Calculate total per-sample percentage methylated after filtering

[Juan Pablo Aguilar Cabezas]

Hi,

I would like to calculate total per-sample percentages.

I have methylKit files created by methyldackel, I created the methylRawList object, then I filtered it by minimum coverage and hi.perc.

I plan to merge all the samples with unite, and then I was told to calculate total methylation percentages per sample by doing the sum(methylated)/ sum(methylated + unmethylated sites).

Can It get/export those values, methylated and unmethylated counts, to calculate the total per-sample methylation?

Thanks;

[Altuna Akalin]

yes, that shouldn't be a problem. You can use percMethylation or equivalent process to calculate percent methylation after unite()

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