Runs cTWAS fine-mapping for regions

finemap_regions(
  region_data,
  LD_map,
  weights,
  L = 5,
  group_prior = NULL,
  group_prior_var = NULL,
  min_var = 2,
  min_gene = 1,
  null_method = c("ctwas", "susie", "none"),
  coverage = 0.95,
  min_abs_corr = 0.1,
  include_cs = TRUE,
  include_prior = FALSE,
  include_mu2 = FALSE,
  include_susie_alpha = TRUE,
  include_susie_result = FALSE,
  snps_only = FALSE,
  force_compute_cor = FALSE,
  save_cor = FALSE,
  cor_dir = NULL,
  LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
  LD_loader_fun = NULL,
  snpinfo_loader_fun = NULL,
  ncore = 1,
  verbose = FALSE,
  logfile = NULL,
  ...
)

Arguments

region_data: region_data to be finemapped
LD_map: a data frame with filenames of LD matrices for the regions.
weights: a list of preprocessed weights.
L: the number of effects or a vector of number of effects for each region.
group_prior: a vector of prior inclusion probabilities for different groups. If NULL, it will use uniform prior inclusion probabilities.
group_prior_var: a vector of prior variances for different groups. If NULL, it will set prior variance = 50 as the default in susie_rss.
min_var: minimum number of variables (SNPs and genes) in a region.
min_gene: minimum number of genes in a region.
null_method: Method to compute null model, options: "ctwas", "susie" or "none".
coverage: A number between 0 and 1 specifying the “coverage” of the estimated confidence sets
min_abs_corr: Minimum absolute correlation allowed in a credible set.
include_cs: If TRUE, add credible sets (CS) to finemapping results.
include_prior: If TRUE, include priors in finemapping results.
include_mu2: If TRUE, include estimated effect size variance (mu2) in finemapping results.
include_susie_alpha: If TRUE, include susie alpha matrix from finemapping results.
include_susie_result: If TRUE, include the "susie" result object in finemapping results.
snps_only: If TRUE, use only SNPs in the region data.
force_compute_cor: If TRUE, force computing correlation (R) matrices
save_cor: If TRUE, save correlation (R) matrices to cor_dir
cor_dir: a string, the directory to store correlation (R) matrices
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 computation over regions
verbose: If TRUE, print detail messages
logfile: the log file, if NULL will print log info on screen
...: Additional arguments of susie_rss.

Value

a list with cTWAS finemapping results.