read_mothur2phyloseq {microbiome} | R Documentation |
Read mothur shared and consensus taxonomy files into a
phyloseq-class
object.
read_mothur2phyloseq(shared.file, consensus.taxonomy.file, mapping.file = NULL)
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 |
Mothur shared and consensus taxonomy files will be converted to
phyloseq-class
.
phyloseq-class
object.
Sudarshan A. Shetty sudarshanshetty9@gmail.com
#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)