Merges region data for cross-boundary genes

merge_region_data(
  boundary_genes,
  region_data,
  region_info,
  LD_map,
  snp_map,
  weights,
  z_snp,
  z_gene,
  estimate_L = TRUE,
  expand = TRUE,
  L = 5,
  maxSNP = Inf,
  LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
  LD_loader_fun = NULL,
  snpinfo_loader_fun = NULL,
  ncore = 1,
  verbose = FALSE,
  logfile = NULL,
  ...
)

Arguments

boundary_genes: a data frame of boundary gene info
region_data: a list of original region_data
region_info: a data frame of region definitions
LD_map: a data frame with filenames of LD matrices and SNP information for the regions.
snp_map: a list of data frames with SNP-to-region map for the reference.
weights: a list of preprocessed weights.
z_snp: A data frame with columns: "id", "z", giving the z-scores for SNPs.
z_gene: A data frame with columns: "id", "z", giving the z-scores for genes.
estimate_L: If TRUE, estimate L for merged regions.
expand: If TRUE, expand merged region_data with full SNPs
L: the number of effects for susie.
maxSNP: Inf or integer. Maximum number of SNPs in a region. Default is Inf, no limit. This can be useful if there are many SNPs in a region and you don't have enough memory to run the program.
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
verbose: If TRUE, print detail messages
logfile: The log filename. If NULL, will print log info on screen.
...: Additional arguments of susie_rss.

Value

a list of merged region data, merged region info, LD_map, snp_map, and merged region IDs.