Plot a subset of the LD matrix

Uses gaston to plot a SNP-annotated LD matrix.

plot_LD(LD_matrix, dat, span = 10, method = c("gaston", "heatmap", "image"))

Arguments

span	This is very computationally intensive, so you need to limit the number of SNPs with span. If span=10, only 10 SNPs upstream and 10 SNPs downstream of the lead SNP will be plotted.

See also

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

Examples

if (FALSE) {
data("BST1")
data("BST1_LD")
plot_LD(LD_matrix = LD_matrix, dat = BST1)
}