Re-build the LD reference panel with given SNPs.

Usage

sHDL.rebuild.ref(
  LD.path,
  gwas.snps,
  LD.path.new,
  nthreads = 1,
  lam.cut = NULL,
  pattern = ".*chr(\\d{1,2})\\.(\\d{1,2})[_\\.].*"
)

LD.path: Path to the .rda file where the Eigen decomposition of LD matrix is stored.
gwas.snps: A vector contains SNP IDs from the GWAS summary statistics.
LD.path.new: The new path to the re-built LD reference.
nthreads: Number of threads to use, default nthreads = 1.
lam.cut: Eigenvalue cutoff for LD matrices, default lam.cut = NULL, which means the same cutoff in the original LD reference panel. For analyses with a limited number of traits and annotations, a lower cutoff (such as 0.1, or even not using a cutoff at all) is recommended. For large-scale analyses, a higher cutoff (such as 1) is recommended, to yield fast computation.
pattern: Chromosome and picece pattern of LD files, default is ".*chr(\d{1,2})\.(\d{1,2})[_\.].*".

The new path to the re-built LD reference.