Flag long and short arms

Oikopleura genomes are special as the long and short arms of their chromosomes have different properties such as GC or repeat content. It can be useful to know if genomic region belongs to long or a short arm.

Usage

flagLongShort(gr, annot, select = c("first", "last", "arbitrary"))

Arguments

gr

A GBreaks or a simple GenomicRanges::GRanges object

annot

A GRanges file containing the coordinate of arms and their nature (such as long, short, XSR or YSR) in a Type metadata column.

select

One method among first, last and arbitrary, to decide on how to handle the regions that match both arms.

Value

Returns a modified version of the object with an extra metadata column, Arm in which the information from the annotation file's Type column was transferred. See the examples below and in the manual of IRanges::findOverlaps for details. on how regions that match both arms are handled.

See also

Other Flagging functions: flagAll(), flagColinearAlignments(), flagDoubleInversions(), flagInversions(), flagPairs(), flagTranslocations()

Author

Charles Plessy

Examples

annot <- GRanges(c("chrA:1-140", "chrA:150-500"), Type = c("short", "long"))

flagLongShort(exampleColinear, annot)
#> GBreaks object with 2 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query      Arm
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <factor>
#>   [1]     chrA   100-150      + | chrB:100-150    short
#>   [2]     chrA   251-300      + | chrB:251-300    long 
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
flagLongShort(exampleColinear, annot, select = "last")
#> GBreaks object with 2 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query      Arm
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <factor>
#>   [1]     chrA   100-150      + | chrB:100-150     long
#>   [2]     chrA   251-300      + | chrB:251-300     long
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
flagLongShort(exampleColinear, annot, select = "arbitrary")
#> GBreaks object with 2 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query      Arm
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <factor>
#>   [1]     chrA   100-150      + | chrB:100-150    short
#>   [2]     chrA   251-300      + | chrB:251-300    long 
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome