micro_otu: Extract OTU table from tidyMicro set

In tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description

A simple wrapper to extract an OTU table from a tidyMicro set

Usage

micro_otu(micro_set, table, taxa_info = cts)

Arguments

micro_set	A tidy_micro data set
table	OTU table of interest
taxa_info	The taxa info to pull

Value

A tibble

Examples

data(mrsa_gen); data(mrsa_clin)

## Creating tidyMicro set
set <- tidy_micro(otu_tabs = mrsa_gen, tab_names = "Genus", clinical = mrsa_clin)

## Filtering out unwanted OTUs
filt.set <- otu_filter(set, prev_cutoff = 1, ra_cutoff = 1, filter_summary = FALSE)

## Extract filtered OTU table
filt.otu.cts <- micro_otu(filt.set, table = "Genus")

## Extract filtered relative abundances table
filt.otu.ra <- micro_otu(filt.set, table = "Genus", taxa_info = ra)

tidyMicro documentation built on Jan. 13, 2021, 6:18 a.m.