does anyone how to make a MicrobiomeMarker object form phyloseq?

General
1

m making analysis of microbiome with qiime2 and i want to make a normalization and a lefse analysis with MicrobiomeMarker, but i'm in troubles because when i try to make a microbiomemarker object i got error messages.

here is the script:

library(phyloseq)

library(microbiomeMarker)

setwd("~/Escritorio/bacte_alfredo/ASVsB/r")

#import objects and make a phyloseq object

ps = import_qiime2(otu_qza = "feature_css.qza", taxa_qza = "taxfix.qza",

  •                sam_tab = "bacte_alfredo_metadata.tsv", tree_qza = "tree.qza")

Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’

microbiomeMarker(ps)

Error in microbiomeMarker(ps) : otu_table is required

a = otu_table(ps)

microbiomeMarker(a)

Error in microbiomeMarker(a) : otu_table is required

microbiomeMarker(otu_table(a))

Error in microbiomeMarker(otu_table(a)) : otu_table is required

marker_table(a)

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

i don know what the #ell is that mean with an otu table and i cannot find a way to get a MicribiomeMarker object.

do you have an idea or tip to get it?

2

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