threshold_count_data {BRACoD.R}

Threshold your microbiome counts data

Description

This function removes samples below a minimum counts and bacteria below a minimum log abundance. Run this before running BRACoD because the algorithm does not perform well when there are many low abundance bacteria that are only present in a few samples.

Usage

threshold_count_data(df_counts, min_counts = 1000, min_ab = 1e-04)

Arguments

df_counts

A dataframe of OTU counts. Samples are rows and bacteria are columns.

min_counts

threshold samples with fewer than this many counts

min_ab

threshold bacteria whose average log abundance is below this

Value

a dataframe of microbiome counts