groupGRangesBy {ORFik} | R Documentation

## 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

[Package ORFik version 1.8.6 Index]