Entering edit mode
2.1 years ago
Bioinfonext
▴
480
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)
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.
Many thanks
