Creates and saves 1) the summary stats file, and 2) the LD matrix. "Columns beta and se are required for fine-mapping. Column maf is needed to output posterior effect size estimates on the allelic scale. All other columns are not required for computations and can be specified arbitrarily."
Source
http://www.christianbenner.com
locus_dir <- echodata::locus_dir;
dat <- echodata::BST1;
LD_matrix <- echodata::BST1_LD_matrix
dir.create(file.path(locus_dir,"FINEMAP"),
showWarnings = FALSE, recursive = TRUE)
out <- echoLD::subset_common_snps(LD_matrix=LD_matrix, dat=dat)
LD_matrix <- out$LD
dat <- out$DT
dat_paths <- echofinemap:::FINEMAP_construct_data(dat=dat,
locus_dir=locus_dir,
LD_matrix=LD_matrix)