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

[Gowri1994]

HI, I have been trying to create "physeq" and encountered the following error while loading the TAX table.

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘tax_table’ for signature ‘matrix'

The code I used is

setwd("/Users/gowri/Desktop/taxonomizr") prepareDatabase('accessionTaxa.sql')

#Test system taxaId<-getId(c('Homo sapiens','Bos taurus','Homo','Alces alces'),'accessionTaxa.sql') print(taxaId)

#TaxiD_table or OTU_table

TaxID=read.table("/Users/gowri/Desktop/rafied_reads.txt", header= T) TaxID1=data.matrix(TaxID)

#Taxonomy_table taxaId2=row.names.data.frame(TaxID) TaxIDtoTaxonomy=getTaxonomy(taxaId2,'accessionTaxa.sql') head(TaxIDtoTaxonomy) write.table(TaxIDtoTaxonomy,"TaxIDtoTaxonomy.txt",sep="\t")

#Sample_table

sample_data=read.table("/Users/gowri/Desktop/grouppp.txt", header= T)

#combine_OTU_data, TAX_data and sample_data OTU = otu_table(TaxID1, taxa_are_rows = TRUE) TAX = tax_table(TaxIDtoTaxonomy)

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘tax_table’ for signature ‘matrix'

Can anyone please help me to resolve this problem?

[ycl6]

Hi @Gowri1994

Can you paste what you get when you try str(TaxIDtoTaxonomy) and head(TaxIDtoTaxonomy)

[valentinavan]

Any idea why this is happening? I am having the same issue and I am not sure why because it has always worked so far, using the same script and the same data. It stopped working. Thanks

[ycl6]

Hi @valentinavan It's hard to tell without seeing your input data. I can have a look at it if you don't mind sharing the data (or part of the data).

[siriusorignblack]

i met the same question and i solved it as following: use tax_table as phyloseq::tax_table rather than only tax_table. because in my situation, it seems there exists some conflicts concerning the tax_table function between phyloseq package and microbiotaprocess package. hope this may have some help for your issue.

[julipeale2001]

phyloseq::tax_table

Worked for me. Thanks

[SafiyaYakubu]

I had the same problem and i solved it by unticking Microbiodataprocess package and microbiome package or not loading them before running the code. They seem to conflict with the tax_table function of phyloseq. Got this hint from siriusorignblack.