dcGOR 1.0.5

Definition for S4 class Anno

Description

Anno has 3 slots: annoData, termData and domainData

Value

Class Anno

Slots

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

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

domainDataAn 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")



An object of S4 class 'Anno'
@annoData: 10 domains, 5 terms 
@termData (InfoDataFrame)
  termNames: 1 2 3 4 5
  tvarLabels: names
@domainData (InfoDataFrame)
  domainNames: 1 2 3 ... 9 10 (10 total)
  dvarLabels: names




# 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



An object of S4 class 'InfoDataFrame'
  rowNames: Term_1 Term_2 Term_3 Term_4 Term_5
  colNames: x y



# 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



An object of S4 class 'InfoDataFrame'
  rowNames: Domain_1 Domain_2 Domain_3 ... Domain_9 Domain_10 (10
    total)
  colNames: x y



# 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



An object of S4 class 'Anno'
@annoData: 10 domains, 5 terms 
@termData (InfoDataFrame)
  termNames: Term_1 Term_2 Term_3 Term_4 Term_5
  tvarLabels: x y
@domainData (InfoDataFrame)
  domainNames: Domain_1 Domain_2 Domain_3 ... Domain_9 Domain_10 (10
    total)
  dvarLabels: x y



# 4) look at various methods defined on class Anno
dim(x)



[1] 10  5



annoData(x)



              Term_1     Term_2     Term_3    Term_4    Term_5
Domain_1  0.38646009 0.29743303 0.83303351 0.1105348 0.6343022
Domain_2  0.58222451 0.01907135 0.84091112 0.6852883 0.7244947
Domain_3  0.07107426 0.12770868 0.11039306 0.5464801 0.8751578
Domain_4  0.23272480 0.44866704 0.10973054 0.3975184 0.4431293
Domain_5  0.84330124 0.02929973 0.77454019 0.4825122 0.6956817
Domain_6  0.54557412 0.69303444 0.92479632 0.5223680 0.4860102
Domain_7  0.04511398 0.21060201 0.87177343 0.6004444 0.3120415
Domain_8  0.60229894 0.10545978 0.07529899 0.4525172 0.4768031
Domain_9  0.32481846 0.11732409 0.08373671 0.7437398 0.2056176
Domain_10 0.88934108 0.93355149 0.94952831 0.7646140 0.2872525



termData(x)



An object of S4 class 'InfoDataFrame'
  rowNames: Term_1 Term_2 Term_3 Term_4 Term_5
  colNames: x y



tData(x)



       x y
Term_1 1 A
Term_2 2 B
Term_3 3 C
Term_4 4 D
Term_5 5 E



domainData(x)



An object of S4 class 'InfoDataFrame'
  rowNames: Domain_1 Domain_2 Domain_3 ... Domain_9 Domain_10 (10
    total)
  colNames: x y



dData(x)



           x y
Domain_1   1 A
Domain_2   2 B
Domain_3   3 C
Domain_4   4 D
Domain_5   5 E
Domain_6   6 F
Domain_7   7 G
Domain_8   8 H
Domain_9   9 I
Domain_10 10 J



termNames(x)



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



domainNames(x)



 [1] "Domain_1"  "Domain_2"  "Domain_3"  "Domain_4"  "Domain_5"  "Domain_6" 
 [7] "Domain_7"  "Domain_8"  "Domain_9"  "Domain_10"



# 5) get the subset
x[1:3,1:2]



An object of S4 class 'Anno'
@annoData: 3 domains, 2 terms 
@termData (InfoDataFrame)
  termNames: Term_1 Term_2
  tvarLabels: x y
@domainData (InfoDataFrame)
  domainNames: Domain_1 Domain_2 Domain_3
  dvarLabels: x y

See also

Anno-method