--- a +++ b/TODOs.txt @@ -0,0 +1,25 @@ +TODOs: + +* To find interesting pairs of genes: + - Look for anti-correlated features used in a model + - Look for features that appear together in trees more than expected. +* test usage of laplace loss function +* define function to annotate model features (currently done as part of plotting) +* switch to CV using OOB of multiple bootstrapped samples? (however CV is easier than BS to understand) +* cluster features +* add text describibg model parameters (n.trees, int.depth, shrinkage) +* generate table with all value presented in graph + +- add training model AUC p-val +- print training model p-val in plot +- predict all CCLE lines +- add lineage barplot in plots +- plot pred features of the same gene of the target feature. +- look for features who don't correlate well with target overall across all models (so should have low Pearson correlation but high relative importance) +- test whether better to color all bars in barplots (by value) + + + +CCLE fixes needed: +- names for Expr$cls +- all mutation features are available for the same number of lines (no?)