occupancy_core: Proportion of Replicates

In MayaGans/CoreMicro: Testing Widely Used Core Microbiome Assignment Methods

Proportion of Replicates

Description

This method assigns taxa to the core if they account for some proportion of the total reads for the sequencing run and if they are present in at least x In this example, a core taxa must account for 0.01 for the entire otu table and be present in at least 50

Usage

occupancy_core(otu_table, prop_rep = 0.5, taxa_as_rows = TRUE)

Arguments

otu_table	a dataframe of OTUs where the first row is the OTU ID and column names refer to sites
taxa_as_rows	logical data must be in a format where the taxa are rows and the sites are columns. The default value is TRUE, if FALSE data will be transposed for downstream analysis.
occupancy_core	some definition

Value

the names of OTUs which meet the proportion of replicate criteria

Examples

occupancy_core(arabidopsis)

MayaGans/CoreMicro documentation built on March 5, 2023, 2:54 a.m.