arrayData-class {arrayMagic}R Documentation

Class arrayData, a simple container for raw data and related information

Description

A simple class to store raw data, annotation information for spots and hybridisations, as well as weights.

Creating Objects

new('arrayData',
intensities = ..., # optional; object of class array
weights = ..., # optional; object of class matrix
spotAttr = ..., # optional; object of class data.frame
hybAttrList = ..., # optional; list of two objects of class data.frame
)

Slots

intensities:
Object of class array; three-dimensional; dim = nrOfSpots x nrOfChannels x nrOfHybridisations; second dimension must contain "green" and "red" and possibly "greenBackground" and "redBackground"; default: NULL
weights:
Object of class matrix; dim = nrOfSpots x nrOfHybridisations; range = [0,1]; default: NULL.
spotAttr:
Object of class data.frame; dim = nrOfSpots x nrOfSpotCharacteristics; default: NULL
hybAttrList:
list of two objects named "green" and "red" of class data.frame; the dimension of each data.frame is given by nrOfHybridisations x nrOfHybridisationCharacteristics ; default: NULL

Methods

intensities<-
(arrayData): Set the intensities of arrayData.
getIntensities
(arrayData): Returns the intensities array.
weights<-
(arrayData): Set the weights of arrayData.
getWeights
(arrayData): Returns the weights object.
spotAttr<-
(arrayData): Set the spotAttr of arrayData.
getSpotAttr
(arrayData): Returns the spotAttr data.frame.
getHybAttr
(arrayData): Returns the "intersection" of the "red" and "green" data.frame of hybAttrList or if one is NULL the other one. The "intersection" are those columns which match in column name and its content otherwise NULL is returned.
getHybAttrGreen
(arrayData): Returns the "green" list element of hybAttrList, i.e. a data.frame.
getHybAttrRed
(arrayData): Returns the "red" list element of hybAttrList, i.e. a data.frame.
hybAttrList<-
(arrayData): Set the hybAttrList of arrayData.
getHybAttrList
(arrayData): Returns the hybAttrList object.
show
(arrayData): Renders information about the arrayData object on standard out.
[
(arrayData,i,j): A subset operator, where i corresponds to the spots and j to the hybridisations.
cbind
(...): Concatenates arrayData objects. Spots/rows are assumed to match; possibly you have to subset and reorder the objects beforehand cf. function cbind.arrayData.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

exprSetRG-class

Examples


intensities <- array(data=runif(120),dim=c(20,2,3))
dimnames(intensities) <- list(NULL, c("green","red"), NULL)
spotAttr <- data.frame(Name=I(rep(c("x","y","k","l","z"),4)),
                       Index=c(1:20))
arrayDataObject <- new("arrayData", intensities=intensities, weights=intensities[,1,],
                       spotAttr=spotAttr, hybAttrList=NULL)
print(arrayDataObject)
hybs <- c(1,3)
spots <- c(1:10, 14)
aD <- arrayDataObject[spots,hybs]
print(aD)
stopifnot( all( getIntensities(arrayDataObject)[spots, , hybs] == getIntensities(aD) ) )
stopifnot( all( getWeights(arrayDataObject)[spots, hybs] == getWeights(aD) ) )
stopifnot( all( getSpotAttr(arrayDataObject)[spots, ] == getSpotAttr(aD) ) )

hybAttr <- data.frame(Name=I(c("hx","hy","hz")),
                      Index=c(1:3))
arrayDataObject <- new("arrayData", intensities=intensities, weights=intensities[,1,],
                       spotAttr=spotAttr, hybAttrList=list(green=hybAttr,red=hybAttr))
hybAttrGreen <- data.frame(Name=I(c("hx","hy","hz")),
                      Index=c(4:6))
aDObject <- new("arrayData", intensities=intensities, weights=intensities[,1,],
                       spotAttr=spotAttr, hybAttrList=list(green=hybAttrGreen,red=hybAttr))
print(arrayDataObject)
cbind(aDObject,aDObject)
hybs <- c(1)
spots <- c(1)
aD <- arrayDataObject[spots,hybs]
print(aD)
stopifnot( all( getIntensities(arrayDataObject)[spots, , hybs] == getIntensities(aD) ) )
stopifnot( all( getWeights(arrayDataObject)[spots, hybs] == getWeights(aD) ) )
stopifnot( all( getSpotAttr(arrayDataObject)[spots, ] == getSpotAttr(aD) ) )
stopifnot( all( getHybAttr(arrayDataObject)[spots, ] == getHybAttr(aD) ) )
stopifnot( all( getHybAttrRed(arrayDataObject)[spots, ] == getHybAttrRed(aD) ) )
stopifnot( all( getHybAttrGreen(arrayDataObject)[spots, ] == getHybAttrGreen(aD) ) )

stopifnot( all( getHybAttrRed(aDObject) == hybAttr) )
stopifnot( all( getHybAttrGreen(aDObject) == hybAttrGreen) )
stopifnot( all( getHybAttr(aDObject) == data.frame(Name=I(c("hx","hy","hz"))) ) )
weights(aDObject) <- intensities[,2,]
intensities(aDObject) <- intensities
spotAttr(aDObject) <- spotAttr
hybAttrList(aDObject) <- list(green=hybAttr,red=hybAttrGreen)
aD <- new("arrayData")
stopifnot(is(aD, "arrayData"))
 

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