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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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How to obtained control and treatment %values instead of the diffmeth % value #249

Closed iramai closed 2 years ago

iramai commented 2 years ago

Hi! I have some doubts when visualizing the obtained results. I am interested in producing a file with raw % values of each sample, as a previous outcome of the diffmeth option (where the methylation difference %value is produced). I thought I could obtained this values from the methylbase outcome with the coverage values but I do not find the way to convert that coverage values for each sample to methylation % values. I do not know if I'm explaining myself well but I will appreciate some kind of feedback in this issue. Thanks in advance, Iraia

alexg9010 commented 2 years ago

Hi @iramai ,

you may check out the percMethylation() function, which gets the percent methylation scores from a methylBase or methylBaseDB object and returns a matrix with percent methylation values per base/region across all samples.

Best Alex

iramai commented 2 years ago

Thank you very much for the aclaration. It works in the same way for the scores from tiled methylBase? Thanks again

alexg9010 commented 2 years ago

Hi @iramai, yes it should summarize the regions that you provide, independent of being base/region/tile.

iramai commented 2 years ago

Ok! Thank!!! I will try both options!