compute_LD: Get LD using 'snpStats' package

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Get LD using snpStats package

Description

Get LD using snpStats package

Usage

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: check_population_1kg(), filter_LD(), get_LD(), get_LD_1KG(), get_LD_1KG_download_vcf(), get_LD_UKB(), get_LD_matrix(), get_LD_vcf(), get_locus_vcf_folder(), ldlinkr_ldproxy_batch(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF()

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.