getCoreRS: Get core rules from phase 3 tpl and til

In crso: Cancer Rule Set Optimization ('crso')

Description

Get core rules from phase 3 tpl and til

Usage

getCoreRS(D, rm, tpl, til, cov.thresh, perf.thresh)

Arguments

D	input matrix D
rm	binary rule matrix
tpl	list of top performances
til	list of top rule set index matrices
cov.thresh	core coverage threshold, defaults is 95
perf.thresh	core performance threshold, default is 90

Examples

library(crso)
data(skcm)
list2env(skcm.list,envir=globalenv())
Q <- log10(P)
rm.full <- buildRuleLibrary(D,rule.thresh = 0.05) # Rule library matrix, dimension: 60 x 71
til.p2 <- makePhaseTwoImList(D,Q,rm.full,k.max = 3,pool.sizes=c(60,20,20),
          max.stored=100,shouldPrint = FALSE)
tpl.p2 <- evaluateListOfIMs(D,Q,rm.full,til.p2)
core.rs <- getCoreRS(D,rm.full,tpl.p2,til.p2) # core.rs should be r1, r2, r3

crso documentation built on July 7, 2019, 5:02 p.m.