From f3954c57723337f537b4931e488f6035c511741f Mon Sep 17 00:00:00 2001 From: Matthias Doering Date: Thu, 22 Mar 2018 15:18:54 +0100 Subject: [PATCH] vignette update --- vignettes/openPrimeR_vignette.Rmd | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/vignettes/openPrimeR_vignette.Rmd b/vignettes/openPrimeR_vignette.Rmd index 9f7ea3d..02159ab 100644 --- a/vignettes/openPrimeR_vignette.Rmd +++ b/vignettes/openPrimeR_vignette.Rmd @@ -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.