shared otus function problem

[pavlo888]

Hi,

I am trying to see the shared OTUs from my phyloseq object.

I am running the function:

shared <- phyloseq_extract_shared_otus(physeqr, samp_names = sample_names(physeqr)) And then I obtain the following error:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘prune_samples’ for signature ‘"array", "phyloseq"’

Any idea what is wrong?

Cheers, Pablo

[vmikk]

Hello Pablo!

As a first guess, is phyloseq package loaded?

library(phyloseq)

And does the examples from the help pages work?

data(esophagus)
ps <- phyloseq_extract_shared_otus(esophagus, samp_names = sample_names(esophagus))
ps
otu_table(ps)

With kind regards, Vladimir

[pavlo888]

Hi Vladimir,

Yes the library is loaded and the example works.

What can I do next?

Cheers, Pablo

[vmikk]

Hello Pablo,

It is difficult to say why it's not working without seeing the data. How many samples are in your physeqr object? Could you post the results of the following commands?

sample_sums(physeqr)
taxa_are_rows(physeqr)

With kind regards, Vladimir

[vmikk]

I will close this issue for now. However, if it is not solved yet, feel free to reopen the issue if necessary.