DNA methylation input

[Akanksha2511]

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]

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.