Open drsora opened 1 month ago
I ran this in my other cohort and get a different error message:
make manhattan and qq plots Reading in /data/sonja/godmc/luric/results/03/positive_control_untransformed_cg07959070.PHENO1.glm.linear.gz GWAS results Error in main() : Wrong column specified for p-values Execution halted
Hi @drsora ,
I’m just back from holiday, so apologies for the slight delay.
Regarding the first error, it seems that the lowest p-value(0.00127855) within the control window is greater than the positive_control_threshold (0.001). The positive_control_threshold can be set in the parameter file depend on the sample size of your cohort. In addition, the Chromosome column may contain characters other than numbers from 1 to 23.
The second error suggests that the P-value is outside the expected range of (0,1).
Would you mind checking the columns of the /data/sonja/godmc/luric/results/03/positive_control_untransformed_cg07959070.PHENO1.glm.linear.gz file
from your two corhorts?
Is column 12 the P-value column? If the P-value is out of the range (0, 1), this could be causing the error. Is column 1 the Chromosome column, and does it only contain values from 1-23? Is column 2 the Position column? Is column 3 the SNP column?
Thanks
Contact Details
sonja.rajic@tuni.fi
Scripts
03g-perform_positive_control.sh
What happened?
03g doesn't run fully, output is below I can't upload 03g because some files are missing, I uploaded a-d
How can the bug be reproduced?
No response
R version
4.4.0 (April, 2024)
Python version
None
Relevant log output