To keep the model of minimum p-value from the file
Hello
My file lists a millions of SNPs with their p-values by additive, dominant, and recessive models. I want to keep the SNPs with a model for which the p-value is the lowest.
Original file.txt
ID,y,z,P-value
rs1,a,b,0.22
rs1,a,b,0.35
rs1,a,b,0.45
rs2,c,d,0.06
rs2,c,d,0.20
rs2,c,d,0.46
rs3,e,f,0.002
rs3,e,f,0.98
rs3,e,f,1.0
The file.txt that I want is...
ID,y,z,P-value
rs1,a,b,0.22
rs2,c,d,0.06
rs3,e,f,0.002
How to do this? Thanks!
1 answer
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This type of questions are more suitable for StackOverflow, see:
since the property of p-value is uniformness under the null hypothesis and it will be totally broken by chosin the min from 3 models, I worn you not to do so - you won't have any basis to do the further analysis after such selection
Thank you for your comment. I just wanted to draw a manhattan plot based on this. But I think I should just show three manhattan plots, based on the model.
Yeap, Manhattan plot would not make any sense if you choose the min =/ 3 plots sounds good!