coerce {convert}R Documentation

Convert Data Objects

Description

Convert between limma, marray and Biobase data objects.

Details

Objects can be converted (coerced) from one class to another using as(object, Class) where object is an object to convert and Class is the name of the class to convert to. The following conversions are provided:
From: To:
RGList marrayRaw
marrayRaw RGList
MAList marrayNorm
marrayNorm MAList
RGList NChannelSet
marrayRaw NChannelSet
MAList ExpressionSet
marrayNorm ExpressionSet
Deprecated
RGList exprSet
MAList exprSet
marrayRaw exprSet

RGList and marrayRaw are coerced to NChannelSet. Channel values are not transformed.

MAList and marrayNorm are coerced so that the ExpressionSet slot contains log-ratios (M-values) and the ExpressionSet object has the same number of columns as the original object. In this case, information on the A-values is lost.

There is intentionally no conversion from RGList or marrayRaw to ExpressionSet, as ExpressionSet is intended for expression values, not intensities.

exprSet objects are deprecated, but converters to this class exist. RGList and marrayRaw objects are coerced to exprSets in such a way that green and red channel intensities are stored in alternate columns of the exprs slot expression matrix. This means that the resulting object has twice as many columns as the original object.

Author(s)

Gordon Smyth and others

See Also

as in the methods package.

Examples

##first set up some fake intensity matrices
testRed = matrix(rnorm(5*2),5,2, 
  dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))
testGreen = matrix(rnorm(5*2),5,2, 
  dimnames=list(paste("gene",1:5, sep=""), c("S1", "S2")))

##some sample/target info
testTarget = data.frame(slide=c("S1", "S2"), Cy3=c("T", "C"),
  Cy5=c("C", "T"), row.names=c("S1", "S2"))

maT = new("marrayInfo", maLabels=c("S1", "S2"),
  maInfo= testTarget)

##now create instances and convert
x <- new("RGList")
x$R = testRed
x$G = testGreen
y <- as(x,"marrayRaw")
z <- as(x, "NChannelSet")

x <- new("marrayRaw")
x@maGf <- testGreen
x@maRf <- testRed
x@maTargets = maT
y <- as(x,"RGList")
z <- as(x, "NChannelSet")

x <- new("MAList")
y <- as(x,"marrayNorm")

##we construct a reasonably complete fake, small 
##instance of the marrayNorm class
x <- new("marrayNorm")
x@maM <- testRed
x@maA <- testGreen
maTargets(x) = maT
y <- as(x,"MAList")
y <- as(x, "ExpressionSet")

x <- new("MAList")
x$M <- testRed
x$A <- testGreen
x$targets = testTarget
y <- as(x,"ExpressionSet")

[Package convert version 1.14.0 Index]