dcGOR 1.0.5

Definition for S4 class Onto

Description

Onto has 2 slots: nodeInfo and adjMatrix

Value

Class Onto

Slots

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

adjMatrixAn 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)

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

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

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

Examples

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



An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 5 terms (parents/from) X 5 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: 1 2 3 4 5
  nodeAttr: term_id




# 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



An object of S4 class 'InfoDataFrame'
  rowNames: Term_1 Term_2 Term_3 Term_4 Term_5
  colNames: term_id term_name term_namespace term_distance



# 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



An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 5 terms (parents/from) X 5 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: Term_1 Term_2 Term_3 Term_4 Term_5
  nodeAttr: term_id term_name term_namespace term_distance



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



[1] 5 5



adjMatrix(x)



          Term_1    Term_2    Term_3     Term_4    Term_5
Term_1 0.5378686 0.3559571 0.1466445 0.87588657 0.7085989
Term_2 0.7232435 0.3623360 0.3810996 0.08324089 0.4138110
Term_3 0.4976214 0.9922084 0.5166277 0.57128948 0.1261319
Term_4 0.2510645 0.1328220 0.4586717 0.25054983 0.7096981
Term_5 0.1073252 0.4619702 0.8470875 0.21365910 0.6273038



nodeInfo(x)



An object of S4 class 'InfoDataFrame'
  rowNames: Term_1 Term_2 Term_3 Term_4 Term_5
  colNames: term_id term_name term_namespace term_distance



nInfo(x)



       term_id term_name term_namespace term_distance
Term_1  Term_1         A      Namespace             1
Term_2  Term_2         B      Namespace             2
Term_3  Term_3         C      Namespace             3
Term_4  Term_4         D      Namespace             4
Term_5  Term_5         E      Namespace             5



nodeNames(x)



[1] "Term_1" "Term_2" "Term_3" "Term_4" "Term_5"



term_id(x)



[1] "Term_1" "Term_2" "Term_3" "Term_4" "Term_5"



term_namespace(x)



[1] "Namespace" "Namespace" "Namespace" "Namespace" "Namespace"



term_distance(x)



[1] 1 2 3 4 5



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



An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 2 terms (parents/from) X 2 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: Term_1 Term_2
  nodeAttr: term_id term_name term_namespace term_distance

See also

Onto-method