summarizeFromPhyloseq: summarizeFromPhyloseq

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

Construct a SummarizedPhyloseq-class object from a phyloseq-class object

Usage

summarizeFromPhyloseq(physeq, level = "all", keep_full_tax = FALSE)

Arguments

physeq	An phyloseq object from the phyloseq package. It must contain an otu_table slot, a sam_data slot, and a tax_table slot. The phy_tree slot and refseq slots are not required.
level	The taxonomy level to summarize. It can be one ore more from Kingdom, Phylum, Class, Order, Family, Genus, and Species. If mutiple phylogenic levels are specified, use a string vector. Default is "all" that parses all levels. The slots that are not specified will be NULL.

Details

This is the main constructor of the SummarizedPhyloseq class. It takes a phyloseq object and calls the link{summarize_taxa}() function for each phylogenic level and return a SummarizedPhyloseq object.

Value

A SummarizedPhyloseq object

Author(s)

Chenghao Zhu

See Also

SummarizedPhyloseq-class

Examples

library(phyloseq)
data(GlobalPatterns)
spy = summarizedFromPhyloseq(GlobalPatterns)

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.