calculateVarFrac_v2: Calculate the fraction of phenotypic variance explained by as...

In vincela/VarExp: Computes phenotypic variance explained by a set of genetic and/or interaction effects

Description

This version takes into account potential rank deficiencies in the correlation matrix and noise in the effect size estimation.

Usage

calculateVarFrac_v2(std_bG, std_bI, matcor, varY, N, type)

Arguments

std_bG	is the vector of standardized genetic effect sizes
std_bI	is the vector of standardized interaction effect sizes
matcor	is the genotype correlation matrix
varY	is the phenotypic variance in the pooled sample
N	is the total sample size
type	indicates wether only genetic or interactions effects should be considered or if both should be considered jointly.

Details

For more details, see Shi et al., Am. J. Hum. Genet., 2016

Value

The fraction of phenotypic variance explained by user-specified effects.

Examples

std_bG = rnorm(5,0,0.01)
std_bI = rnorm(5,0,0.001)
matcor = cor(matrix(runif(5*5,1,5),nrow=5))
varY = 2.25
N = 100000
calculateVarFrac_v2(std_bG, std_bI, matcor, varY, N, "G")
calculateVarFrac_v2(std_bG, std_bI, matcor, varY, N, "I")
calculateVarFrac_v2(std_bG, std_bI, matcor, varY, N, "J")

vincela/VarExp documentation built on May 29, 2019, 12:42 p.m.