filter_species_abunds: Filter species found in few samples and/or low abundance

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

Filter species found in few samples and/or low abundance

Description

Filter species found in few samples and/or low abundance

Usage

filter_species_abunds(
  species_dat,
  filter_type = "mean",
  minMeanAbund = 0,
  minSampFrac = 0
)

Arguments

species_dat	OTU table
filter_type	Either "mean" or "fracNonzero"
minMeanAbund	minimum mean relative abundance for inclusion of a taxon
minSampFrac	minimum fraction of samples with nonzero abundance for inclusion of a taxon

Value

Filtered species table

Examples

filter_species_abunds(species_dat)

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