Estimates cTWAS parameters using EM

est_param(
  region_data,
  init_group_prior = NULL,
  init_group_prior_var = NULL,
  niter_prefit = 3,
  niter = 30,
  min_p_single_effect = 0.8,
  use_null_weight = TRUE,
  min_snps = 2,
  min_genes = 1,
  ncore = 1,
  logfile = NULL,
  verbose = FALSE,
  ...
)

Arguments

region_data: a list object indexing regions, variants and genes.
init_group_prior: a vector of initial values of prior inclusion probabilities for SNPs and genes.
init_group_prior_var: a vector of initial values of prior variances for SNPs and gene effects.
niter_prefit: the number of iterations of the E-M algorithm to perform during the initial parameter estimation step
niter: the number of iterations of the E-M algorithm to perform during the complete parameter estimation step
min_p_single_effect: Regions with probability >= min_p_single_effect of having at most one causal effect will be selected for the final EM step.
use_null_weight: If TRUE, allow for a probability of no effect in susie
min_snps: minimum number of SNPs in a region.
min_genes: minimum number of genes in a region.
ncore: The number of cores used to parallelize computation over regions
logfile: The log filename. If NULL, print log info on screen.
verbose: If TRUE, print detail messages
...: Additional arguments of susie_rss.

Value

a list with estimated parameters