makePhaseThreeImList: Make phase 3 im list from phase 2 im list

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

Description

Make phase 3 im list from phase 2 im list

Usage

makePhaseThreeImList(D, Q, rm.ordered, til.ee, pool.sizes, max.stored,
  max.nrs.borrow, shouldPrint)

Arguments

D	binary matrix of events by samples
Q	penalty matrix of events by samples
rm.ordered	matrix of rules ordered by phase one
til.ee	list of rule set matrices (im list) from phase two
pool.sizes	pool sizes for phase two
max.stored	max number of rule sets saved
max.nrs.borrow	max number of new rule sets per k, default is 10^5
shouldPrint	Print progress updates? Default is TRUE

Value

phase 3 top im list

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(60,10,10),
          max.stored=100,shouldPrint = FALSE)
til.p3 <- makePhaseThreeImList(D,Q,rm.ordered = rm.full,til.ee = til.p2, pool.sizes=c(60,20,20),
         max.stored=100,max.nrs.borrow=100,shouldPrint = TRUE)

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