qiime2r - typo?

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1

Hi guys!
Thank you for your really nice job @jbisanz , this library is very useful!
But when I try to import my files and create a phyloseq object it return me an Error
If I run:

physeq<-qza_to_phyloseq(
features="aedes_h2o_host.qza",
tree="rooted-tree_h2o_host.qza",
"taxonomy_h20_host_138vsearch.qza",
metadata = "map_aedes_h2o_host.tsv"
)

return:
Error in parse_taxonomy(taxonomy) :
Table does not match expected format (conames(obj) are Feature.ID, Taxon, Confience)

that's because my taxonomy file have as colnames:

colnames(taxonomy$data)
[1] "Feature.ID" "Taxon" "Consensus"

I think because I use Vsearch plugin.
I fix importing taxonomy qza and changing the colnames as:

taxonomy<-read_qza("taxonomy_h20_host_138vsearch.qza")
'names(taxonomy$data)[names(taxonomy$data) == "Consensus"] <- "Confidence"'

I hope that could be useful for other people
Thank again for everything

2

Typo corrected in the error message, and now both Confidence and Consensus will be allowed in that third column. Reinstall from github and should be fixed.

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3

An off-topic reply has been split into a new topic: Error in parse_taxonomy(taxonomy)

Please keep replies on-topic in the future.