makePhaseThreeImList {crso}

Make phase 3 im list from phase 2 im list

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)