main: main function for simulation

In KaiqianZhang/prsim: Simulations for PRS Analysis

Description

main function for simulation

Usage

main(
  sim_label = 1,
  N_YRI,
  N_CEU,
  N_CHB,
  p_YRI,
  p_CEU,
  p_CHB,
  h2_YRI,
  h2_CEU,
  h2_CHB,
  prare_YRI,
  prare_CEU,
  prare_CHB,
  dist = "gaussian",
  ld = "strong",
  chunk_size,
  cores_used
)

Arguments

sim_label	denotes the x-th simulation
N_YRI	the number of YRI individuals
N_CEU	the number of CEU individuals
N_CHB	the number of CHB individuals
p_YRI	the proportion of causal SNPs in YRI population
p_CEU	the proportion of causal SNPs in CEU population
p_CHB	the proportion of causal SNPs in CHB population
h2_YRI	heritability of this phenotype in YRI population
h2_CEU	heritability of this phenotype in CEU population
h2_CHB	heritability of this phenotype in CHB population
prare_YRI	proportion of causal rare SNPs in YRI population
prare_CEU	proportion of causal rare SNPs in CEU population
prare_CHB	proportion of causal rare SNPs in CHB population
dist	distribution of effect sizes, default is "gaussian". Options can be "gaussian", "exponential", "laplace". Note that LDpred simulates non-zero effect sizes from laplace distribution.
ld	linkage disequilibrium. Options can be "strong" or "weak". We simulate nearby snps together when ld is strong. We simulate snps evenly spread over all variants when ld is weak.
chunk_size	the size of chunk we perform matrix multiplication
cores_used	the number of cores used in parallel computing

Value

phenotypes for three populations and effect sizes for three populations

KaiqianZhang/prsim documentation built on Feb. 7, 2022, 10:58 p.m.