Trouble with qiime2R

I just wanted to say thanks, I have been trouble shooting getting the export boom files into R and the import was the first to work correctly. Currently not sure wy I’m having trouble, but it may be something to do with the merging of the taxonomy + otu_table.

One quick comment though when I import it over, for some reason the row specified as titles/column titles does not import correctly:

[1] “V2” “V3” “V4” “V5” “V6” “V7” “V8” “V9” “V10” “V11” “V12” “V13” “V14” “V15” “V16” “V17” “V18” “V19” “V20” “V21” “V22” “V23”
[23] “V24” “V25” “V26” “V27” “V28”

Hi Ben, Could you send me a copy of the table and I can figure out what is going on?



Hi Jordan sure, which files do you need, the metadata table? Ben

Upload.assessment.txt (90.7 KB)

edit: I would like to add that the columns import correctly, it's just the titles that do not, I was able to do analysis putting V# to send information to R to be able to select my samples.

Ahh, yes this was a bug on the import of the metadata table where the column names were becoming a row of the table. If you pull the latest version from github this should be fixed. Let me know if you still have problems.


Great, will test it today, thank you again. Ben

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One quick recommendation, the column titles end up being:

[1] “ta1” “ta2” “ta3” “ta4” “ta5” “ta6” “ta7”

You can use this code to give your column titles:

colnames(tax_table(OBJECT.GOES.HERE))=c(“Domain”, “Phylum”, “Class”, “Order”, “Family”, “Genus”, “OTU”)