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

    p0 <- read_biom2phyloseq()
    #biom.file <- qiita1629.biom"
    #meta.file <- qiita1629_mapping.csv"
    #p0 <- read_biom2phyloseq(biom.file = biom.file,
    #                       metadata.file = meta.file,
    #                       taxonomy.file = NULL)

[Package microbiome version 1.12.0 Index]