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Heritability Estimation Error!! #464

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Taylor19973 opened this issue Nov 14, 2024 · 0 comments
Open

Heritability Estimation Error!! #464

Taylor19973 opened this issue Nov 14, 2024 · 0 comments

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@Taylor19973
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Taylor19973 commented Nov 14, 2024

I have this problem, but the N and Z columns are both numeric and it still doesn't work. Is this problem occurring on my end (as in error in the data input) or on the package's end? Please kindly advise! Thank you very much!

str(dt1)
$ SNP: chr "rs3790767" "rs867355" "rs3790762" "rs10799805" ...
$ A1 : chr "A" "A" "G" "C" ...
$ A2 : chr "C" "G" "A" "T" ...
$ N : num 256498 256498 256498 256498 256498 ...
$ Z : num 6.03 6.04 6.05 6.04 6.01 ...

  • attr(*, ".internal.selfref")=

h2_res_dt1 <- ldsc_h2(munged_sumstats = dt1, ancestry = "EUR")
✔ Using EUR reference from Pan-UKB [277ms]
✔ Reading LD Scores [1.2s]
✔ Reading weights [997ms]
✔ Reading M [274ms]
✔ Reading summary statistics from dataframe [90ms]
✔ Reading summary statistics [437ms]
ℹ 308/4685 SNPs remain after merging with LD-score files
ℹ Removed 5 SNPs with Chi^2 > 256.498; 303 SNPs remain
✔ Merging summary statistics with LD-score files [5s]
Error in t(weighted.LD[select.from[i]:select.to[i], ]) %*% weighted.chi[select.from[i]:select.to[i], :
Non-integer argument
✖ Estimating heritability [295ms]

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