Filter LD

data("BST1") data("BST1_LD_matrix") LD_list <- list(LD = BST1_LD_matrix, DT = BST1) LD_list <- echoLD:::filter_LD(LD_list, min_r2 = .2)

filter_LD(LD_list, remove_correlates = FALSE, min_r2 = 0, verbose = FALSE)

Arguments

LD_list	List containing SNP-level data (DT), and LD matrix (LD).
remove_correlates	A list of SNPs. If provided, all SNPs that correlates with these SNPs (at r2>=min_r2) will be removed from both DT and LD list items..
min_r2	Correlation threshold for remove_correlates.
verbose	Print messages.

See also

Other LD: LD_1KG_download_vcf(), LD_1KG(), LD_custom(), LD_ukbiobank(), compute_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()