Web app for calculating GWAS power using empirical allele frequency estimates.
Use git lfs clone https://github.com/rivas-lab/gbe-power-app.git to pull in
the files tracked with LFS.
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.
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.
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.