How to calculate TPR, true positive rate,for tissue sharing between two different tissues?
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Entering edit mode
4.8 years ago
anamaria ▴ 220

Hello,

I have to calculate sharing of EQTLs between two different tissues (retina and LCL), π1 statistic. Can you please point me to the methodology on this issue?

I tried using qvalue function:

library(qvalue)
qval_obj=qvalue(pvalR)
pi1=1-qval_obj$pi0

but after running:

qval_obj=qvalue(pvalR)
Error in smooth.spline(lambda, pi0, df = smooth.df) : 
  missing or infinite values in inputs are not allowed

or

 qval_obj=qvalue(pvalR,lambda=0.5)
Error in pi0est(p, ...) : 
  ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda.

I checked:

max(pvalR)
[1] 0.000352731
min(pvalR)
[1] 1.84872e-127

Please advise,

Thanks Ana

tpr • 1.1k views
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