DawnRank-package: DawnRank
In MartinFXP/DawnRank: What the package does (short line)

DawnRank calculates the pathway impact a mutated gene has on a individual patient using a PageRank inspired algorithm. Mutations in genes with greater pathway impact are likely to be driver genes in cancer. DawnRank can calculate individual pathway impacts and predict drivers from groups of patients

Package:	DawnRank
Type:	Package
Version:	1.1
Date:	2013-10-15
License:	GPL

Jack Hou <jackhou2@illinois.edu> Maintainer: Martin Pirkl <martin.pirkl@bsse.ethz.ch>

###using a small subset of the TCGA dataset and a small KEGG gene interaction network,
###We will show how to get DawnRank Results

library(DawnRank)

#load the mutation data
data(brcaExampleMutation)

#load the tumor expression data
data(brcaExampleTumorExpression)

#load the normal expression data
data(brcaExampleNormalExpression)

#load the pathway data
data(brcaExamplePathway)

#load the gold standard
data(goldStandard)

#normalize the tumor and normal data to get the differential expression
normalizedDawn<-DawnNormalize(tumorMat=brcaExampleTumorExpression,normalMat=brcaExampleNormalExpression)

#get the DawnRank Score
dawnRankScore<-DawnRank(adjMatrix=brcaExamplePathway,mutationMatrix=brcaExampleMutation,expressionMatrix=normalizedDawn, mu=3,goldStandard=goldStandard)

#look at the DawnRank scores for a few patients
dawnRankFrame<-dawnRankScore[[3]]
head(dawnRankFrame)

#get the aggregate DawnRank scores
aggregateDawnRankScore<-condorcetRanking(scoreMatrix=dawnRankScore[[2]],mutationMatrix=brcaExampleMutation)

#look at top 10 ranked genes
top10<-aggregateDawnRankScore[[2]][1:10]
top10

#get the individual cutoff for patient TCGA-A2-A04P
dawnRankFrame$isCGC<-dawnRankFrame$isGoldStandard
library(maxstat)
patspeccutoff(patient="TCGA-A2-A04P",ms=dawnRankFrame,default=95)->significance