DNA methylation input - Githubissues

fraenkel-lab / OmicsIntegrator

This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.

http://fraenkel.mit.edu/omicsintegrator

BSD 2-Clause "Simplified" License

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DNA methylation input #34

Open Akanksha2511 opened 5 years ago

Akanksha2511 commented 5 years ago

Hi,

Can we use differential methylated region file (attached) as input for omicsintegrator ? I gave it a try but its writing one chromosome several times in the events_to_genes file (attached). Is this because I am using DMR file instead of peak file ?
events_to_genes.txt

DMRs.txt

Can you please help me with this? thanks

sgosline commented 5 years ago

Hi there. There are two issues with using methylation data: 1- Methylation corresponds only with repression of neighboring genes, and Garnet makes the assumption in the regression that genes can be activated or repressed. Though I suppose this could be ok. 2- Your file differs from a standard BED file in that it doesn't have any quantifiable measure of activity in column 4, which we use later in the regression.