Investigate why heatmaps don't provide confidence in DML identification

[yaaminiv]

I remade some heatmaps with DML identified from methyKit in this script. The resultant heatmaps don't give me confidence in the DML identified:

ploidy-DML heatmap:

pH-DML heatmap:

@sr320 do you mind visualizing the DML with IGV? Based on that, I want to see if it's worth rerunning methylKIt but without covariates. Right now, ploidy-DML were identified using pH data as a covariate, and pH-DML were identified using ploidy data as a covariate.

ploidy-DML list: https://github.com/RobertsLab/project-oyster-oa/blob/master/analyses/Haws_07-DML-characterization/DML-ploidy-25-Cov5-NO-SNPs.bed
pH-DML: https://github.com/RobertsLab/project-oyster-oa/blob/master/analyses/Haws_07-DML-characterization/DML-pH-25-Cov5-NO-SNPs.bed
Previous DML IGV: https://github.com/RobertsLab/project-oyster-oa/blob/master/analyses/Haws_07-DML-characterization/dml.xml