read_mothur2phyloseq: Read Mothur Output into a Phyloseq Object

Description Usage Arguments Details Value Author(s) Examples

View source: R/read_mothur2phyloseq.R

Description

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

Usage

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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 sudarshanshetty9@gmail.com

Examples

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