Cancer Rule Set Optimization ('crso')

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Documentation for package ‘crso’ version 0.1.1

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buildRuleLibrary Make full rule library of all rules that satisfy minimum coverage threshold.
evaluateListOfIMs Evaluate list of rule set matrices
getBestRsList Get list of best rule sets of size K for all K
getCoreK Determine core K from phase 3 tpl and til
getCoreRS Get core rules from phase 3 tpl and til
getGCDs Get Generalized Core Duos
getGCEs Get Generalized Core Events
getGCRs Get Generalized Core Rules
getPoolSizes Get pool sizes for phase 2
getRulesAsStrings Represent binary rule matrix as strings
makeFilteredImList Make filtered im list from phase 3 im list
makePhaseOneOrderedRM Order rules according to phase one importance ranking
makePhaseThreeImList Make phase 3 im list from phase 2 im list
makePhaseTwoImList Output list of top rule sets for each k in 1:k.max
makeSubCoreList Get list of core rules from random subsets of samples
skcm.list Example data set derived from TCGA skin cutaneous melanoma (SKCM) data.