R: Get the stop sites from a GRangesList of orfs grouped by orfs

stopSites {ORFik}

R Documentation

Get the stop sites from a GRangesList of orfs grouped by orfs

Description

In ATGTTTTGC, get the position of the C.

Usage

stopSites(grl, asGR = FALSE, keep.names = FALSE, is.sorted = FALSE)

Arguments

`grl`	a `GRangesList` object
`asGR`	a boolean, return as GRanges object
`keep.names`	if asGR is False, do you still want to keep a named vector
`is.sorted`	a speedup, if you know the ranges are sorted

Value

if asGR is False, a vector, if True a GRanges object

Examples

gr_plus <- GRanges(seqnames = c("chr1", "chr1"),
                   ranges = IRanges(c(7, 14), width = 3),
                   strand = c("+", "+"))
gr_minus <- GRanges(seqnames = c("chr2", "chr2"),
                    ranges = IRanges(c(4, 1), c(9, 3)),
                    strand = c("-", "-"))
grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus)
stopSites(grl, is.sorted = FALSE)

[Package ORFik version 1.0.0 Index]