Screens regions with strong signals

Screens regions with strong signals

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,
  min_gene_pval = min_snp_pval,
  use_twas_min_pval = FALSE,
  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.

min_gene_pval

Select regions with minimum gene p-values < min_gene_pval. By default, it is set to the same value as 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.