I am using ChAMP to process EPIC methylation array data. While delving into the source code for
champ.DMR for another reason, I noticed that it defined the linear model used in the DMRcate method as
~ pheno. Further delving revealed that
DMRcate::cpg.annotate, which itself requires a model with an intercept (e.g. it is has this in the function
stopifnot(colnames(design) == "(Intercept)")).
Is there any way to circumvent this and input a model into
DMRcate (and thus, into
champ.DMR) that has no intercept, as in
0 + pheno? This is necessary as other methods (like
champ.DMP) already use a no intercept model.