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