4
votes
Accepted
Inflated p-values in quantitative trait analysis
Permutation as suggested by @StupidWolf's comment is essential to understand what's going on. If permutation makes this pattern go away, then you have a problem with your model specification, there's ...
- 3,804
3
votes
Accepted
Odds ratio and enrichment of SNPs in gene regions?
The first approach only address the question of how likely are you to end up with the observed over-representation given the MAF distribution.
My suggestion is to use the second approach, but I am not ...
- 1,678
1
vote
Accepted
tensorQTL interaction issue
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no homozygous ones needed for QTL calculation.
I used plink2 to ...
- 31
1
vote
What are the largest fully publicly available molecular QTL datasets?
The largest eQTL datasets I can think of is probably eQTLGen. This is a meta-analysis of many studies using >30,000 samples from whole blood. This might be less ideal if you want cell-type-specific ...
- 857
Only top scored, non community-wiki answers of a minimum length are eligible