conglomerate_taxa: Conglomerate taxa by sample on a given classification level....

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

Conglomerate taxa by sample on a given classification level. Function from the phylosmith-package.

Description

Conglomerate taxa by sample on a given classification level from the tax_table.

Usage

conglomerate_taxa(phyloseq_obj, classification, hierarchical = TRUE,
use_taxonomic_names = TRUE)

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.
classification	Column name as a string or numeric in the tax_table for the factor to conglomerate by.
hierarchical	Whether the order of factors in the tax_table represent a decreasing hierarchy (TRUE) or are independent (FALSE). If FALSE, will only return the factor given by classification.
use_taxonomic_names	If (TRUE), will use the hierarchical taxonomic name from Domain to classification level. If (FALSE) will uses the classification level with a numerical assignment.

Value

phyloseq-object

See Also

tax_glom()

Examples

conglomerate_taxa(soil_column, 'Phylum')

schuyler-smith/phylosmith documentation built on Aug. 17, 2024, 10:19 a.m.