MACAU Run 1
I ran MACAU to assess the influence of Oly shell length on methylation counts, given relatedness. I used wet weight as a covariate. Check out this jupyter notebook for details.
Results, which are located in the https://github.com/sr320/paper-oly-mbdbs-gen repo, in theanalyses/macau/ subdirectory, is a table with many columns. Thus far I have pulled the p-vlaues out to visualize a quick heatmap. I did this in the 04-raw-count-files.Rmd notebook (probably will move that elsewhere).
The heat map was generated by filtering the raw methylated count data with only loci that MACAU identified as DMLs, witht he very conservative p-value of 0.001. The samples mostly cluster by population, with the exception of samples 12 ans 18 - those are two South Sound samples (#10-18) that cluster with Hood Canal samples (#1-9).