condorcetRanking: Aggregate gene ranking over all patients

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

Description

/codecondorcetRanking Returns aggregate gene list over all patients.

Usage

condorcetRanking(scoreMatrix, mutationMatrix, pen = 0.85, parallel = NULL,
  par = T, dovec = T)

Arguments

mutationMatrix	the mutation matrix. Rows are genes, columns are patients
pen	the penality parameter in the condorcet algorithm for missing data. Default 0.85
scoreMatrixa	matrix containing all the given DawnRank scores per patient. Rows are genes, columns are patients

Value

the ranks. A list of 2 including a [[1]] a matrix of all pairwise comparisons, [[2]] the final rankings based on the Condorcet score

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)
significance<-patspeccutoff(patient="TCGA-A2-A04P",ms=dawnRankFrame,
default=95)

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