diff --git a/ldsc.py b/ldsc.py index 6801dbde..5c2aafac 100755 --- a/ldsc.py +++ b/ldsc.py @@ -842,7 +842,8 @@ def ldscore(args, log): raise ValueError("Must set either --frqfile and --ref-ld or --frqfile-chr and --ref-ld-chr") if args.rg: - sumstats.estimate_rg(args, log) + sumstats.estimate_genetic_correlation(args, log) + # sumstats.estimate_rg(args, log) elif args.h2: sumstats.estimate_h2(args, log) elif args.h2_cts: diff --git a/ldscore/sumstats.py b/ldscore/sumstats.py index b101cac4..03c07c7d 100644 --- a/ldscore/sumstats.py +++ b/ldscore/sumstats.py @@ -162,7 +162,8 @@ def read_reference_ld_scores(args: Any, logger: Any) -> pd.DataFrame: elif args.ref_ld_chr: pattern = ps.sub_chr(args.ref_ld_chr, "[1-22]") logger.log(f"Reading reference panel LD Scores from {pattern} ...") - ref_ld = ps.ldscore_fromlist(split_paths(args.ref_ld_chr)) + ref_ld = ps.ldscore_fromlist(split_paths(args.ref_ld_chr), num=NUM_CHROMOSOMES) + # ref_ld = ps.ldscore_fromlist(split_paths(args.ref_ld_chr)) else: raise ValueError("No reference LD Scores provided.") except Exception as e: @@ -225,7 +226,8 @@ def read_m(args: Any, logger: Any, num_annotations: int) -> np.ndarray: if args.ref_ld: m_annot_list = ps.M_fromlist(split_paths(args.ref_ld), common=(not args.not_M_5_50)) elif args.ref_ld_chr: - m_annot_list = ps.M_fromlist(split_paths(args.ref_ld_chr), common=(not args.not_M_5_50)) + m_annot_list = ps.M_fromlist(split_paths(args.ref_ld_chr), num=NUM_CHROMOSOMES, common=(not args.not_M_5_50)) + # m_annot_list = ps.M_fromlist(split_paths(args.ref_ld_chr), common=(not args.not_M_5_50)) else: raise ValueError("No reference LD Scores provided for M.") @@ -260,7 +262,8 @@ def read_regression_weight_ld_scores(args: Any, logger: Any) -> pd.DataFrame: elif args.w_ld_chr: pattern = ps.sub_chr(args.w_ld_chr, "[1-22]") logger.log(f"Reading regression weight LD Scores from {pattern} ...") - w_ld = ps.ldscore_fromlist(split_paths(args.w_ld_chr)) + w_ld = ps.ldscore_fromlist(split_paths(args.w_ld_chr), num = NUM_CHROMOSOMES) + # w_ld = ps.ldscore_fromlist(split_paths(args.w_ld_chr)) else: raise ValueError("No regression weight LD Scores provided.") except Exception as e: