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BXD power calculator

Statement of need

The BXD power app (https://dashbrook1.shinyapps.io/bxd_power_calculator_app/) seeks to provide a quick and easy graphical interface for users to calculate the theortical power to detect an effect in a two parent recombinant inbred population. This GitHub provides the scripts which the app is based on. A power calculator such as this is needed as all grants require a calculation of the applications power to detect the effect of interest, and this app can provide values and figures for applicants to use.

Installation

Installation simply requires server.R, ui.R and run_app.R to be downloaded to the same folder, and the run_app.R script to be run. The user can specify the location of their directory with the setwd command in run_app.R, if needed.

Test

To test that the app is working correctly, open the app and wait for plots to appear. Set heritability to 0.4, locus effect size to 0.4, biological replicates between 2 and 10, and power threshold to 0.8, observing that the plots update after each user input. The main plot should now appear as shown below:

-Figure 1

Now go to the table below, and click on "Total animals needed" to sort by the minimum number of animals needed. The table should now look like this:

-Figure 2

Now return to the inputs, and alter the minimum number of biological replicates to 10. The figure to the left should now appear like this:

-Figure 3

Issues

Issues can be raised through the github issue tracker.

Contributing

Contribute to source code by forking the Github repository, and sending us pull requests.

Its also possible to just post comments on code / commits.

Or be a maintainer, and adopt a function

Cite

Citation will be added, after publication.

License

The source code is released under the GNU GENERAL PUBLIC LICENSE Version 3 (GPLv3). See LICENSE.txt.

Contact

Code managed by David Ashbrook - Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, USA

About

App for visualizing probability (beta) of detecting a QTL as a function of heritability, strains, and replicates within strain

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