generate_gwas_ss: Modify SNP effects to account for LD

In explodecomputer/simulateGP: Functions for Simulating Genotype-Phenotype Relationships

Modify SNP effects to account for LD

Description

After generating the set of causal effects at each SNP, use an LD correlation matrix to transform the effects to reflect the correlation structure at the SNPs. Note if running many repeats, only need to generate the LD-modified params once and then can repeatedly re-sample using generate_gwas_ss

Usage

generate_gwas_ss(
  params,
  nid,
  vy = 1,
  minmaf = 0.001,
  ld = NULL,
  ldobj = NULL,
  ldobjlist = NULL,
  ldobjfiles = NULL,
  ldobjdir = NULL,
  gwasglue2 = FALSE,
  nthreads = 1
)

Arguments

params	Output from generate_gwas_params
nid	sample size
vy	Variance of trait
minmaf	minimum allowed maf. default=0.01 to prevent instability
ld	LD correlation matrix. Must be same dimension as params
ldobj	LD objects (e.g. see test_ldobj)
ldobjlist	List of LD objects
ldobjfiles	Array of filenames containing LD object files (e.g. see generate_ldobj)
ldobjdir	Directory containing output from generate_ldobj
gwasglue2	Logical, creates a gwasglue2 SummarySet when @param ldobj is not NULL (default FALSE).
nthreads	Number of threads (can be slow for complete GWAS and large LD regions)

Value

Updated params

explodecomputer/simulateGP documentation built on April 3, 2024, 2:38 a.m.