qza_to_phyloseq: generates a phyloseq object from .qza artifacts

In jbisanz/qiime2R: qiime2R

generates a phyloseq object from .qza artifacts

Description

Construct a phyloseq object from multiple qiime2 artifacts (.qza). Embedded metadata for provenance is not maintained in this function and instead read_qza() should be used.

Usage

qza_to_phyloseq(features, tree, taxonomy, metadata, tmp)

Arguments

features	file path for artifact containing a feature (OTU/SV) table
tree	file path for artifact containing a tree
taxonomy	file path for artifact containg taxonomy
metadata	file path for a qiime2-compliant TSV metadata file
tmp	a temporary directory that the object will be decompressed to.

Value

a phyloseq object

Examples

## Not run: physeq<-qza_to_phyloseq(features="data/table.qza", tree="data/rooted-tree.qza", taxonomy="data/taxonomy.qza", metdata="data/sample-metadata.qza")

jbisanz/qiime2R documentation built on Dec. 17, 2024, 4:09 p.m.