abundance_and_occupancy_core: Proportion of Reads and Replicates:

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

Proportion of Reads and 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 0.02 for the entire otu table and be present in at least 50

Usage

abundance_and_occupancy_core(
  otu_table,
  prop_rep = 0.5,
  prop_reads = 2e-04,
  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
prop_reads	percentage of reads
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	percentage of replicates

Value

the names of OTUs which meet the proportion of reads and replicate criteria

Examples

abundance_and_occupancy_core(arabidopsis)

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