download_ribosomal_ref_seqs: Uses the provided OTU table to generate a contribution table...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Uses the provided OTU table to generate a contribution table based on the PICRUSt 16S normalization and genomic content tables

Description

Uses the provided OTU table to generate a contribution table based on the PICRUSt 16S normalization and genomic content tables

Usage

download_ribosomal_ref_seqs(db = "AGORA", out_path)

Arguments

db	Either AGORA or embl_gems
picrust_norm_file	File path to PICRUSt 16S normalization reference data
picrust_ko_table_directory	Directory of PICRUSt genome OTU predictions
picrust_ko_table_suffix	File naming of PICRUSt genome OTU predictions
copynum_column	Whether to include a copy number column in the contribution table
otu_rel_abund	Whether to convert OTU table to relative abundances first

Value

Table of PICRUSt-based contribution abundances for all OTUs

Examples

generate_contribution_table_using_picrust(otu_table, picrust_norm_file, picrust_dir, picrust_suffix)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.