read_phyloseq: Import phyloseq Data

In microbiome/microbiome: Microbiome Analytics

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.

Value

phyloseq-class object

Author(s)

Sudarshan A. Shetty [e-mail]

Examples

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

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.