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 1.12.0 Index]