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vignette update
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Matthias Doering committed Mar 22, 2018
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7 changes: 1 addition & 6 deletions vignettes/openPrimeR_vignette.Rmd
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Expand Up @@ -265,12 +265,7 @@ optimal.primers <- design_primers(template.df[1:2,], mode.directionality = "fw",
settings = design.settings)
```

`optimal.primers` is a list in which the optimal primers are stored in `optimal.primers$opti` and the corresponding filtered primers are stored in `optimal.primers$filtered`. The optimal primer sets for all evaluated melting temperatures are stored in `optimal.primers$all_results`. We can use the `summary()` function to get an overview of the properties of the designed primers:

```{r view_designed_primers, message = FALSE, warning = FALSE}
# Create an overview of the optimal primers
print(summary(optimal.primers$opti))
```
`optimal.primers` is a list in which the optimal primers are stored in `optimal.primers$opti` and the corresponding filtered primers are stored in `optimal.primers$filtered`. The optimal primer sets for all evaluated melting temperatures are stored in `optimal.primers$all_results`.

The primer design function can be customized in many ways. The `init.algo` argument can be used to specify how the initial set of primers is generated. By default, this is done by extracting substrings from the template sequences ('naive'). A tree-based initialization strategy producing degenerate primers can be activated by setting `init.algo` to 'tree', which is favorable for related template sequences.

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