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Update vignette with code for getting taxid from scientific name usin…
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…g taxize.
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sdgamboa committed Mar 11, 2024
1 parent 9cd2015 commit dbb8ddd
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13 changes: 11 additions & 2 deletions vignettes/bugphyzz.Rmd
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Expand Up @@ -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:

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