| 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
## Not run:
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)
## End(Not run)