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Changes to get the ldscore rg option to work on a test data set #7

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Changes to get the ldscore rg option to work on a test data set #7

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3 changes: 2 additions & 1 deletion ldsc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
9 changes: 6 additions & 3 deletions ldscore/sumstats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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.")

Expand Down Expand Up @@ -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:
Expand Down