picrust_otu: Predict OTU functional potential via PICRUSt

In themetagenomics: Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

Description

Given an OTU abundance table prepared with the GreenGenes reference database, this function predicts the functional content using either COG or KO precalculated mapping tables that map the taxonomic abundance for a given OTU to functional abundance content across a set of functional genes.

Usage

picrust_otu(file_path, otu_id_targets)

Arguments

file_path	Path to the precalculated table
otu_id_targets	Character vector of OTU IDs to predict

Value

A list containing

gene_ids

String vector of KO IDs, the column names in genome_table_out.

pimeta_ids

String vector of names for the PICRUSt metadata categories, the column names of pimeta_table_out.

matches

String vector of OTU IDs from otu_id_targets that were present in the mapping file.

genemeta

String vector of functional metadata corresponding to gene_ids

genome_table_out

Integer matrix of gene counts across topics

pimeta_table_out

Numeric matrix of method specific metadata (NSTI)

themetagenomics documentation built on May 1, 2020, 1:06 a.m.