prepare: Prepare CpG sites and expression for modeling
In iloveless1/methylXprs: Associates DNA Methylation with Matched gene Expression

Prepare CpG sites and expression for modeling

prepare(
  Counts = Counts,
  Methy = Methy,
  Methylation.Annotation = Methylation.Annotation,
  annotated_RNA = annotated_RNA,
  idx = idx,
  dist
)

`Counts`	A matrix of RNA counts
`Methy`	A matrix of Methylation M-values
`Methylation.Annotation`	A GRanges object containing CpG site locations. must have same order as `Methy`
`annotated_RNA`	A GRanges object containing RNA annotation. Must have same order as `Counts`