makeORFNames: Make ORF names per orf

In ORFik: Open Reading Frames in Genomics

Description

grl must be grouped by transcript If a list of orfs are grouped by transcripts, but does not have ORF names, then create them and return the new GRangesList

Usage

makeORFNames(grl, groupByTx = TRUE)

Arguments

grl	a GRangesList
groupByTx	logical (T), should output GRangesList be grouped by transcripts (T) or by ORFs (F)?

Value

(GRangesList) with ORF names, grouped by transcripts, sorted.

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)
makeORFNames(grl)

ORFik documentation built on March 27, 2021, 6 p.m.