Thats the deviation from the expected 0.5.
If you have 100 reads overlapping a het SNP, if 25 coming from ref and 75 coming from alt, Allelic Ratio (AR) w.r.t ref allele is
25/100 = 0.25 . So the deviation is
If there is no allelic imbalance, the ref reads would be 50 and alternate reads would be 50, AR is 0.5 and deviation would be
0.5-0.5=0, i.e no allelic imbalance.
I would just do
ref/total to have AR. No need to do (
0.5-ref/total). You need to do a binomial test to see the "significant" deviation.
PS: It doesnt matter if numerator is ref or alt count. When you interpret, it should be w.r.t what you use as numerator. Like in gene expression fold change, depending on if you compare condition1 vs condition2 or condition2 vs condition1
modified 8 weeks ago
8 weeks ago by
geek_y ♦ 9.8k