gbe-power-app

Web app for calculating GWAS power using empirical allele frequency estimates.

Cloning

Use git lfs clone https://github.com/rivas-lab/gbe-power-app.git to pull in the files tracked with LFS.

Running the app

First install the GeneticsDesign package from Bioconductor to obtain the needed dependencies:

source("https://bioconductor.org/biocLite.R")
biocLite("GeneticsDesign")

Then install my version of "GeneticsDesign" in data using R CMD install data/GeneticsDesign_1.45.0.tar.gz. Start RStudio and open shinyapp/ui.R and click the "Run App" button above the file contents. You can use the arrow next to the "Run App" button to choose whether to launch the app in RStudio or your browser. Note that the app relies on data that is tracked with git LFS, so be it might make sense to make sure all the LFS data has been pulled in using git lfs pull.

Pushing the app to shinyapps.io

Use

library(rsconnect)
rsconnect::deployApp('path/to/your/app')

to push the app to the web. Note that you must install the GeneticsDesign package using

library(devtools)
install_github("cdeboever3/GeneticsDesign")

for this to work.

App description

Design Summary Table

The design summary table tells you how many genes are powered at 0.8 given the study design parameters. The gene in the "Gene" box is not used for this table. Currently, the calculation is kind of slow, so it may take ~1 minute to generate the table.