Get LD using snpStats package

Get LD using snpStats package

compute_LD(
  ss,
  select_snps = NULL,
  stats = c("R"),
  symmetric = TRUE,
  depth = "max",
  as_sparse = TRUE,
  verbose = TRUE
)

Arguments

stats	A character vector specifying the linkage disequilibrium measures to be calculated. This should contain one or more of the strings: "LLR", "OR", "Q", "Covar", "D.prime", "R.squared", ad "R"
symmetric	When no y argument is supplied this argument controls the format of the output band matrices. If TRUE, symmetric matrices are returned and, otherwise, an upper triangular matrices are returned
depth	When y is not supplied, this parameter is mandatory and controls the maximum lag between columns of x considered. Thus, LD statistics are calculated between x[,i] and x[,j] only if i and j differ by no more than depth
LD_folder	Locus-specific LD output folder.

Source

snpStats Bioconductor page LD tutorial

See also

Other LD: LD_1KG_download_vcf(), LD_1KG(), LD_custom(), LD_ukbiobank(), filter_LD(), get_locus_vcf_folder(), ldlinkr_ldproxy_batch(), load_or_create(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF(), translate_population()