Post by Mema on Mar 6, 2017 18:37:17 GMT
Hello,
Is it MUST to specifying the --prevalence function when we using case-control data (0 and 1) for GWAS analysis (using--mlma or --mlma-loco) , or its just an option?
And what if i don't know the real population prevalence? can i put any random value (0.01 to 0.99) to start the analysis, and what is the best starting prevalence value ?
- Because i tried both ways (adding or not adding --prevalence function) to the analysis and it gave me the same out put :
Chr SNP bp A1 A2 Freq b se p.
So can you also please tell me how can i get an output with log(odds ratio) with its corresponding standard
error, in order to use it for the conditional and joint genome-wide association analysis?
Best regards
Medhat
Is it MUST to specifying the --prevalence function when we using case-control data (0 and 1) for GWAS analysis (using--mlma or --mlma-loco) , or its just an option?
And what if i don't know the real population prevalence? can i put any random value (0.01 to 0.99) to start the analysis, and what is the best starting prevalence value ?
- Because i tried both ways (adding or not adding --prevalence function) to the analysis and it gave me the same out put :
Chr SNP bp A1 A2 Freq b se p.
So can you also please tell me how can i get an output with log(odds ratio) with its corresponding standard
error, in order to use it for the conditional and joint genome-wide association analysis?
Best regards
Medhat