read_biom2phyloseq {microbiome}R Documentation

Read BIOM File into a Phyloseq Object

Description

Read biom and mapping files into a phyloseq-class object.

Usage

read_biom2phyloseq(biom.file = NULL, taxonomy.file = NULL,
  metadata.file = NULL, ...)

Arguments

biom.file

A biom file with '.biom' extension

taxonomy.file

NULL the latest version has taxonomic information within the biom

metadata.file

A simple metadata/mapping file with .csv extension

...

Arguments to pass for import_biom

Details

Biom file and mapping files will be converted to phyloseq-class.

Value

phyloseq-class object.

Author(s)

Sudarshan A. Shetty sudarshanshetty9@gmail.com

Examples

## Not run: 
biom.file <- qiita1629.biom"
meta.file <- qiita1629_mapping.csv"
p0 <- read_biom2phyloseq(biom.file = biom.file, 
                       metadata.file = meta.file, 
                       taxonomy.file = NULL)

## End(Not run)

[Package microbiome version 1.4.2 Index]