Anno-class: Definition for S4 class Anno

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description

Anno has 3 slots: annoData, termData and domainData

Value

Class Anno

Slots

annoData

An object of S4 class AnnoData, containing data matrix with the column number equal to nrow(termData) and the row number equal to nrow(domainData).

termData

An object of S4 class InfoDataFrame, describing information on columns in annoData.

domainData

An object of S4 class InfoDataFrame, describing information on rows in annoData.

Creation

An object of this class can be created via: new("Anno", annoData, termData, domainData)

Methods

Class-specific methods:

• dim(): retrieve the dimension in the object

• annoData(): retrieve the slot 'annoData' in the object

• termData(): retrieve the slot 'termData' (as class InfoDataFrame) in the object

• domainData(): retrieve the slot 'domainData' (as class InfoDataFrame) in the object

• tData(): retrieve termData (as data.frame) in the object

• dData(): retrieve domainData (as data.frame) in the object

• termNames(): retrieve term names (ie, row names of termData) in the object

• domanNames(): retrieve domain names (ie, row names of domainData) in the object

Standard generic methods:

• str(): compact display of the content in the object

• show(): abbreviated display of the object

• as(matrix, "Anno"): convert a matrix to an object of class Anno

• as(dgCMatrix, "Anno"): convert a dgCMatrix (a sparse matrix) to an object of class Anno

• [i,j]: get the subset of the same class

Access

Ways to access information on this class:

• showClass("Anno"): show the class definition

• showMethods(classes="Anno"): show the method definition upon this class

• getSlots("Anno"): get the name and class of each slot in this class

• slotNames("Anno"): get the name of each slot in this class

• selectMethod(f, signature="Anno"): retrieve the definition code for the method 'f' defined in this class

See Also

Anno-method

Examples

# create an object of class Anno, only given a matrix
annoData <- matrix(runif(50),nrow=10,ncol=5)
as(annoData, "Anno")

# create an object of class Anno, given a matrix plus information on its columns/rows
# 1) create termData: an object of class InfoDataFrame
data <- data.frame(x=1:5, y=I(LETTERS[1:5]), row.names=paste("Term",
1:5, sep="_"))
termData <- new("InfoDataFrame", data=data)
termData
# 2) create domainData: an object of class InfoDataFrame
data <- data.frame(x=1:10, y=I(LETTERS[1:10]),
row.names=paste("Domain", 1:10, sep="_"))
domainData <- new("InfoDataFrame", data=data)
domainData
# 3) create an object of class Anno
# VERY IMPORTANT: make sure having consistent names between annoData and domainData (and termData)
annoData <- matrix(runif(50),nrow=10,ncol=5)
rownames(annoData) <- rowNames(domainData)
colnames(annoData) <- rowNames(termData)
x <- new("Anno", annoData=annoData, domainData=domainData,
termData=termData)
x
# 4) look at various methods defined on class Anno
dim(x)
annoData(x)
termData(x)
tData(x)
domainData(x)
dData(x)
termNames(x)
domainNames(x)
# 5) get the subset
x[1:3,1:2]

dcGOR documentation built on May 2, 2019, 6:14 p.m.