common_taxa: Find taxa shared between treatments of a phyloseq object....

In schuyler-smith/phyloschuyler: Functions to help analyze data as phyloseq objects

Find taxa shared between treatments of a phyloseq object. Function from the phylosmith-package.

Description

Inputs a phyloseq-class object and finds which taxa are shared between all of the specified treatments from data in the sample_data()), or every sample in the dataset.

Usage

common_taxa(phyloseq_obj, treatment = NULL, subset = NULL, n = "all")

Arguments

phyloseq_obj	A phyloseq-class object. It must contain sample_data()) with information about each sample, and it must contain tax_table()) with information about each taxa/gene.
treatment	Column name as a string or numeric in the sample_data. This can be a vector of multiple columns and they will be combined into a new column.
subset	A factor within the treatment. This will remove any samples that to not contain this factor. This can be a vector of multiple factors to subset on.
n	Number of treatment groups that need to share the taxa to be considered a common taxa.

Value

vector

See Also

unique_taxa

Examples

common_taxa(soil_column, treatment = "Treatment",
subset = "Amended", n = "all")

schuyler-smith/phyloschuyler documentation built on Aug. 16, 2024, 5:36 a.m.