Mset out of unmethylated and methylated signals (minfi)

Question

[daria.kostiniuk]

Hey, I am trying to figure out raw GEO data GSE152026. Well apparently it is not completely raw and is available in form of csv file which contains methylated and unmethylated signals, as well as detection p values. I would like to construct rgset or mset to proceed with qs, filtering the probes of interest and normalization. The problem is that I can't find a way to convert the signals into minfi objects, and the documentation always starts with idat files. How could I possibly construct minfi objects with methylated/unmethylated signal data? Thank you!

[Basti]

I do not have time to test because the file is very big but you can convert the data.frame of signals into a MethylSet :

rgSet=read.table(your_df)
mSet=MethylSet(Meth = dplyr::select(rgSet,ends_with("Methylated.signal",ignore.case = FALSE))%>% 
                 rename_with(~ str_remove(., ".Methylated.signal"), everything()), Unmeth = dplyr::select(rgSet,ends_with("Unmethylated.Signal",ignore.case = FALSE))%>% 
                 rename_with(~ str_remove(., ".Unmethylated.Signal"), everything()))
##your rgSet may contain different colnames
mSet@annotation=c(array = "IlluminaHumanMethylationEPIC", annotation = "ilm10b2.hg19") #adapt annotation file
featureNames(mSet)= ... #adapt feature names (EPIC probes)