Description Usage Arguments Details Value Author(s) Examples
View source: R/read_mothur2phyloseq.R
Read mothur shared and consensus taxonomy files into a
phyloseq-class
object.
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #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)
|
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