txNames {ORFik}R Documentation

Get transcript names from orf names

Description

names must either be a column called names, or the names of the grl object

Usage

txNames(grl, unique = FALSE)

Arguments

grl

a GRangesList grouped by ORF or GRanges object

unique

a boolean, if true unique the names, used if several orfs map to same transcript and you only want the unique groups

Value

a character vector of transcript names, without _* naming

See Also

Other ORFHelpers: defineTrailer, longestORFs, mapToGRanges, orfID, startCodons, startSites, stopCodons, stopSites, uniqueGroups, uniqueOrder

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_1 = gr_plus, tx2_1 = gr_minus)
# there are 2 orfs, both the first on each transcript
txNames(grl)


[Package ORFik version 1.4.0 Index]