read_mothur2phyloseq: Read Mothur Output into a Phyloseq Object

In microbiome/microbiome: Microbiome Analytics

Read Mothur Output into a Phyloseq Object

Description

Read mothur shared and consensus taxonomy files into a phyloseq-class object.

Usage

read_mothur2phyloseq(shared.file, consensus.taxonomy.file, mapping.file = NULL)

Arguments

shared.file	A shared file produced by mothur. Identified from the .shared extension
consensus.taxonomy.file	Consensus taxonomy file produced by mothur. Identified from with the .taxonomy extension. See http://www.mothur.org/wiki/ConTaxonomy_file.
mapping.file	Metadata/mapping file with .csv extension

Details

Mothur shared and consensus taxonomy files will be converted to phyloseq-class.

Value

phyloseq-class object.

Author(s)

Sudarshan A. Shetty [e-mail]

Examples

#otu.file <- system.file(
#"extdata/Baxter_FITs_Microbiome_2016_fit.final.tx.1.subsample.shared",
#   package='microbiome')

#tax.file <- system.file(
#"extdata/Baxter_FITs_Microbiome_2016_fit.final.tx.1.cons.taxonomy",
#   package='microbiome')

#meta.file <- system.file(
#"extdata/Baxter_FITs_Microbiome_2016_mapping.csv",
#   package='microbiome')

#p0 <- read_mothur2phyloseq(
#       shared.file=otu.file,
#       consensus.taxonomy.file=tax.file,
#       mapping.file=meta.file)

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