install.packages("devtools")
library(devtools)
install_github("weitinging/MinNetRank")
install.packages("MinNetRank")
library(MinNetRank)
library(MinNetRank)
#load the adjacency network
data("AdjacencyMatrix")
#load the known cancer genes
data("KnownGenes")
#load the mutation data
data("LihcMutation")
#load the tumor expression data
data("LihcTumorExpression")
#load the normal expression data
data("LihcNormalExpression")
#Using AdjacencyMatrix
##Using the mutation and expression data
Network = "AdjacencyMatrix"
LihcMinNetRank = MinNetRank(Network, SNP=LihcMutation, TumorExpression=LihcTumorExpression, NormalExpression=LihcNormalExpression, CGC=KnownGenes, beta = 0.4841825)
write.table(LihcMinNetRank, file='TCGA-LIHC.MinNetRank.Result.xls', quote =F, sep="\t", row.names = FALSE)
##Using the mutation data
Network = "AdjacencyMatrix"
LihcMinNetRankMutation = MinNetRank(Network, SNP=LihcMutation, CGC=KnownGenes, beta = 0.4841825)
write.table(LihcMinNetRankMutation, file='TCGA-LIHC.MinNetRank.Mutation.xls', quote =F, sep="\t", row.names = FALSE)
##Using the expression data
Network = "AdjacencyMatrix"
LihcMinNetRankExp = MinNetRank(Network, TumorExpression=LihcTumorExpression, NormalExpression=LihcNormalExpression, CGC=KnownGenes, beta = 0.4841825)
write.table(LihcMinNetRankExp, file='TCGA-LIHC.MinNetRank.Expression.xls', quote =F, sep="\t", row.names = FALSE)
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