def row_from_comps(comps, TF, var, N): snp = comps[TF.SNPName] if not snp in var: return None chr = "chr"+comps[TF.SNPChr] pos = comps[TF.SNPChrPos] reference_allele, effect_allele = PB8KFileInfo.alleles(TF, comps) zscore = float(comps[TF.OverallZScore]) se = math.sqrt(float(var[snp])/N) beta = zscore*se OR = str(math.exp(beta)) #check ldpred coord_genotype parse_sum_stats_standard() for what is a1 and a2 p = str(stats.norm.sf(abs(zscore)) * 2) row = (chr, snp, reference_allele, effect_allele, pos, OR, p,) return row
def row_from_comps(gene, comps, TF): snp = comps[TF.SNPName] reference_allele, effect_allele = PB8KFileInfo.alleles(TF, comps) zscore = comps[TF.OverallZScore] row = (snp, gene, zscore, reference_allele, effect_allele,) return row