Question: Performing Logistic Regression On Plink
0
gravatar for tom.d.brocklehurst
5.3 years ago by
United Kingdom
tom.d.brocklehurst0 wrote:

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

plink • 2.7k views
ADD COMMENTlink modified 5.3 years ago by zx87547.5k • written 5.3 years ago by tom.d.brocklehurst0
1

Is plink manual --logistic not helpful?

ADD REPLYlink written 5.3 years ago by zx87547.5k

How will this help me identify the value for lambda?

ADD REPLYlink written 5.3 years ago by tom.d.brocklehurst0
1
gravatar for zx8754
5.3 years ago by
zx87547.5k
London
zx87547.5k wrote:

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.

ADD COMMENTlink written 5.3 years ago by zx87547.5k
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