read_biom2phyloseq: Read BIOM File into a Phyloseq Object

In microbiome: Microbiome Analytics

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 [e-mail]

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)

Example output

Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2020 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>


Attaching package: ‘microbiome’

The following object is masked from ‘package:ggplot2’:

    alpha

The following object is masked from ‘package:base’:

    transform

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.