makeFilteredImList: Make filtered im list from phase 3 im list

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

Description

Make filtered im list from phase 3 im list

Usage

makeFilteredImList(D, Q, rm, til, filter.thresh)

Arguments

D	binary matrix of events by samples
Q	penalty matrix of events by samples
rm	matrix of rules ordered by phase one
til	im list from phase 3
filter.thresh	minimum percentage of samples assigned to each rule in rs

Value

filtered 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(60,20,20),max.stored=100,shouldPrint = FALSE)
filtered.im.list <- makeFilteredImList(D,Q,rm.full,til.p2,filter.thresh = 0.05)

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