calc_EG_Var: Function to calculate the variance of conditional expected...

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

This is the variance for the simplified function calc_EG. It used the formula var(X)=E(X^2)-E(X)^2, where E(X) is the same as the result of calc_EG.

Usage

calc_EG_Var(M, p, rdv)

Arguments

M	genotype likelihoods P(D_{ij}|G=AA, Aa\ or\ aa) for one locus, matrix of dimension number of samples by 3 (double);
p	genotype frequencies P(G=AA, Aa\ or\ aa) (double); output from function calc_EM.
rdv	read depth (vector of integers) for all samples

Value

the variance of E(P(G_{ij}|D_{ij})).

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.