DawnRank: DawnRank

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

Description

This is the main method of the DawnRank method. DawnRank calculates the importance of a gene in a pathway through its connectivity to downstream genes and the differential expression of the downstream genes.

Usage

  DawnRank(adjMatrix, expressionMatrix, mutationMatrix,
    mu = 20, maxit = 100, epsilon = 1e-04,
    goldStandard = NULL)

Arguments

adjMatrix,	the adjacency matrix
expressionMatrix,	the normalized expression matrix (multiple patients)
mutationMatrix,	a logical matrix containing mutation information
mu,	the proposed free parameter
maxit,	the maximum number of iterations to use, default 100
epsilon,	the lower magnitude cutoff, default 0.0001
goldStandard,	A list of common driver genes, used as a comparison. This is optional, default=NULL

Value

the ranks. A list of 3 including a [[1]] output of all the ranks, [[2]] output of all the ranks (percentile), [[3]] mutated ranks, [[4]] the steps of convergence

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.