During runing ChAMP, some users required some extra features like paired calculation, sample matching .e.g. So I wrote some scripts here for users to use, in most case, users just need to source these script, then run them along with normal ChAMP pipeline.
champ.PairedDMP.R: To find paired Differential Methylation Probes in your Beta matrix (M matrix).
champ.PairedDMR.R: Using bumphunter algorithm to get paired DMR result.
MatchSample.R: To help user to find mismatched sample between pd csv file and IDAT folder.