chrA   300-390      + | collinear alignment
#>    [7]     chrA   391-399      + | bridge region      
#>    [8]     chrA   400-490      + | collinear alignment
#>    [9]     chrA   491-499      + | bridge region      
#>   [10]     chrA   500-590      + | collinear alignment
#>   [11]     chrA   591-600      * | end region         
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome