phyloseq object

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1

Hi read this post (Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R) 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.

3

Hi @komal,

From these commands, it looks like you were successful:

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 :lizard:

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5

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