read_phyloseq: Import phyloseq Data

In microbiome: Microbiome Analytics

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 [e-mail]

See Also

write_phyloseq

Examples

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

Example output

Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2020 Leo Lahti, 
    Sudarshan Shetty et al. <microbiome.github.io>


Attaching package: ‘microbiome’

The following object is masked from ‘package:ggplot2’:

    alpha

The following object is masked from ‘package:base’:

    transform

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.