proportion of correlated regions

[humanpaingeneticslab]

Hi Everyone,

I was wondering if someone could share some R code that takes for input the results of supergnova and estimates the proportion of correlated regions. Here's what I have so far;

Best to All,
Marc.

R --no-save --quiet
library( "ashr" )

#----- load supergnova results
my <- read.table(
"supanova_insomnia.txt",
header=TRUE, sep=" ", as.is=TRUE,
stringsAsFactors=FALSE, quote="" )

#----- estimate proportion of correlated regions
J <- ash( my[,"rho"], sqrt( my[,"var"] ), mixcompdist="halfnormal" )
sum( 1 - J$result$lfdr ) / nrow( my ) # <----- is this correct?