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hansenlab / minfi

Devel repository for minfi
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blockFinder #119

Open Zitong-Li opened 6 years ago

Zitong-Li commented 6 years ago

Hello, Kasper:

I was using minfi package and the function blockFinder() with GenomicRatioSet, and the function failed and returns: "need OpenSea types in granges(object)".

I looked in to the code of the blockFinder() function and found in line 16: idx <- which(granges(object)$type == "OpenSea") .

As far as my knowledge, granges() types is a S4 type object now and not supporting "$" operator any more, only with seqnames, ranges, and strand information and the island information is metadata saved in mcols(GenomicRatioObject). I tried to add island information to granges(GenomicRatioObject)$type by hand and it's not working. Could you help me about this？

Thank you very much!

Zitong-Li commented 6 years ago

OK I found the solution myself. I need to add a metadata column of UCSC Island information to the GenomicRatioSet object myself to make the blockFinder function to work.

mcols(object)$type<-getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19,what="Islands.UCSC")[,2]