[R] qq plot issue with ab line

[Ana Marija]

Hello,

I made the plot in attach with this function:

qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
{
  nn = length(p)
  xx =  -log10((1:nn)/(nn+1))
  plot( xx,  -sort(log10(p)),
        main = MAIN, sub= SUB, cex.sub=1.3,
        xlab=expression(Expected~~-log[10](italic(p))),
        ylab=expression(Observed~~-log[10](italic(p))),
        cex.lab=1.0,mgp=c(2,1,0))
  abline(0,1,col='red')
  if(BH) ## BH = include Benjamini Hochberg FDR
  {

    abline(-log10(0.05),1, col='black',lty=1)
    text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
    abline(-log10(0.10),1, col='black',lty=1)
    text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
    abline(-log10(0.25),1, col='black',lty=1)
    text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
    #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
           #col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
    if (BF)
    {
      abline(h=-log10(0.05/nn), col='black') ## bonferroni
    }
  }
}


biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
qqunif(biob272$V2)


> head(biob272)
         V1       V2
1 rs2089177 0.581204
2 rs4360974 0.418456
3 rs6502526 0.416670
4 rs8069906 0.568030
5 rs9895995 0.266746
6 rs9905280 0.510032

But the red, abline doesn't look like it is 1:1 line.

Can you please advise?

Thanks
Ana

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