read_csv2phyloseq: Read Simple OTU Tables into a Phyloseq Object

In microbiome/microbiome: Microbiome Analytics

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 [e-mail]

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)

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