cor.X.function: Function to edit the correlation matrix of expected genotype...

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

Description

Given the original case or control genotype matrix, return the edited correlation matrix. In the check_hom_matrix, we are trying to solve the problem that the whole column is homozygous. But this NA correlation pairs happens when one column is not homozygous, but when paired with another column, the non-missing values might be homozygous. And it will return the edited correlation matrix while check_hom_matrix return the edited genotype probability matrix.

Usage

cor.X.function(X1, hom = 1, multiplier = 1, snp_loop)

Arguments

hom	with value 1 or 2. 1 means making changes with the 1st nonNA element, 2 means making changes with a random nonNA element
multiplier	with value 1 or 2, 1 is dividing by 2 and 2 is mulitpling by 2.
snp_loop	will tell the relative location of the probablematic snp.
X	the expected condidtional genotype probablity matrix for grouped rare variants

Value

cor.X the edited correlation from the expected condidtional genotype probablity matrix

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