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