qza_to_phyloseq: generates a phyloseq object from .qza artifacts

Description Usage Arguments Value Examples

View source: R/qza_to_phyloseq.R

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

1
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

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## 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 Nov. 12, 2021, 3:09 p.m.