read_phyloseq {microbiome} | R Documentation |
Read the otu, taxonomy and metadata from various formats.
read_phyloseq(otu.file = NULL, taxonomy.file = NULL, metadata.file = NULL, type = c("simple", "mothur", "biom"), sep = ",")
otu.file |
File containing the OTU table (for mothur this is the file with the .shared extension) |
taxonomy.file |
(for mothur this is typically the consensus taxonomy file with the .taxonomy extension) |
metadata.file |
File containing samples x variables metadata. |
type |
Input data type: 'mothur' or 'simple' or 'biom' type. |
sep |
CSV file separator |
See help(read_mothur2phyloseq) for details on the Mothur input
format; and help(read_biom2phyloseq) for details on the biom format.
The simple format refers to the set of CSV files written by the
write_phyloseq
function.
phyloseq-class
object
Sudarshan A. Shetty sudarshanshetty9@gmail.com
write_phyloseq
## Not run: # pseq <- read_phyloseq(otu.file, # taxonomy.file, # metadata.file, # type=c('mothur', 'simple', 'biom')) ## End(Not run)