save_pq: A wrapper of write_pq to save in all three possible formats

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

A wrapper of write_pq to save in all three possible formats

Description

A wrapper of write_pq to save in all three possible formats

Usage

save_pq(physeq, path = NULL, ...)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
path	a path to the folder to save the phyloseq object
...	Other arguments passed on to write_pq() or utils::write.table() function.

Details

Write :

• 4 separate tables

• 1 table version

• 1 RData file

Value

Build a folder (in path) with four csv tables (refseq.csv, otu_table.csv, tax_table.csv, sam_data.csv) + one table with all tables together + a rdata file (physeq.RData) that can be loaded using base::load() function + if present a phylogenetic tree in Newick format (phy_tree.txt)

Author(s)

Adrien Taudière

See Also

write_pq()

Examples

save_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.