Performing Logistic Regression On Plink

Question

[tom.d.brocklehurst]

Using plink, I have been asked to perform logistic regression, calculating 95% confidence intervals, using covariate and identify the value for lambda. The covariate is supplied as a .txt file.

I have read some papers, mainly "Basic statistical analysis in genetic case-control studies” (Clarke et al. 2011, Nature Protocols 6: 121-33),but I am not sure which input to follow.

Thanks

[zx8754]

Is plink manual --logistic not helpful?

[tom.d.brocklehurst]

How will this help me identify the value for lambda?

Answer 1

[zx8754]

In the cited paper, they mention an inflation factor λ, if this is what you after then use --adjust together with --logistic option and it will create a log file with lambda value. Then this value can be used with output modifiers command --lambda.

Note: Add --ci 0.95 option to get 95% confidence intervals.