# phyloseq object
**URL:** https://forum.qiime2.org/t/phyloseq-object/28831
**Category:** Library Support
**Created:** [January 8, 2024, 10:49am UTC](https://forum.qiime2.org/t/phyloseq-object/28831 "2024-01-08T10:49:01Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@komal](https://forum.qiime2.org/u/komal)
#### Post date: [January 8, 2024, 10:49am UTC](https://forum.qiime2.org/t/phyloseq-object/28831/1 "2024-01-08T10:49:01Z")
Hi read this post ([Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R](https://forum.qiime2.org/t/tutorial-integrating-qiime2-and-r-for-data-visualization-and-analysis-using-qiime2r/4121)) for creating phyloseq object for Differential analysis. However I am unable to understand if the phyloseq object created and if so how to use to for further analysis
My commands in r studio:
library(qiime2R)
library(phyloseq)
SVs\<-read\_qza("table.qza")
metadata\<-read\_q2metadata("sample-metadata.tsv")
taxonomy\<-read\_qza("taxonomy.qza")
tree\<-read\_qza("rooted\_tree.qza")
physeq\<-qza\_to\_phyloseq(
features="table.qza",
tree="rooted\_tree.qza",
"taxonomy.qza",
metadata = "sample-metadata.tsv"
)
physeq
My output:
library(qiime2R)
> library(phyloseq)
>
> SVs\<-read\_qza("table.qza")
> metadata\<-read\_q2metadata("sample-metadata.tsv")
> taxonomy\<-read\_qza("taxonomy.qza")
> tree\<-read\_qza("rooted-tree.qza")
> tree\<-read\_qza("rooted\_tree.qza")
> physeq\<-qza\_to\_phyloseq(
- features="table.qza",
- tree="rooted-tree.qza",
- "taxonomy.qza",
- metadata = "sample-metadata.tsv"
- )
> physeq\<-qza\_to\_phyloseq(
- features="table.qza",
- tree="rooted\_tree.qza",
- "taxonomy.qza",
- metadata = "sample-metadata.tsv"
- )
> physeq
> phyloseq-class experiment-level object
> otu\_table() OTU Table: [681 taxa and 86 samples]
> sample\_data() Sample Data: [86 samples by 4 sample variables]
> tax\_table() Taxonomy Table: [681 taxa by 7 taxonomic ranks]
> phy\_tree() Phylogenetic Tree: [681 tips and 675 internal nodes]
Is my phyloseq object created?
Thank you.
---
### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [January 8, 2024, 4:25pm UTC](https://forum.qiime2.org/t/phyloseq-object/28831/2 "2024-01-08T16:25:24Z")
---
### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [January 8, 2024, 4:46pm UTC](https://forum.qiime2.org/t/phyloseq-object/28831/3 "2024-01-08T16:46:44Z")
Hi @komal,
From these commands, it looks like you were successful:
> [@komal](#):
>
> > physeq\<-qza\_to\_phyloseq(
>
> - features="table.qza",
> - tree="rooted\_tree.qza",
> - "taxonomy.qza",
> - metadata = "sample-metadata.tsv"
> - )
>
> > physeq
> > phyloseq-class experiment-level object
> > otu\_table() OTU Table: [681 taxa and 86 samples]
> > sample\_data() Sample Data: [86 samples by 4 sample variables]
> > tax\_table() Taxonomy Table: [681 taxa by 7 taxonomic ranks]
> > phy\_tree() Phylogenetic Tree: [681 tips and 675 internal nodes]
You assigned `physeq` as the resultant object from running `qza_to_phyloseq()`, and the output of `physeq` is showing up as `phyloseq-class experiment-level object`, which is the descriptor for a phyloseq object.
Cheers 🦎
---
### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [January 8, 2024, 4:46pm UTC](https://forum.qiime2.org/t/phyloseq-object/28831/4 "2024-01-08T16:46:47Z")
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [February 8, 2024, 10:47pm UTC](https://forum.qiime2.org/t/phyloseq-object/28831/5 "2024-02-08T22:47:06Z")
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