Extract central blocks in translocations

Extract central blocks in translocations

Usage

filterTranslocations(gb, rename = TRUE, remove = FALSE)

Arguments

gb

A GBreaks object processed with flagTranslocations.

rename

Replace range names by their numeric order before subsetting.

remove

Filter out instead of filtering in.

Value

Returns the GBreaks object in which all ranges that are not the central part of an inversion 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: flagTranslocations(), showTranslocations()

Examples

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