read_csv2phyloseq {microbiome} | R Documentation

## Read Simple OTU Tables into a Phyloseq Object

### Description

Read simple OTU tables, mapping and taxonomy files into a `phyloseq-class` object.

### Usage

    read_csv2phyloseq(
      otu.file = NULL,
      taxonomy.file = NULL,
      metadata.file = NULL,
      sep = ","
    )

### Arguments

`otu.file` | A simple otu_table with '.csv' extension
`taxonomy.file` | A simple taxonomy file with '.csv' extension
`metadata.file` | A simple metadata/mapping file with .csv extension
`sep` | CSV file separator

### Details

Simple OTU tables, mapping and taxonomy files will be converted to `phyloseq-class`.

### Value

`phyloseq-class` object.

### Author(s)

Sudarshan A. Shetty sudarshanshetty9@gmail.com

### Examples

    # NOTE: the system.file command reads these example files from the
    # microbiome R package. To use your own local files, simply write
    # otu.file <- "/path/to/my/file.csv" etc.

    #otu.file <-
    #   system.file("extdata/qiita1629_otu_table.csv",
    #   package='microbiome')

    #tax.file <- system.file("extdata/qiita1629_taxonomy_table.csv",
    #        package='microbiome')

    #meta.file <- system.file("extdata/qiita1629_mapping_subset.csv",
    #     package='microbiome')

    #p0 <- read_csv2phyloseq(
    #        otu.file=otu.file,
    #        taxonomy.file=tax.file,
    #        metadata.file=meta.file)

[Package microbiome version 1.12.0 Index]