calc_EG_general: More general function to calculate the 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

Calculate the conditional expected genotype probability given the observed sequencing data D_{ij} from formula E(P(G_{ij}|D_{ij}))=∑_{g=0}^2 gP(G_{ij}=g|D_{ij}), where P(G_{ij}=g|D_{ij})=P(D_{ij}|G_{ij}=g)*P(G_{ij}=g)/P(D_{ij}). It is called from generate_seqdata.

Usage

calc_EG_general(M, p, rdv)

Arguments

M	genotype likelihoods with dimension of number of sample by 3 (double), each column is the genotype likelihood P(D_{ij}|G=AA, Aa\ or\ aa) for one locus; uses output from calc_pobs_ndepth for simulation data.
p	genotype frequencies P(G=AA, Aa\ or\ aa) for each variant; output from function calc_EM.
rdv	read depth for all samples, should be a vector of integer with length equal to number of samples.

Value

a vector of containing conditional expected genotype probability. Length should be the same as rdv.

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