Onto-class: Definition for S4 class Onto
In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description Value Slots Creation Methods Access See Also Examples

Onto has 2 slots: nodeInfo and adjMatrix

Class Onto

nodeInfo: An object of S4 class InfoDataFrame, describing information on nodes/terms.
adjMatrix: An object of S4 class AdjData, containing adjacency data matrix (for a direct graph), with rows for parent (arrow-outbound) and columns for children (arrow-inbound)

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

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

Standard generic methods:

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

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

Onto-method

# 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]