orfSignature: Signature for each ORF

In microseq: Basic Biological Sequence Handling

Signature for each ORF

Description

Creates a signature text for orfs in an orf.table.

Usage

orfSignature(orf.table, full = TRUE)

Arguments

orf.table	A tibble with ORF information.
full	Logical indicating type of signature.

Details

A signature is a text that uniquely identifies each ORF in an orf.table, which is a GFF-table with columns Seqid, Start, End and Strand.

The full signature (full = TRUE) contains the Seqid, Start, End and Strand information for each ORF, separated by semicolon ";". This text is always unique to each ORF. If full = FALSE the Signature will not contain the starting position information for each ORF. This means all nested ORFs ending at the same stop-codon will then get identical Signatures. This is useful for identifying which ORFs are nested within the same LORF.

Note that the signature you get with full = FALSE contains Seqid, then End if on the positive Strand, Start otherwise, and then the Strand.

Value

A text vector with the Signature for each ORF.

Author(s)

Lars Snipen.

See Also

findOrfs.

Examples

# Using a genome file in this package
genome.file <- file.path(path.package("microseq"),"extdata","small.fna")

# Reading genome and finding orfs
genome <- readFasta(genome.file)
orf.tbl <- findOrfs(genome)

# Compute signatures
signature.full <- orfSignature(orf.tbl)
signature.reduced <- orfSignature(orf.tbl, full = FALSE)

microseq documentation built on Aug. 21, 2023, 5:10 p.m.