process.ORF.annotations: Import ORF annotations, a contig-id,len,ORF-id table and a...

In rbhwilliams/orf.lcam: Processing taxonomic and functional data from lcamapper

Description

Import ORF annotations, a contig-id,len and ORF-id table and a set of contigs and generate an ORF-level output at the 100 percent hit rate for a given taxonomic level

Usage

process.ORF.annotations(taxScan,contig2orfTable,contigsToUse,level)

Arguments

taxScan	is a character vector, returned from read.tax
contig2orfTable	is a data.frame containing mappings between contigs and ORFs, as returned from process.orf.fasta.file
contigsToUse	a subset of contigs contained within contig2orfTable that you wish to study; most often this is a size-filtered set
level	one letter chars for DPCOFGS taxomonic levels

Value

returns an object of class list with the following elements

contig2orfList	is a (contig-named) list, whose elements are congnate ORF-ids
taxaToExtract	is a vector containing the number of ORFs annotated to a given taxonomic entity at the 100 percent hit rate level
taxScanSelected	is subset of taxScan that you have selected via contigsToUse

rbhwilliams/orf.lcam documentation built on May 27, 2019, 3 a.m.