phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I am having a problem when building a new phyloseq object from manually imported data using phyloseq(). If I run:
phyloseq <- phyloseq(OTU, TAX, tree)
I get this error:
## Error in paste (..., sep = sep) :
## 4 arguments passed to .Internal(paste) which requires 3
Adding only one of the components (either OTU-table or Tax-table) at a time, gives the same error:
phyloseq <- phyloseq(OTU)
## Error in paste (..., sep = sep) :
## 4 arguments passed to .Internal(paste) which requires 3
All other steps are -as far as I'm aware of- working perfectly fine. It's only this final step of combining the components that gives an error.
head(tax, n=3)
## Kingdom Phylum Class Order Family Genus Species
## Zotu1 "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Prevotellaceae" "Prevotella_9" "copri"
## Zotu2 "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "Ruminococcaceae" "Faecalibacterium" NA
## Zotu3 "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "Lachnospiraceae" "Agathobacter" NA
TAX <- tax_table(tax)
asv <- column_to_rownames(asv, var = "sample_id")
ASV <- otu_table(asv, taxa_are_rows = F)
Anyone know what is the problem here? Many thanks!
I am having a problem when building a new phyloseq object from manually imported data using
phyloseq(). If I run:I get this error:
Adding only one of the components (either OTU-table or Tax-table) at a time, gives the same error:
phyloseq <- phyloseq(OTU)All other steps are -as far as I'm aware of- working perfectly fine. It's only this final step of combining the components that gives an error.
head(tax, n=3)Anyone know what is the problem here? Many thanks!