diff --git a/vignettes/bugphyzz.Rmd b/vignettes/bugphyzz.Rmd index f342a5dd..1e60445a 100644 --- a/vignettes/bugphyzz.Rmd +++ b/vignettes/bugphyzz.Rmd @@ -270,10 +270,19 @@ knitr::kable(gsea_tbl) Finally, a user could get all of the signature names to which a given taxon belongs to. Only taxids should be used. -An example using _Escherichia coli_ (taxid: 562): +An example using _Escherichia coli_ (taxid: 562). + +Get taxid for _E. coli_ using taxize: + +```{r, message=FALSE} +taxid <- as.character(taxize::get_uid("Escherichia coli")) +taxid +``` + +Get all signature names related to the _E. coli_ taxid: ```{r} -getTaxonSignatures(tax = "562", bp = bp) +getTaxonSignatures(tax = taxid, bp = bp) ``` ## Session information: