makePhaseOneOrderedRM: Order rules according to phase one importance ranking

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

Description

Order rules according to phase one importance ranking

Usage

makePhaseOneOrderedRM(D, rm.start, spr, Q, trn, n.splits, shouldPrint)

Arguments

D	Binary matrix of N events and M samples
rm.start	Starting binary rule matrix (i.e., rule library)
spr	Random rule sets per rule in each phase one iteration. Default is 40.
Q	Penalty matrix, negative log of passenger probability matrix.
trn	Target rule number for stopping iterating. Default is 16.
n.splits	number of splits for parallelization. Default is all available cpus.
shouldPrint	Print progress updates? Default is TRUE

Value

binary rule matrix ordered by phase one importance ranking

Examples

data(skcm)
list2env(skcm.list,envir=globalenv())
Q <- log10(P)
rm.full <- buildRuleLibrary(D,rule.thresh = 0.06) # Rule library matrix, dimension: 36s x 71
rm.ordered <- makePhaseOneOrderedRM(D,rm.full,spr = 1,Q,trn = 34,shouldPrint = TRUE)
# note, for real applications, spr should be at least 40.

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