Question: Creating GRanges object
0
gravatar for lalchungnungabt17
9 weeks ago by
lalchungnungabt170 wrote:

I have a methylation data in GenomicRatioSet (i call it Mset).

  1. I extracted the methylation beta values MB_betas=getBeta(Mset)

  2. Next, i extracted the co-ordinates as you have suggested MB_granges=granges(Mset)

  3. I wanted to assign the meta-column of the GRanges i have obtained in the previous step. mcols(MBgranges)=MBbetas

*Is this the correct to create the GRanges object? I seem to have a strange result, which likely to come from the assigning the meta-data not in the correct order as original and can't figure it out OR is this the correct way of doing it?*

Thank you very much for your help in advance

ADD COMMENTlink written 9 weeks ago by lalchungnungabt170

Why do you want to have a GRanges with the methylation data in the mcols, rather than just using the GenomicRatioSet as intended? Is there something that you plan on doing that cannot be accomplished using the usual minfi pipeline?

ADD REPLYlink written 9 weeks ago by James W. MacDonald49k
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