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DegreeAnalysis <-
function(Vertices,Edges,SaveFileName=""){
# Degree Analysis of real vertices
#
# input
# Vertices: vertices for network construction
# Edges: Edges for network construction
# SaveFileName: basic file name for saving figure.
#
# output
# Degrees: Degrees of real vertices
#
# Junliang Shang
# 3.30/2014
#library(igraph)
gdf <- graph.data.frame(Edges,directed=F,Vertices)
gdfDegree <- degree(gdf)
gdfDegree <- gdfDegree[1:length(Vertices[Vertices[,3]=="1",1])]
gdfDegreeName <- names(gdfDegree)
TgdfDegree <- rep(0,length(gdfDegreeName))
for (i in 1:length(gdfDegreeName)){
TgdfDegree[i] <- gdfDegree[[i]]
}
Degrees <- cbind(gdfDegreeName,TgdfDegree)
Degrees <- Degrees[order(as.numeric(Degrees[,2]),decreasing=T),]
colnames(Degrees) <- c("SNP","Degree")
dev.new()
set.seed(8)
hist(gdfDegree,col="gray",border="yellow",xlab="Degree",main=NA)
title(main=list("Histogram of real vertice degree",font=3))
# savePlot(filename=paste(SaveFileName,"_DA",sep=""),type="tiff")
list(Degrees=Degrees)
}
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