aneuploidyVariabilityTest

Create a test to see if chromosome 18 is duplicated or removed more often than other chromosomes.

To do (3/18/2018)

1. Change resampling method to bootstrap

   • take N samples with replacement, where N is the the number of cells.
   • 1000 bootstraps

2. Compare bootstrap distribution between each pair of chromosomes

   • Wilcoxon or t-test to assess for similarity in variability between pairs of chromosomes
   • Possibly KS test as well
   • Generate heatmap with p-values (23x23 matrix)

3. Linear regression - identify features that predict chromosome variability

   • Do this by chromosome and by bin
   • Example features include # of genes, size of chromosome/segment, # of TFs in segment, gene density, open chromatin regions
   • Y is the observed frequency, Xs are the observed features

4. Visualization of p-values - use all pairwise comparisons. Plot the number of significantly different chromosomes on the x axis.

5. Network - assess similarity between pairwise comparisons.

6. Use association rules to determine multiple regions that are co-deleted or co-amplified

   • See "mining of massive datasets," Chapter 6.1

Brainstorming on 3/18/2018: