| read_csv2phyloseq {microbiome} | R Documentation |
Read simple OTU tables, mapping and taxonomy files into a
phyloseq-class object.
read_csv2phyloseq(otu.file = NULL, taxonomy.file = NULL, metadata.file = NULL, sep = ",")
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 |
Simple OTU tables, mapping and taxonomy files will be converted
to phyloseq-class.
phyloseq-class object.
Sudarshan A. Shetty sudarshanshetty9@gmail.com
## 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)