startCodons {ORFik}R Documentation

Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs

Description

In ATGTTTTGC, get the positions ATG. It takes care of exons boundaries, with exons < 3 length.

Usage

startCodons(grl, is.sorted = FALSE)

Arguments

grl

a GRangesList object

is.sorted

a boolean, a speedup if you know the ranges are sorted

Value

a GRangesList of start codons, since they might be split on exons

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)
startCodons(grl, is.sorted = FALSE)
[Package ORFik version 1.0.0 Index]