write_phyloseq {microbiome}R Documentation

Exporting phyloseq Data in CSV Files

Description

Writes the otu, taxonomy and metadata in csv files.

Usage

write_phyloseq(x, type = "all", path = getwd())

Arguments

x

phyloseq-class object

type

'OTU' or 'TAXONOMY' or 'METADATA'

path

Path to the directory/folder where the data will be written. Uses the working directory by default.

Value

Output file path (a string)

See Also

read_phyloseq

Examples

## Not run: 
data(dietswap)
pseq <- dietswap
# By default writes all info at once (ie OTU/TAXONOMY/METADATA)
write_phyloseq(pseq) 
write_phyloseq(pseq, 'OTU')
write_phyloseq(pseq, 'TAXONOMY')
write_phyloseq(pseq, 'METADATA')

## End(Not run)

[Package microbiome version 1.2.1 Index]