make_framebot_tax_table: make_framebot_tax_table

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description

Create a taxonomy table from FunGene Pipeline output.

Usage

make_framebot_tax_table(clstr_machine, taxa_machine)

Arguments

clstr_machine	match_cluster_machine_name.txt from my FunGene Pipeline script
taxa_machine	match_taxa_machine_names.txt from my FunGene Pipeline script

Details

My FunGene pipeline script (see john-quensen.com) produces one file matching representative sequence machine names with cluster numbers and a second matching representative sequence machine names with taxa names found by FrameBot. This function parses and combines the two files to produce a phyloseq tax_table. Ranks are Genus, Species, and Strain. Classification is the closest match to sequence in the FrameBot reference database. The percent identity to the closest match is appended to the name of the closest match (strain level in the tax_table).

Value

A tax_table of class phyloseq.

Note

See the workshop page Command Line FunGene Pipeline at john-quensen.com for the FunGene Pipeline script.

Author(s)

John Quensen

Examples

match.clst <- system.file("extdata", "match_cluster_machine_name.txt", package="RDPutils")
match.taxa <- system.file("extdata", "match_taxa_machine_names.txt", package="RDPutils")
my_taxa <- make_framebot_tax_table(clstr_machine=match.clst, taxa_machine=match.taxa) 

jfq3/RDPutils documentation built on Nov. 8, 2019, 1:05 p.m.