I am still a little unclear about what is left to do in the project.

• It looks like we have some MARIO results to look at
• Phenotype RELI analysis (still in discovery phase?)
• Should I aggregate ancestry or not?
• What about aggregating by cell type?

Outstanding things

TODO Figure 3A

• Make version with the consistent order as an alternative (HOMER)

Figure 4

• Median can be used to aggregate cell type in the phenotype heatmap
• Need Direction from Matt and Leah

Figure 5

• Mario Plots
• Need Direction from Matt and Leah

Figure 6

• Highlight SNPs associated with SLE allelic in MARIO
• SNPmoods finds SNPs that breaks a motif