DMRcate design
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Jitendra ▴ 10
@nabiyogesh-11718
Last seen 1 day ago
United Kingdom

Hi all,

I am trying to use DMRcate first time for epic array data.

I have done the limma association analysis using below model design but not sure how to design model metrix for DMRcate for same type of BMI and CpG sites association analysis; Could you help me if below DMRcate design correct or wrong?

Limma linear regression;

#model matrix

    var<-model.matrix(~BMI + as.factor(Gender) + Age +CD8T +CD4T +NK + Bcell +Mono ,data=targets2)

    fit<-lmFit(mval,var)


    fit2<-eBayes(fit,trend=TRUE, robust=TRUE)

    probe<-topTable(fit2,adjust="BH",coef=2,num=Inf)

DMRcate analysis;

library(DMRcate)
myMs <- logit2(myBetas)

myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)

design <- model.matrix(~BMI + as.factor(Gender) + Age +CD8T +CD4T +NK + Bcell +Mono ,data=targets2)

myannotation <- cpg.annotate(myMs.noSNPs, analysis.type="differential",design=design, coef=2)

Many thanks,

Epigenetics EpigeneticsWorkflow DMRcate • 682 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

The help page for cpg.annotate says this:

design: Study design matrix. Identical context to differential
          analysis pipeline in 'limma'. Must have an intercept if
          'contrasts=FALSE'.  Applies only when 'analysis.type %in%
          c("differential", "ANOVA", "diffVar")'.
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Entering edit mode

Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?

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That's what identical context means.

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Thanks, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANOVA", /"diffVar"" as we are looking for BMI associated CpG regions methylation patterns. Could anyone please help with this.

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