def get_r_human_readable(pop: str, var1: str, var2: str, ref_genome: str = "GRCh37"): bm = ld_matrix(pop).bm() ht = ld_index(pop).ht() chrom, pos, ref, alt = var1.split("-") var1 = (hl.parse_locus(f"{chrom}:{pos}", ref_genome), [ref, alt]) chrom, pos, ref, alt = var2.split("-") var2 = (hl.parse_locus(f"{chrom}:{pos}", ref_genome), [ref, alt]) return get_r_for_pair_of_variants(bm, ht, var1, var2)
def get_r_within_gene_in_pop(pop: str, gene: str): """ Gets LD information (`r`) for all pairs of variants within `gene` for a given `pop`. Warning: this returns a table quadratic in number of variants. Exercise caution with large genes. :param pop: Population for which to get LD information :param gene: Gene symbol as string :return: Table with pairs of variants """ return get_r_within_gene( ld_matrix(pop).bm(), ld_index(pop).ht(), gene, None, 'GRCh37')