I'd like to perform some nice visualization of my methylation data - Illumina EPIC array. I analyze my data using minfi package, so at the end I have GenomicRatioSet, MethylSet and other.
The problem is MethyGenoSet object which ios hard to obtain... Of course there is an easy way, jus analyze your data with methylumi then convert your normalized set to get MethyGenoSet object. Unfortunately methylumi package doesn't support EPIC array - so far. What is more, some errors occured with normalization using this package... Then I decided to stay with minfi which works nice.
So what I did so far:
gmset <- preprocessIllumina(RGSet, bg.correct = TRUE, normalize = "controls") #normalization with illumina function (methyl set as output) gmset <- mapToGenome(gmset) #(genomic methylset) yyy <- MethyGenoSet(rowRanges(gmset), getBeta(gmset), getMeth(gmset), getUnmeth(gmset)) #attempt to create this object Error in `rownames<-`(`*tmp*`, value = .get_colnames_from_assays(assays)) : invalid rownames length
I'll be grateful fo arny suggestions how to solve this issue.