dcGOR 1.0.5

Definition for S4 class Cnetwork

Description

Cnetwork is an S4 class to store a contact network, such as the one from RWR-based contact between samples/terms by dcRWRpipeline. It has 2 slots: nodeInfo and adjMatrix

Value

Class Cnetwork

Slots

nodeInfoAn object of S4 class InfoDataFrame, describing information on nodes/domains.

adjMatrixAn object of S4 class AdjData, containing symmetric adjacency data matrix for an indirect domain network

Creation

An object of this class can be created via: new("Cnetwork", 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

Standard generic methods:

  • str(): compact display of the content in the object
  • show(): abbreviated display of the object
  • as(matrix, "Cnetwork"): convert a matrix to an object of class Cnetwork
  • as(dgCMatrix, "Cnetwork"): convert a dgCMatrix (a sparse matrix) to an object of class Cnetwork
  • [i]: get the subset of the same class

Access

Ways to access information on this class:

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

Examples

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



An object of S4 class 'Cnetwork'
@adjMatrix: a weighted symmetric matrix of 5 samples/terms X 5 samples/terms 
@nodeInfo (InfoDataFrame)
  nodeNames: 1 2 3 4 5
  nodeAttr: id




# create an object of class Cnetwork, 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



An object of S4 class 'InfoDataFrame'
  rowNames: Domain_1 Domain_2 Domain_3 Domain_4 Domain_5
  colNames: id level description



# 2) create an object of class Cnetwork
# 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("Cnetwork", adjMatrix=adjM, nodeInfo=nodeI)
x



An object of S4 class 'Cnetwork'
@adjMatrix: a weighted symmetric matrix of 5 samples/terms X 5 samples/terms 
@nodeInfo (InfoDataFrame)
  nodeNames: Domain_1 Domain_2 Domain_3 Domain_4 Domain_5
  nodeAttr: id level description



# 3) look at various methods defined on class Cnetwork
dim(x)



[1] 5 5



adjMatrix(x)



           Domain_1   Domain_2  Domain_3  Domain_4  Domain_5
Domain_1 0.28674904 0.67940568 0.2612663 0.3498324 0.2858638
Domain_2 0.07508181 0.02144015 0.8738172 0.5003737 0.4241023
Domain_3 0.85388949 0.99335998 0.6187192 0.1840178 0.4115077
Domain_4 0.64491955 0.88064373 0.4329641 0.6983444 0.6659519
Domain_5 0.78162055 0.23141078 0.2724255 0.6361669 0.6488376



nodeInfo(x)



An object of S4 class 'InfoDataFrame'
  rowNames: Domain_1 Domain_2 Domain_3 Domain_4 Domain_5
  colNames: id level description



nInfo(x)



               id level description
Domain_1 Domain_1  SCOP           A
Domain_2 Domain_2  SCOP           B
Domain_3 Domain_3  SCOP           C
Domain_4 Domain_4  SCOP           D
Domain_5 Domain_5  SCOP           E



nodeNames(x)



[1] "Domain_1" "Domain_2" "Domain_3" "Domain_4" "Domain_5"



# 4) get the subset
x[1:2]



An object of S4 class 'Cnetwork'
@adjMatrix: a weighted symmetric matrix of 2 samples/terms X 2 samples/terms 
@nodeInfo (InfoDataFrame)
  nodeNames: Domain_1 Domain_2
  nodeAttr: id level description

See also

Cnetwork-method