calc_psingle: Function to compute the genotype likelihood of a read given...

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 function uses the formula P(D=g|G=G_1G_2)=1/2*P(D=g|G_1)+1/2*P(D=g|G_2) and p(D=g|G_1=g)=1-e,p(D=other\ call|G_1=g)=e/3 to compute the genotype likelihood P(D=g|G=G_1G_2,e), more details are in Appendix B of the paper. It is called from functions calc_pobs_ndepth and calc_Mr.

Usage

calc_psingle(sing_read, A1, A2, error)

Arguments

sing_read	single read, e.g. A.
A1	allele 1 in the true genotype, e.g. if G_1G_2=AC then A1='A'
A2	allele 2 in the true genotype, e.g. A2='C'
error	sequencing error, decimal with value between 0 and 1.

Value

likelihood of observing sing_read given genotype (A1A2) and error rate

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