qtl_pheno_simu {rNeighborGWAS}

Simulating phenotype values with neighbor effects.

Description

A function to simulate phenotype values with multiple sources of variation controlled

Usage

qtl_pheno_simu(
  b_self,
  b_nei,
  eigenK_self,
  eigenK_nei,
  b_ratio = c(1, 1),
  pveB,
  pve
)

Arguments

b_self

A n x 1 genotype vector to design major additive genetic effect.

b_nei

A vector of an explanatory variable for neighbor effects

eigenK_self

Products of eigen() with self covariance matrices that are used as explanatory variables for the phenotype.

eigenK_nei

Products of eigen() with neighbor covariance matrices that are used as explanatory variables for the phenotype.

b_ratio

Ratio for contributions of eigenK_self and eigenK_nei to the phenotype.

pveB

Proportion of variance explained by genetic effects attributable to the fixed effects (i.e., b_.. vector).

pve

Proportion of variance explained by all genetic effects (i.e., b_.. and eigenK_..)

Value

A list of simulated phenotypes

• y Simulated phenotype values

• beta_self major self-genetic effects

• beta_nei major neighbor effects

• sigma_self self polygenic effects

• sigma_nei neighbor polygenic effects

• epsilon residuals

• res_pveB realized proportion of variation explained by major-effect genes

• res_pve realized proportion of variation explained by major-effect genes and polygenic effects

Author(s)

Eiji Yamamoto, and Yasuhiro Sato