makePhaseThreeImList {crso} | R Documentation |
Make phase 3 im list from phase 2 im list
makePhaseThreeImList(D, Q, rm.ordered, til.ee, pool.sizes, max.stored, max.nrs.borrow, shouldPrint)
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 |
phase 3 top im list
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)