Description Usage Arguments Value
This is a black box function which performs the statistical test on a single SNP.
1 | Test_ASE_Outliers(Eg_std, eh1, eh2, r0, p0)
|
Eg_std |
Genetic standard deviation, the square root of genetic variation in regulation in general population in natural log scale (numeric value). |
eh1 |
Integer value for of expression of haplotype 1. |
eh2 |
Integer value of expression of haplotype 2. |
r0 |
The ratio of the eh1 allele (i.e., eh1/(eh1+eh2)) in the absence of any regulatory difference (reference bias due to alignment). The simplest way to get such an estimate would be to get the median ratio between eh1 and eh2 across the entire library. |
p0 |
An average noise rate p(R->A) or p(A->R), i.e., the probability of seeing an allele due to noise when it is essentially not there (for GTEx v7: LAMP = 0.0003). |
Undajusted 2-sided p-value, testing whether: H0:There does not exist a significantly abnormal allelic imbalance for this SNP, vs. H1: Allelic ratio significantly deviates from normal population.
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