micropan (version 1.2)

lorfs: Longest ORF

Description

Filtering a gff.table with ORF information to keep only the LORFs.

Usage

lorfs(gff.table)

Arguments

gff.table

A gff.table (data.frame) with genomic features information.

Value

A gff.table with a subset of the rows of the argument gff.table. After this filtering the Type variable in gff.table is changed to "LORF". If you want to retirve the LORF sequences, use gff2fasta.

Details

For every stop-codon there are usually mutliple possible start-codons in the same reading frame (nested ORFs). The LORF (Longest ORF) is defined as the longest of these nested ORFs, i.e. the ORF starting at the most upstream start-codon matching the stop-codon.

See Also

readGFF, findOrfs, gff2fasta.

Examples

# NOT RUN {
# See the example in the Help-file for findOrfs.

# }