Question: coef in dmrcate
0
gravatar for yoursbassanio
2.0 years ago by
yoursbassanio0 wrote:

Hi All

What should be the coef in cpg.annotate if my intereste is "Condition". In bumphunting the coef is 2 as it calls for the column number of designmatrix. But in dmrcate manual I saw it to be index. So is it that my coef=1?

designMatrix <- model.matrix(~Condition+T1+T2+T3+T4)

 

designMatrix

    (Intercept) Condition T1 T2 T3 T4

1             1       0      8.90                0.87       0.5        1.40

 

Looking forward

MVinu

ADD COMMENTlink modified 2.0 years ago by James W. MacDonald49k • written 2.0 years ago by yoursbassanio0
Answer: coef in dmrcate
1
gravatar for James W. MacDonald
2.0 years ago by
United States
James W. MacDonald49k wrote:

I am not sure what you mean by 'I saw it to be index', but you can be sure that the dmrcate manual doesn't indicate that you should use the intercept column. The coef argument is how you specify which coefficient you are interested in testing, so in your case it would be coef=2.

ADD COMMENTlink written 2.0 years ago by James W. MacDonald49k

Thanks james for the answer. In the dmrcate manual under the cpg.annoate its as follows "coef The column index in design corresponding to the phenotype comparison."

 

 

ADD REPLYlink written 2.0 years ago by yoursbassanio0

Right. I could translate that to be 'the column number of your design matrix that contains the coefficient you care about'. Does that make more sense?

ADD REPLYlink written 2.0 years ago by James W. MacDonald49k
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