Screens regions with strong signals to be used in fine-mapping step.

screen_regions(
  region_data,
  LD_map,
  weights,
  group_prior = NULL,
  group_prior_var = NULL,
  L = 5,
  min_var = 2,
  min_gene = 1,
  filter_L = TRUE,
  filter_nonSNP_PIP = FALSE,
  min_L = 1,
  min_nonSNP_PIP = 0.5,
  min_abs_corr = 0.1,
  LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
  LD_loader_fun = NULL,
  snpinfo_loader_fun = NULL,
  ncore = 1,
  logfile = NULL,
  verbose = FALSE,
  ...
)

Arguments

region_data: a list object indexing regions, variants and genes.
LD_map: a data frame with filenames of LD matrices and SNP information for each of the regions.
weights: a list of preprocessed weights.
group_prior: a vector of two prior inclusion probabilities for SNPs and genes.
group_prior_var: a vector of two prior variances for SNPs and gene effects.
L: the number of effects for susie.
min_var: minimum number of variables (SNPs and genes) in a region.
min_gene: minimum number of genes in a region.
filter_L: If TRUE, screening regions with estimated credible sets (L) = min_L.
filter_nonSNP_PIP: If TRUE, screening regions with total non-SNP PIP >= min_nonSNP_PIP.
min_L: If screening by nubmer of credible sets (L), regions with L >= min_L will be selected to run finemapping using full SNPs.
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_abs_corr: Minimum absolute correlation allowed in a credible set.
LD_format: file format for LD matrix. If "custom", use a user defined LD_loader_fun() function to load LD matrix.
LD_loader_fun: a user defined function to load LD matrix when LD_format = "custom".
snpinfo_loader_fun: a user defined function to load SNP information file, if SNP information files are not in standard cTWAS reference format.
ncore: The number of cores used to parallelize susie over regions.
logfile: The log filename. If NULL, will print log info on screen.
verbose: If TRUE, print detail messages.
...: Additional arguments of susie_rss.

Value

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