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

## Not run: 
# 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)


## End(Not run)

[Package microbiome version 1.4.2 Index]