getCoreK: Determine core K from phase 3 tpl and til

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

Description

Determine core K from phase 3 tpl and til

Usage

getCoreK(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.K <- getCoreK(D,rm.full,tpl.p2,til.p2)
# core.K should be 3 almost always for this example, can run a few time to confirm

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