construct_otu_table: construct_otu_table

Description Usage Arguments Examples

View source: R/construct_otu_table.R

Description

construct_otu_table can construct a OTU table with a phyloseq object.

Usage

1
construct_otu_table(phyloseq, level = "all")

Arguments

phyloseq

A phyloseq object contain otu table, taxonomy table, sample metadata and phylogenetic tree.

level

The coloumn name of the level wanted to select. Default is "all". If "all" then retain all taxonomy level and seperate by "; ", else ONLY retain the given taxonomy level, drop everything else. Level name should be one of "all", "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species".

Examples

1
construct_otu_table(demo_phyloseq_object, level = "Genus") %>% .[,1:5]

yeguanhuav/visual16S documentation built on Aug. 11, 2019, 8:51 a.m.