read_biom2phyloseq: Read BIOM File into a Phyloseq Object

In microbiome/microbiome: Microbiome Analytics

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,
  sep = ",",
  ...
)

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
sep	Separator of the metadata file in case it isn't comma-delimited. Default is ","
...	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)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.