filter_counts: Filter low presence taxa from a count matrix.

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Filter low presence taxa from a count matrix.

Description

Filter low presence taxa from a count matrix.

Usage

filter_counts(counts, abundance = 10, presence = 0.1)

Arguments

counts	A count matrix with samples as rows and taxa as columns.
abundance	Smallest acceptable mean abundance for a taxon.
presence	A taxon has to be present in at least this percentage of samples to pass the filter.

Value

Count matrix with some taxa removed.

Examples

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Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.