Estimates cTWAS parameters using EM with cTWAS SER model

Usage

est_param(
  region_data,
  init_group_prior = NULL,
  init_group_prior_var = NULL,
  group_prior_var_structure = c("shared_all", "shared_type", "shared_context",
    "shared_nonSNP", "independent", "fixed"),
  niter_prefit = 3,
  niter = 50,
  min_var = 2,
  min_gene = 1,
  min_group_size = 100,
  min_p_single_effect = 0.8,
  null_method = c("ctwas", "susie", "none"),
  EM_tol = 1e-04,
  force_run_niter = FALSE,
  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 different groups.
init_group_prior_var: a vector of initial values of prior variances for different groups.
group_prior_var_structure: a string indicating the structure to put on the prior variance parameters. "shared_all" allows all groups to share the same variance parameter. "shared_type" allows all groups in one molecular QTL type to share the same variance parameter. "shared_context" allows all groups in one context (tissue, cell type, condition) to share the same variance parameter. "shared_nonSNP" allows all non-SNP groups to share the same variance parameter. "independent" allows all groups to have their own separate variance parameters. "fixed" sets prior variance parameters to values in init_group_prior_var.
niter_prefit: the maximum number of iterations of the E-M algorithm to perform during the initial parameter estimation step.
niter: the maximum number of iterations of the E-M algorithm to perform during the complete parameter estimation step.
min_var: minimum number of variables (SNPs and genes) in a region.
min_gene: minimum number of genes in a region.
min_group_size: Minimum number of variables in a group.
min_p_single_effect: Regions with probability greater than min_p_single_effect of having at most one causal effect will be used selected for the complete parameter estimation step.
null_method: Method to compute null model, options: "ctwas", "susie" or "none".
EM_tol: A small, non-negative number specifying the convergence tolerance of log-likelihood for the EM iterations.
force_run_niter: If TRUE, run all the niter EM iterations.
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.

Value

a list with estimated parameters