dcGOR (version 1.0.2)

Onto-class: Definition for S4 class Onto

Description

Onto has 2 slots: nodeInfo and adjMatrix

Value

• Class Onto

Creation

An object of this class can be created via: new("Onto", 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} term_id():{retrieve term id (ie, column 'term_id' of nodeInfo) in the object, if any} term_name():{retrieve term id (ie, column 'term_name' of nodeInfo) in the object, if any} term_namespace():{retrieve term id (ie, column 'term_namespace' of nodeInfo) in the object, if any} term_distance():{retrieve term id (ie, column 'term_distance' of nodeInfo) in the object, if any}

itemize

• str():

item

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

Access

Ways to access information on this class:

• showClass("Onto"):

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

See Also

Onto-method

Examples

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

# create an object of class Onto, given a matrix plus information on nodes
# 1) create nodeI: an object of class InfoDataFrame
data <- data.frame(term_id=paste("Term", 1:5, sep="_"),
term_name=I(LETTERS[1:5]), term_namespace=rep("Namespace",5),
term_distance=1:5, row.names=paste("Term", 1:5, sep="_"))
nodeI <- new("InfoDataFrame", data=data)
nodeI
# 2) create an object of class Onto
# 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("Onto", adjMatrix=adjM, nodeInfo=nodeI)
x
# 3) look at various methods defined on class Onto
dim(x)
adjMatrix(x)
nodeInfo(x)
nInfo(x)
nodeNames(x)
term_id(x)
term_namespace(x)
term_distance(x)
# 4) get the subset
x[1:2]