abundance_core: Summation of Reads:

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

Summation of Reads:

Description

This method assigns taxa to the core if they are in the top X Taxa are ranked in abundance and the cumulative sum is recorded. Any taxa which appears before some cutoff percentage is included in the core. In this example, a taxa will be assigned to the core if they account for the first 75

Usage

abundance_core(otu_table, readn = 0.75, 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
readn	count of reads needed
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.

Value

the names of OTUs which meet the proportion of reads criteria

Examples

abundance_core(arabidopsis)

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