DawnNormalize: DawnNormalize

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

Description

DawnNormalize takes a tumor and normal expression matrix and returns a standardized absolute differential expression matrix

Usage

DawnNormalize(tumorMat, normalMat)

Arguments

tumorMat,	a matrix representing the tumor expression
normalMat,	a matrix representing the normal expression

Value

the differential expression matrix, it is absolute standarized matrix

Examples

###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

MartinFXP/DawnRank documentation built on Sept. 10, 2021, 11:25 p.m.