filter_LD: Filter LD

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

Filter LD

Description

Filter LD

Usage

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

Arguments

LD_list	List containing SNP-level data (dat), 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 dat and LD list items..
min_r2	Correlation threshold for remove_correlates.
verbose	Print messages.

See Also

Other LD: check_population_1kg(), compute_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()

Examples

LD_list <- list(LD = echodata::BST1_LD_matrix,
                DT = echodata::BST1)
LD_list2 <- echoLD::filter_LD(LD_list = LD_list, min_r2 = .2)

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