shinyGPA: Run ShinyGPA app
In carter-allen/GPA: GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/shinyGPA.R

Run ShinyGPA app.

1	shinyGPA( out=NULL )

out

output of fitAll function.

shinyGPA runs the ShinyGPA app. It takes the output of the fitAll function, which fits the GPA model for all possible pairs of GWAS datasets, as input.

Provides visualization to investigate pleiotropic architecture using GWAS results.

Dongjun Chung, Emma Kortemeier

Kortemeier E, Ramos PS, Hunt KJ, Kim HJ, Hardiman G, and Chung D (2018), "ShinyGPA: An interactive and dynamic visualization toolkit for genetic studies," PLOS One, 13(1): e0190949.

fitAll.

# simulator function

simulator <- function( risk.ind, nsnp=20000, alpha=0.6 ) {
  
  m <- length(risk.ind)
  
  p.sig <- rbeta( m, alpha, 1 )
  pvec <- runif(nsnp)
  pvec[ risk.ind ] <- p.sig
  
  return(pvec)
}

# run simulation

set.seed(12345)
nsnp <- 1000
alpha <- 0.3
pmat <- matrix( NA, nsnp, 5 )

pmat[,1] <- simulator( c(1:200), nsnp=nsnp, alpha=alpha )
pmat[,2] <- simulator( c(51:250), nsnp=nsnp, alpha=alpha )
pmat[,3] <- simulator( c(401:600), nsnp=nsnp, alpha=alpha )
pmat[,4] <- simulator( c(451:750), nsnp=nsnp, alpha=alpha )
pmat[,5] <- simulator( c(801:1000), nsnp=nsnp, alpha=alpha )

# Fit GPA for all possible pairs of GWAS datasets

out <- fitAll( pmat, maxIter = 100 )

# Run the ShinyGPA app using the ouput from fitAll()

# shinyGPA(out)