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rg values not in the [-1,1] bound&NAN Values #472

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AyselenKuru opened this issue Jan 13, 2025 · 1 comment
Open

rg values not in the [-1,1] bound&NAN Values #472

AyselenKuru opened this issue Jan 13, 2025 · 1 comment

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@AyselenKuru
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AyselenKuru commented Jan 13, 2025

This was already discussed in Issue #89, but in that case, the SE values were high. What happens if the SE values are within normal parameters( this case has high SE but I am asking in general)? I double-checked my GWAS data, and it is corrected, so that might be causing the problem. Is there any way to resolve this issue?

On a related note, I am also encountering NaN values in my analysis. The sample size is not small, but the heritability of PD.sumstatz is extremely low. Below, I will provide the rg and h2 results.

I am working on this as part of a college project, and unfortunately, I work alone and no one to ask about thisin project. Any help would be greatly appreciated.
p1 p2 rg se z p h2_obs h2_obs_se h2_int h2_int_se gcov_int gcov_int_se

PD.sumstats.gz ALS_80610.sumstats.gz NA NA NA NA 0.08834 0.04898 1.008 0.06257 0.05391 0.04835
PD.sumstats.gz LBD_6618.sumstats.gz NA NA NA NA -1.169 0.495 1.176 0.0625 0.007518 0.03848
PD.sumstats.gz ALS.sumstats.gz NA NA NA NA 0.1065 0.1195 1.004 0.06415 0.02845 0.04698
PD.sumstats.gz MS.sumstats.gz NA NA NA NA -0.1977 0.1847 1.102 0.08088 -0.08452 0.04831
PD.sumstats.gz MS2.sumstats.gz NA NA NA NA -0.1435 0.1991 1.061 0.05696 0.09332 0.04602

Total Observed scale h2: -2.5984 (1.1618)
Lambda GC: 0.9547
Mean Chi^2: 0.9495
Intercept: 1.0838 (0.0604)
Ratio: NA (mean chi^2 < 1)

Thanks in advance,
Ice

@aksarkar
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@AyselenKuru If your PD GWAS includes proxy cases, you will get downwards biased estimates of heritability. Refer to https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010208

You will need to obtain PD GWAS without proxy cases to get reasonable estimates.

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