Modify SNP effects to account for LD — generate_gwas

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

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