Computes LD for weight variants using reference LD

Usage

compute_weight_LD_from_ref(
  weights,
  region_info,
  LD_map,
  snp_map = NULL,
  LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
  LD_loader_fun = NULL,
  snpinfo_loader_fun = NULL,
  ncore = 1
)

Arguments

weights: a list of preprocessed weights.
region_info: a data frame of region definitions.
LD_map: a data frame with filenames of LD matrices and SNP information for the regions. Required when load_predictdb_LD = FALSE.
snp_map: a list of SNP-to-region map for the reference. If NUll, it will reads SNP info from the "SNP_file" column of LD_map.
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.

Value

a list of processed weights, with LD of weight variants included.