QTL-QTL interaction

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nata...@gmail.com

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Jul 5, 2021, 5:48:59 AMJul 5
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Hi
I don't understand how can a/d be larger than 1 in the case of a binary trait. And how is the SE so big?
These are my fitqtl results after addqtl and addpair:

$FOB3_bin
fitqtl summary
Method: Haley-Knott regression 
Model:  binary phenotype
Number of observations : 118 
Full model result
----------------------------------  
Model formula: y ~ Q1 + Q2 + Q3 
                                  est                 SE                t
Intercept         -0.2722688  0.2461408 -1.10615077
L...@30.0a    0.5833693  0.3649499  1.59849135
L...@30.0d    2.2229040  0.6213122  3.57775695
LG...@6.6a    -1.8501205 14.6417859 -0.12635894
LG...@6.6d   10.3528849 14.6465690  0.70684711
LG...@21.0a  0.5553481 14.6439920  0.03792327
LG...@21.0d -8.9403417 14.6415530 -0.61061431

thanks
Nataly

nata...@gmail.com

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Jul 5, 2021, 5:57:25 AMJul 5
to R/qtl discussion
basil=cross
s.aq=summary(addqtl)
here is the code I used for my 3 binary traits:

for(i in 1:3){
  p<-phenames(basil)[i+n]
  if(length(qtlist.bin[[p]][,1])>0){
    q<-rbind(qtlist.bin[[p]][,-c(3,4)],s.aq[[p]])
    rqtl2.bin[[p]]<-refineqtl(basil,p,makeqtl(basil,q[,1],q[,2],what="prob"),maxit.fitqtl=1e+6,tol=0.05,method="hk",model="binary")
    out.ap.bin[[p]]<-addpair(basil,q[,1],p,rqtl2.bin[[p]],maxit=1e+6,tol=0.2,method="hk",model="binary")
    qtlpairs[[p]]<-summary(out.ap.bin[[p]],thresholds=m.bin[p,])
    s.fq[[p]]<-summary(out.fq[[p]]<- fitqtl(basil,p,rqtl2.bin[[p]],maxit=1e+6,tol=0.01,method="hk",model="binary",get.ests=T))
  }

Is it because of the maxit / tol parameters?
ב-יום שני, 5 ביולי 2021 בשעה 12:48:59 UTC+3, nata...@gmail.com כתב/ה:

Karl Broman

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Jul 5, 2021, 7:09:55 AMJul 5
to R/qtl discussion
With the binary trait model, it is using logistic regression, so there are no constraints on the parameters.

karl

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