Genetic correlation issue
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filippo abbondanza
Sep 6, 2019, 9:28:25 AM9/6/19
to ldsc_users
Hi,
I have done GWASs on handedness and I wanted to compute h2 and the genetic correlation with handedness from the UKBB. When I try to compute rg I got the following error (below). The h2 of my trait is positive (0.0415). I read that someone asked something similar in the group and you pointed to the h2 being negative, which doesn't seem to be the case in here
Thanks in advance!
Filippo
Call:
./ldsc.py \
--ref-ld-chr eur_w_ld_chr/ \
--out pegQ_sex_adj_Right_handedness_UKBB \
--rg pegQ_sex_corrected.sumstats.gz,right_hand_UKBB.sumstats.gz \
--w-ld-chr eur_w_ld_chr/
Beginning analysis at Fri Sep 6 01:03:10 2019
Reading summary statistics from pegQ_sex_corrected.sumstats.gz ...
Read summary statistics for 359485 SNPs.
Reading reference panel LD Score from eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 355178 SNPs remain.
After merging with regression SNP LD, 355178 SNPs remain.
Computing rg for phenotype 2/2
Reading summary statistics from right_hand_UKBB.sumstats.gz ...
Read summary statistics for 1217311 SNPs.
After merging with summary statistics, 355178 SNPs remain.
337916 SNPs with valid alleles.
ERROR computing rg for phenotype 2/2, from file right_hand_UKBB.sumstats.gz.
Traceback (most recent call last):
File "/storage/home/users/fa36/LDSC/ldsc/ldscore/sumstats.py", line 410, in estimate_rg
rghat = _rg(loop, args, log, M_annot, ref_ld_cnames, w_ld_cname, i)
File "/storage/home/users/fa36/LDSC/ldsc/ldscore/sumstats.py", line 539, in _rg
intercept_gencov=intercepts[2], n_blocks=n_blocks, twostep=args.two_step)
File "/storage/home/users/fa36/LDSC/ldsc/ldscore/regressions.py", line 705, in __init__
np.multiply(hsq1.tot_delete_values, hsq2.tot_delete_values))
FloatingPointError: invalid value encountered in sqrt
Summary of Genetic Correlation Results
p1 p2 rg se z p h2_obs h2_obs_se h2_int h2_int_se gcov_int gcov_int_se
pegQ_sex_corrected.sumstats.gz right_hand_UKBB.sumstats.gz NA NA NA NA NA NA NA NA NA NA
Call:
./ldsc.py \
--h2 pegQ_sex_corrected.sumstats.gz \
--ref-ld-chr eur_w_ld_chr/ \
--out pegQ_sex_corrected \
--w-ld-chr eur_w_ld_chr/
Beginning analysis at Wed Sep 4 13:45:42 2019
Reading summary statistics from pegQ_sex_corrected.sumstats.gz ...
Read summary statistics for 359485 SNPs.
Reading reference panel LD Score from eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 355178 SNPs remain.
After merging with regression SNP LD, 355178 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0138 (0.1202)
Lambda GC: 0.9868
Mean Chi^2: 0.9978
Intercept: 0.9962 (0.0102)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Wed Sep 4 13:46:09 2019
Total time elapsed: 26.77s
Call:
./ldsc.py \
--h2 pegQ_sex_corrected.sumstats.gz \
--ref-ld-chr eur_w_ld_chr/ \
--out pegQ_sex_corrected \
--w-ld-chr eur_w_ld_chr/
Beginning analysis at Wed Sep 4 13:45:42 2019
Reading summary statistics from pegQ_sex_corrected.sumstats.gz ...
Read summary statistics for 359485 SNPs.
Reading reference panel LD Score from eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 355178 SNPs remain.
After merging with regression SNP LD, 355178 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0138 (0.1202)
Lambda GC: 0.9868
Mean Chi^2: 0.9978
Intercept: 0.9962 (0.0102)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Wed Sep 4 13:46:09 2019
Total time elapsed: 26.77s
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