Anno-class: Definition for S4 class Anno
In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

Anno-class

R Documentation

Definition for S4 class Anno

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

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]

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.