GenPheno {AllelicSeries}

Generate Phenotypes

Description

Generate Phenotypes

Usage

GenPheno(
  anno,
  beta,
  covar,
  geno,
  reg_param,
  binary = FALSE,
  include_residual = TRUE,
  indicator = FALSE,
  method = "none",
  prop_causal = 1,
  random_signs = FALSE,
  random_var = 0,
  weights = c(0, 1, 2)
)

Arguments

anno

(snps x 1) annotation vector.

beta

(3 x 1) coefficient vector for bmvs, dmvs, and ptvs respectively.

covar

Covariate matrix.

geno

(n x snps) genotype matrix.

reg_param

Regression parameters.

binary

Generate binary phenotype? Default: FALSE.

include_residual

Include residual? If FALSE, returns the expected value. Intended for testing.

indicator

Convert raw counts to indicators? Default: FALSE.

method

Genotype aggregation method. Default: "none".

prop_causal

Proportion of variants which are causal.

random_signs

Randomize signs? FALSE for burden-type genetic architecture, TRUE for SKAT-type.

random_var

Frailty variance in the case of random signs. Default: 0.

weights

Aggregation weights.

Value

(n x 1) numeric vector.