Description Usage Arguments Value Examples
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.
1 2 3 | DawnRank(adjMatrix, expressionMatrix, mutationMatrix,
mu = 20, maxit = 100, epsilon = 1e-04,
goldStandard = NULL)
|
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 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | ###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)
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