How to use methylKit to summarize DNA methylation information over pre-defined regions and then do differential methylation calculation

[liquan kou]

Hi:

    I'm using methylKit to do BS analysis. In the  paper 'methylKit a comprehensive R package for the analysis of genome-wide DNA methylation profiles', in the part“Summarizing DNA methylation information over pre-defined regions or tiling windows” , it shows the use of pre-defined regions and tiling windows.

    Now I can use the tile windows method to conduct fixed bp length analysis. However, I still don't know how to use the pre-defined regions method to verify promoters or CpG islands and then make differential methylation calculation.

    Can you give me some advice or instance on this?

Best Regards!

Kou

[Altuna Akalin]

you need to have the coordinates of the CpG islands or promoters. There are available at UCSC genome browser for example. There might be also annotation packages in BioC that could have those coordinates. If you have a GRanges object that has the coordinates of CpGs or promoters you can use regionCounts() function, please see examples there

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