dcGOR (version 1.0.2)

Dnetwork-class: Definition for S4 class Dnetwork

Description

Dnetwork is an S4 class to store a domain network, such as the one from semantic similairty between pairs of domains by dcDAGdomainSim. It has 2 slots: nodeInfo and adjMatrix

Value

• Class Dnetwork

Creation

An object of this class can be created via: new("Dnetwork", nodeInfo, adjMatrix)

Methods

Class-specific methods:

• dim():

{retrieve the dimension in the object} adjMatrix():{retrieve the slot 'adjMatrix' in the object} nodeInfo():{retrieve the slot 'nodeInfo' (as class InfoDataFrame) in the object} nInfo():{retrieve nodeInfo (as data.frame) in the object} nodeNames():{retrieve node/term names (ie, row names of nodeInfo) in the object} id():{retrieve domain id (ie, column 'id' of nodeInfo) in the object, if any} level():{retrieve domain level (ie, column 'level' of nodeInfo) in the object, if any} description():{retrieve domain description (ie, column 'description' of nodeInfo) in the object, if any}

itemize

• str():

item

• show():
• as(matrix, "Dnetwork"):
• as(dgCMatrix, "Dnetwork"):
• [i]:

Access

Ways to access information on this class:

• showClass("Dnetwork"):

{show the class definition} showMethods(classes="Dnetwork"):{show the method definition upon this class} getSlots("Dnetwork"):{get the name and class of each slot in this class} slotNames("Dnetwork"):{get the name of each slot in this class} selectMethod(f, signature="Dnetwork"):{retrieve the definition code for the method 'f' defined in this class}

See Also

Dnetwork-method

Examples

# create an object of class Dnetwork, only given a matrix
adjM <- matrix(runif(25),nrow=5,ncol=5)
as(adjM, "Dnetwork")

# create an object of class Dnetwork, given a matrix plus information on nodes
# 1) create nodeI: an object of class InfoDataFrame
data <- data.frame(id=paste("Domain", 1:5, sep="_"),
level=rep("SCOP",5), description=I(LETTERS[1:5]),
row.names=paste("Domain", 1:5, sep="_"))
nodeI <- new("InfoDataFrame", data=data)
nodeI
# 2) create an object of class Dnetwork
# VERY IMPORTANT: make sure having consistent names between nodeInfo and adjMatrix
adjM <- matrix(runif(25),nrow=5,ncol=5)
colnames(adjM) <- rownames(adjM) <- rowNames(nodeI)
x <- new("Dnetwork", adjMatrix=adjM, nodeInfo=nodeI)
x
# 3) look at various methods defined on class Dnetwork
dim(x)
adjMatrix(x)
nodeInfo(x)
nInfo(x)
nodeNames(x)
id(x)
level(x)
description(x)
# 4) get the subset
x[1:2]