get_physeq_tbls: Get phyloseq tables

In antonioggsousa/micrUBIfuns: Set of functions for microbiome analyses

Description

Given a phyloseq object with 'otu_table', 'tax_table', 'sam_data' (required) it gives a list with those tables.

Usage

get_physeq_tbls(physeq, tax_rank = NULL, rm_na = FALSE, feature_w_tax = FALSE)

Arguments

physeq	phyloseq-class object with 'otu_table', 'tax_table', 'sam_data' slots (required).
tax_rank	taxonomic rank (character). One of the taxonomic ranks among the column names of 'tax_table()' of the 'physeq' object given.
rm_na	include (TRUE) or not (FALSE) NAs (logical), i.e., taxa without classification at the taxonomic level specified at 'tax_rank'. It only works if 'tax_rank' was provided. Otherwise it is ignored.
feature_w_tax	substitute the feature labels (in columns) by the taxa names specified at 'tax_rank' level (logical). Default is 'FALSE'. It only works if 'tax_rank' was provided. Otherwise it is ignored.

Value

A list with the 'feature' ('otu_table'), 'taxonomy' ('tax_table'), and 'metadata' ('sample_data') tables. If the 'tax_rank' is specified, it will give 'feature' and 'taxonomy' summarized at that 'tax_rank' level. If 'feature_w_tax' is equal 'TRUE' (only works together with 'tax_rank'), the column names in the 'feature' table will be the taxa names at 'tax_rank' level specied.

antonioggsousa/micrUBIfuns documentation built on Nov. 14, 2020, 1:40 a.m.