Question

coef in dmrcate

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yoursbassanio ▴ 10

@yoursbassanio-12717

Last seen 3.6 years ago

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

dmrcate bumphunter methylation epic • 1.5k views

ADD COMMENT • link updated 7.0 years ago by James W. MacDonald 65k • written 7.0 years ago by yoursbassanio ▴ 10

score 1 · Answer 1 · 2017-04-18

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 hour ago

United States

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 COMMENT • link 7.0 years ago James W. MacDonald 65k

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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 REPLY • link 7.0 years ago yoursbassanio ▴ 10

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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 REPLY • link 7.0 years ago James W. MacDonald 65k