Gets correlation matrices for a single region.

Source: R/ctwas_region_cor.R

Loads precomputed correlation matrices if available in cor_dir, otherwise, computes correlation matrices if no precomputed correlation matrices, or force_compute_cor = TRUE.

get_region_cor(
  region_id,
  sids,
  gids,
  LD_map,
  weights,
  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,
  verbose = FALSE
)

Arguments

region_id

a character string of region id.

sids

SNP IDs in the region

gids

gene IDs in the region

LD_map

a data frame with filenames of LD matrices and SNP information for the regions.

weights

a list of preprocessed weights

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.

verbose

If TRUE, print detail messages

Value

correlation matrices (R_snp, R_snp_gene and R_gene)