I want to combine the packages minfi and wateRmelon to analyse my EPIC methylation data. I loaded my data as an RGChannelSetExtended into R with Minfi. Next I wanted to filter out low quality samples and probes with the pfilter function of wateRmelon. Downside: the function returns a Methylset, which I cannot use in the preprocessNoob function of Minfi (it requires a RGChannelSet). In the older versions of watermelon I noticed it was possible to return a RGChannelSetExtended.
Is there anyone who can help me with this problem?