<p>I wish to convert a kraken2 or metaphlan2 report into the R package to analyze using Phyloseq.</p>
<p>I have performed obtained an importation and Phyloseq analysis, but the result was not correct.</p>
<pre class="lang-r prettyprint-override"><code>library(&quot;phyloseq&quot;)
library(&quot;biomformat&quot;) 
otu_Rat11 &lt;- read_biom(&quot;Rat11.biom&quot;) 

otumat_Rat11 = as(biom_data(otu_Rat11), &quot;matrix&quot;) 
OTU_Rat11 &lt;- otu_table(otumat_Rat11, taxa_are_rows=TRUE) 
str(OTU_Rat11)
#Formal class 'otu_table' [package &quot;phyloseq&quot;] with 2 
#slots ..@ .Data : num [1:1018, 1] 942 433 3007 116765 15103 ... .. ..- 
#attr(*, &quot;dimnames&quot;)=List of 2 .. .. ..:ℎ[1:1018]&quot;186826&quot;&quot;33958&quot;&quot;1578&quot;
#&quot;33959&quot;.........:chr[1:1018] &quot;186826&quot; &quot;33958&quot; &quot;1578&quot; &quot;33959&quot;......... :
# chr &quot;sa1&quot; ..@ taxa_are_rows: logi TRUE

taxmat_Rat11 = as.matrix(observation_metadata(otu_Rat11), rownames.force=TRUE)
TAX_Rat11 = tax_table(taxmat_Rat11)

physeq_Rat11 = phyloseq(OTU_Rat11, TAX_Rat11)
str(physeq_Rat11) 
#Formal class 'phyloseq' [package &quot;phyloseq&quot;] with 5 slots ..@ otu_table:Formal 
#class 'otu_table' [package &quot;phyloseq&quot;] with 2 slots .. .. ..@ .Data : num 
#[1:1018, 1] 942 433 3007 116765 15103 ... .. .. .. ..- attr(*, &quot;dimnames&quot;)=List
# of 2 .. .. .. .. ..:ℎ[1:1018]&quot;186826&quot;&quot;33958&quot;&quot;1578&quot;&quot;33959&quot;.............: chr 
#[1:7] &quot;taxonomy1&quot; &quot;taxonomy2&quot; &quot;taxonomy3&quot; &quot;taxonomy4&quot; ... ..@ sam_data : NULL ..
#@ phy_tree : NULL ..@ refseq : NULL –
</code></pre>
<p>Now I try to obtain @ sam_data</p>
<pre><code>sampledata = sample_data(otu_Rat11) 
#Error in access(object, &quot;sam_data&quot;, errorIfNULL) : sam_data slot is empty.
</code></pre>
<p>What do with sample data and how to merge several phyloseq-format datasets from different metagenomes?</p>

CC BY-SA 4.0
2020-07-24T10:16:32.713Z
Is it possible to have an example file for `Rat11.biom`? It's easier to debug with a reproducible result.
What do you mean by "the result was not correct"?
What's your code for merging several phyloseq-format datasets from different metagenomes?
Ryan SY Kwan
CC BY-SA 4.0
2021-07-29T00:32:56.630Z
I'm working on this procedure with some difficult. Could you please tell me how do you convert kraken2 report files into the biom format?
Jianwei
CC BY-SA 4.0
2021-12-21T15:59:01.160Z
I had received the same error. My metadata file was in a matrix format, I converted it into a data.frame and it worked. Pls try and see if it works.
Pooja Kunte
<r>
Kraken2 or metaphlan2 report to phyloseq
# Kraken2 or metaphlan2 report to phyloseq

(Asked by: username_0 on 2020-07-16)

I wish to convert a kraken2 or metaphlan2 report into the R package to analyze using Phyloseq.
I have performed obtained an importation and Phyloseq analysis, but the result was not correct.
library("phyloseq")
library("biomformat") 
otu_Rat11 <- read_biom("Rat11.biom") 

otumat_Rat11 = as(biom_data(otu_Rat11), "matrix") 
OTU_Rat11 <- otu_table(otumat_Rat11, taxa_are_rows=TRUE) 
str(OTU_Rat11)
#Formal class 'otu_table' [package "phyloseq"] with 2 
#slots ..@ .Data : num [1:1018, 1] 942 433 3007 116765 15103 ... .. ..- 
#attr(*, "dimnames")=List of 2 .. .. ..:ℎ[1:1018]"186826""33958""1578"
#"33959".........:chr[1:1018] "186826" "33958" "1578" "33959"......... :
# chr "sa1" ..@ taxa_are_rows: logi TRUE

taxmat_Rat11 = as.matrix(observation_metadata(otu_Rat11), rownames.force=TRUE)
TAX_Rat11 = tax_table(taxmat_Rat11)

physeq_Rat11 = phyloseq(OTU_Rat11, TAX_Rat11)
str(physeq_Rat11) 
#Formal class 'phyloseq' [package "phyloseq"] with 5 slots ..@ otu_table:Formal 
#class 'otu_table' [package "phyloseq"] with 2 slots .. .. ..@ .Data : num 
#[1:1018, 1] 942 433 3007 116765 15103 ... .. .. .. ..- attr(*, "dimnames")=List
# of 2 .. .. .. .. ..:ℎ[1:1018]"186826""33958""1578""33959".............: chr 
#[1:7] "taxonomy1" "taxonomy2" "taxonomy3" "taxonomy4" ... ..@ sam_data : NULL ..
#@ phy_tree : NULL ..@ refseq : NULL –

Now I try to obtain @ sam_data
sampledata = sample_data(otu_Rat11) 
#Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty.

What do with sample data and how to merge several phyloseq-format datasets from different metagenomes?

**Tags:** r
> **Comments:**
> **username_1**: Is it possible to have an example file for `Rat11.biom`? It's easier to debug with a reproducible result. What do you mean by "the result was not correct"? What's your code for merging several phyloseq-format datasets from different metagenomes?  
> **username_2**: I'm working on this procedure with some difficult. Could you please tell me how do you convert kraken2 report files into the biom format?  
> **username_3**: I had received the same error. My metadata file was in a matrix format, I converted it into a data.frame and it worked. Pls try and see if it works.  

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## 0 answers

