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getp <- function(lr,lr0,ties.method = "average") {
# Adapted from J.D.Storey, see qvalue::empPvals
# Get resampled p-values, pulling across variables (e.g., genes)
# lr: observed statistics
# lr0: null statistics (i.e. from resampled residuals)
m = length(lr)
m0 = length(lr0)
v = c(rep(TRUE,m),rep(FALSE,m0))
v = v[rev(order(c(lr,lr0)))]
u = 1:length(v)
w = 1:m
p = ((u[v==TRUE]-w))/(length(lr0))
#to account for the extreme observed values
#p = ((u[v==TRUE]-w)+1)/(length(lr0)+2)
p = p[rank(-lr, ties.method = ties.method)]
p = pmax(p, 1/m0)
return(p)
}
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