groupGRangesBy: Group GRanges

In JokingHero/ORFik: Open Reading Frames in Genomics

Group GRanges

Description

It will group / split the GRanges object by the argument 'other'. For example if you would like to to group GRanges object by gene, set other to gene names.
If 'other' is not specified function will try to use the names of the GRanges object. It will then be similar to 'split(gr, names(gr))'.

Usage

groupGRangesBy(gr, other = NULL)

Arguments

gr	a GRanges object
other	a vector of unique names to group by (default: NULL)

Details

It is important that all intended groups in 'other' are uniquely named, otherwise duplicated group names will be grouped together.

Value

a GRangesList named after names(GRanges) if other is NULL, else names are from unique(other)

Examples

ORFranges <- GRanges(seqnames = Rle(rep("1", 3)),
                     ranges = IRanges(start = c(1, 10, 20),
                                      end = c(5, 15, 25)),
                     strand = "+")
ORFranges2 <- GRanges("1",
                      ranges = IRanges(start = c(20, 30, 40),
                                       end = c(25, 35, 45)),
                      strand = "+")
names(ORFranges) = rep("tx1_1", 3)
names(ORFranges2) = rep("tx1_2", 3)
grl <- GRangesList(tx1_1 = ORFranges, tx1_2 = ORFranges2)
gr <- unlist(grl, use.names = FALSE)
## now recreate the grl
## group by orf
grltest <- groupGRangesBy(gr) # using the names to group
identical(grl, grltest) ## they are identical

## group by transcript
names(gr) <- txNames(gr)
grltest <- groupGRangesBy(gr)
identical(grl, grltest) ## they are not identical

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.