read_phyloseq {microbiome}R Documentation

Import phyloseq Data

Description

Read the otu, taxonomy and metadata from various formats.

Usage

read_phyloseq(
  otu.file = NULL,
  taxonomy.file = NULL,
  metadata.file = NULL,
  type = c("simple", "mothur", "biom"),
  sep = ","
)

Arguments

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

Details

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.

Value

phyloseq-class object

Author(s)

Sudarshan A. Shetty sudarshanshetty9@gmail.com

See Also

write_phyloseq

Examples

#  pseq <- read_phyloseq(otu.file, 
#                     taxonomy.file, 
#                     metadata.file, 
#                     type=c('mothur', 'simple', 'biom'))

[Package microbiome version 1.14.0 Index]