Nothing

```
################################################################
# function:
# aveNumEdges takes one parameter:
# objgraph is the graph object
# aveNumEdges counts the number of edges in the graph and divides
# that by the number of nodes in the graph to give the
# average number of edges. A double representing the average
# number of edges will be returned.
#
# created by: Elizabeth Whalen
# last updated: July 22, 2002
################################################################
aveNumEdges<-function(objgraph)
numEdges(objgraph)/length(nodes(objgraph))
################################################################
# function:
# calcProb takes two parameters:
# origgraph is the original graph from which the subgraph was made
# subgraph is the subgraph made from the original graph
# calcProb calculates the probability of having the number of edges
# found in the subgraph given that it was made from origgraph.
# The hypergeometric distribution is used to calculate the
# probability (using the pdf).
#
# created by: Elizabeth Whalen
# last updated: July 22, 2002
################################################################
calcProb <- function(subgraph, origgraph)
{
origNumNodes<-length(nodes(origgraph))
subNumNodes<-length(nodes(subgraph))
origNumEdges<-numEdges(origgraph)
subNumEdges<-numEdges(subgraph)
dyads <- (origNumNodes * (origNumNodes - 1) / 2) - origNumEdges
sampledyads <- subNumNodes * (subNumNodes - 1) / 2
prob<-dhyper(subNumEdges,origNumEdges,dyads,sampledyads)
prob
}
################################################################
# function:
# calcSumProb takes two parameters:
# g is the original graph from which the subgraph was made
# sg is the subgraph made from the original graph
# calcSumProb calculates the probability of having greater than or equal
# to the number of edges found in the subgraph given that it was made
# from origgraph.
# The hypergeometric distribution is used to calculate the summed
# probability (using the cdf).
#
# notes: This calculates the upper tail of the hypergeometric
# distribution.
#
# created by: Elizabeth Whalen
# last updated: July 22, 2002
################################################################
calcSumProb <- function(sg, g)
{
origNumNodes<-length(nodes(g)) #g
subNumNodes<-length(nodes(sg)) #gs
origNumEdges<-numEdges(g) #L
subNumEdges<-numEdges(sg) #Ls
dyads <- (origNumNodes * (origNumNodes - 1) / 2) - origNumEdges
sampledyads <- subNumNodes * (subNumNodes - 1) / 2
prob<-phyper(subNumEdges,origNumEdges,dyads,sampledyads,lower.tail=FALSE)
prob
}
################################################################
# function:
# mostEdges takes one parameter:
# objGraph is the graph object
# mostEdges finds the node that has the most edges in the graph.
# The index of the node, the node id (ex. affy id, locus
# link id, ...), and the number of edges for that node is returned
# in a list.
#
# created by: Elizabeth Whalen
# last updated: August 2, 2002
################################################################
mostEdges<-function(objGraph)
{
oEdges<-edges(objGraph)
lens <- sapply(oEdges, length)
mx <- max(lens)
return(names(oEdges)[match(mx, lens)])
}
################################################################
# function:
# numNoEdges takes one parameter:
# objGraph is the graph object
# numNoEdges calculates the number of nodes that have an edge list
# of NULL (i.e. no edges) and returns an integer representing
# the number of NULL edge lists in the graph.
#
# created by: Elizabeth Whalen
# last updated: July 22, 2002
################################################################
numNoEdges<-function(objGraph)
{
els <- sapply(edges(objGraph), length)
sum(els==0)
}
##########################################################
##RG/2003
##########################################################
##listEdges: list all edges for every pair of nodes in the graph
##so if there N nodes then there are N choose 2 possible entries
##dropNULL=T/F says whether to drop those pairs with no edges
listEdges <- function(object, dropNULL=TRUE)
{
if( !is(object, "graphNEL") )
stop("'listEdges' only works for graphNEL objects")
Nd <- nodes(object)
Nn <- length(Nd)
EL <- object@edgeL
eList <- NULL
for(i in seq_len(Nn)) {
Node <- Nd[i]
ELi <- EL[[i]]
for( j in seq(along=ELi$edges) ) {
toN <- Nd[ELi$edges[j]]
btwn <- paste(sort(c(Node, toN)), collapse=":")
newN <-new("simpleEdge",
bNode=Node, eNode=toN,
weight=if( is.null(ELi$weights[j])) 1 else ELi$weights[j] ,
directed = edgemode(object)=="directed",
edgeType=if(is.null(ELi$type[j])) "" else
ELi$type[j])
if( is.null(eList[[btwn]]) )
eList[[btwn]] <- list(newN)
else
eList[[btwn]] <- list(eList[[btwn]], newN )
}
}
return(eList)
}
listLen <- function(list)
.Call(graph_listLen, list)
```

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