Screens regions with strong signals

Usage

screen_regions(
  region_data,
  group_prior = NULL,
  group_prior_var = NULL,
  min_var = 2,
  min_gene = 1,
  min_nonSNP_PIP = 0.5,
  min_snp_pval = 5e-08,
  null_method = c("ctwas", "susie", "none"),
  ncore = 1,
  logfile = NULL,
  verbose = FALSE
)

Arguments

region_data: a list object indexing regions, variants and genes.
group_prior: a vector of prior inclusion probabilities for different groups.
group_prior_var: a vector of prior variances for different groups.
min_var: minimum number of variables (SNPs and genes) in a region.
min_gene: minimum number of genes in a region.
min_nonSNP_PIP: If screening by non-SNP PIPs, regions with total non-SNP PIP >= min_nonSNP_PIP will be selected to run finemapping using full SNPs.
min_snp_pval: Select regions with minimum SNP p-values < min_snp_pval.
null_method: Method to compute null model, options: "ctwas", "susie" or "none".
ncore: The number of cores used to parallelize susie over regions.
logfile: The log filename. If NULL, print log info on screen.
verbose: If TRUE, print detail messages.

Value

a list, containing a data frame of selected region data, and a data frame of screening summary for all regions.