Error regarding userGWAS function
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Lucy Kim
Jul 11, 2024, 11:28:29 PM (6 days ago) Jul 11
to Genomic SEM Users
Hi all,
I ran into problem using userGWAS function. And I'm getting the error regarding infinite or missing valuses in 'x'.
After getting this error, I tried to find any zero value or NA in summary statistics, but could not find any.
There were 25 warnings (use warnings() to see them)
[1] "Please note that an update was made to userGWAS on Sept 1 2023 so that the default behavior is to fix the measurement model using the fix_measurement argument."
[1] "Starting GWAS Estimation"
Error in .userGWAS_main(i, int, n_phenotypes, n, I_LD, V_LD, S_LD, std.lv, :
task 39 failed - "infinite or missing values in 'x'"
Calls: userGWAS -> %dopar% -> <Anonymous>
Execution halted
Should I filter out SNPS with having P-values with zero in the analysis?
Or is there any solution to this?
I ran into problem using userGWAS function. And I'm getting the error regarding infinite or missing valuses in 'x'.
After getting this error, I tried to find any zero value or NA in summary statistics, but could not find any.
There were 25 warnings (use warnings() to see them)
[1] "Please note that an update was made to userGWAS on Sept 1 2023 so that the default behavior is to fix the measurement model using the fix_measurement argument."
[1] "Starting GWAS Estimation"
Error in .userGWAS_main(i, int, n_phenotypes, n, I_LD, V_LD, S_LD, std.lv, :
task 39 failed - "infinite or missing values in 'x'"
Calls: userGWAS -> %dopar% -> <Anonymous>
Execution halted
Should I filter out SNPS with having P-values with zero in the analysis?
Or is there any solution to this?
Best,
Lucy
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