I'm following the r/qtl book to analyse my QTLs. I got 3 peaks respectively in 3 chromosomes, as shown in the attached picture 1, one of which on chromosome 8 is with huge confidence interval. So I think there may be more than one genes in that peak and I want to use methods for multiple QTLs to separate them.
I first ran scaneone, and got the results as shown in attached picture 2. Then I controlled the QTL on chr8 by running makeqtl and addqtl of position 8@118, and the result showed me that there may be another peak at 8@24 (as shown in attached picture 3). So I expected that if I control the QTLS on chr2 and chr3, then I will find two peaks seperately at 8@120 and 8@24 on chr8.
But the problem came. After I ran add pair command, the result gave me two peaks at 8@75 and 8@100 with very weak evidence (shown in attached picture 4). So I don't understand why the result is so different from what I expected according to the results from previous steps.
Btw, when I plot the addpair result, I got the graph as shown in attached picture 5, indicating three locations interacting in chr8. But the evidence is very weak.
Could somebody explain a bit for me? Are there more than one gene in the peak on chr8? If so, did I do the right thing to separate them? Thanks in advance!
Here is my code:
out1.bin <- scanone(AllChrSuperNew1, pheno.col=2, method=c("em"))
qtl8 <- makeqtl(AllChrSuperNew1,chr = 8, pos =118.8633 ,what="prob")
summary(fitqtl(AllChrSuperNew1,pheno.col=2,method = "hk",qtl=qtl8,get.ests = TRUE))
out1.c8 <- addqtl(AllChrSuperNew1,pheno.col=2,qtl=qtl8)
qtl23 <- makeqtl(AllChrSuperNew1,chr= c(2,3),pos=c(136.8572,151.0700),what="prob")
out1.ap <- addpair(AllChrSuperNew1,qtl=qtl23,chr=8,method = "hk",verbose=FALSE)