Show translocations and their flanking blocks.

Show translocations and their flanking blocks.

Usage

showTranslocations(gb, rename = TRUE, detect = TRUE)

Arguments

gb

A GBreaks object.

rename

Replace range names by their numeric order before subsetting.

detect

Run again flagTranslocations() if TRUE, else reuse the tra flag or fail if it is absent.

Value

Returns the GBreaks object in which all ranges that are not part of a translocation triplet have been discarded. If the object was missing the tra metadata column, return the object after discarding all of its ranges.

See also

Other Translocation functions: filterTranslocations(), flagTranslocations(), removeTranslocations()

Examples

showTranslocations(exampleTranslocation)
#> GBreaks object with 3 ranges and 2 metadata columns:
#>     seqnames    ranges strand |        query   tra
#>        <Rle> <IRanges>  <Rle> |    <GRanges> <Rle>
#>   1     chrA   100-200      + | chrB:100-200  TRUE
#>   2     chrA   201-300      + | chrC:201-300 FALSE
#>   3     chrA   301-400      + | chrB:301-400 FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome