Nothing
# SETAS.R
setAs("marrayRaw", "RGList", function(from, to) {
# Gordon Smyth
# 20 Dec 2003
y <- new(to)
ifposlen <- function(x) if(length(x)) return(x) else return(NULL)
y$R <- ifposlen(from@maRf)
y$G <- ifposlen(from@maGf)
y$Rb <- ifposlen(from@maRb)
y$Gb <- ifposlen(from@maGb)
y$weights <- ifposlen(from@maW)
y$printer$ngrid.r <- ifposlen(from@maLayout@maNgr)
y$printer$ngrid.c <- ifposlen(from@maLayout@maNgc)
y$printer$nspot.r <- ifposlen(from@maLayout@maNsr)
y$printer$nspot.c <- ifposlen(from@maLayout@maNsc)
y$printer$notes <- ifposlen(from@maLayout@maNotes)
y$genes <- ifposlen(from@maGnames@maInfo)
y$genes$Labels <- ifposlen(from@maGnames@maLabels)
attr(y$genes,"notes") <- ifposlen(from@maGnames@maNotes)
y$genes$Sub <- ifposlen(from@maLayout@maSub)
y$genes$Plate <- ifposlen(from@maLayout@maPlate)
y$genes$Controls <- ifposlen(from@maLayout@maControls)
y$targets <- ifposlen(from@maTargets@maInfo)
y$targets$Labels <- ifposlen(from@maTargets@maLabels)
y$notes <- ifposlen(from@maNotes)
y
})
##There is intentionally no setAs function with this signature
##Robert Gentleman, Nov 22, 2006
#setAs("marrayRaw", "ExpressionSet", function(from)
setAs("marrayNorm", "MAList", function(from, to)
# Gordon Smyth
# 20 Dec 2003. Last modified 18 April 2005.
{
y <- new(to)
ifposlen <- function(x) if(length(x)) return(x) else return(NULL)
y$A <- ifposlen(from@maA)
y$M <- ifposlen(from@maM)
y$weights <- ifposlen(from@maW)
y$printer$ngrid.r <- ifposlen(from@maLayout@maNgr)
y$printer$ngrid.c <- ifposlen(from@maLayout@maNgc)
y$printer$nspot.r <- ifposlen(from@maLayout@maNsr)
y$printer$nspot.c <- ifposlen(from@maLayout@maNsc)
y$printer$notes <- ifposlen(from@maLayout@maNotes)
y$genes <- ifposlen(from@maGnames@maInfo)
y$genes$Labels <- ifposlen(from@maGnames@maLabels)
attr(y$genes,"notes") <- ifposlen(from@maGnames@maNotes)
y$genes$Sub <- ifposlen(from@maLayout@maSub)
y$genes$Plate <- ifposlen(from@maLayout@maPlate)
y$genes$Controls <- ifposlen(from@maLayout@maControls)
y$targets <- ifposlen(from@maTargets@maInfo)
y$targets$Labels <- ifposlen(from@maTargets@maLabels)
y$notes <- ifposlen(from@maNotes)
##modified with Gordon's suggestions
##y$maNormCall <- from@maNormCall
##if(as.character(y$maNormCall)=="<undef>") y$maNormCall <- NULL
if(from@maNormCall != getClass("call")@prototype) y$maNormCall <- from@maNormCall
y
})
setAs("marrayNorm", "ExpressionSet", function(from){
##Robert Gentleman
##22 November 2006
nM <- new("MIAME")
notes(nM) <- paste(from@maNotes,
":: Converted from marrayNorm object, exprs are log-ratios")
exprs <- maM(from)
colnames(exprs) <- NULL
if (any(duplicated(maLabels(maGnames(from))))) {
rownames(exprs) <- seq_len(nrow(exprs))
fData <- data.frame(maGnames=maLabels(maGnames(from)))
} else {
rownames(exprs) <- maLabels(maGnames(from))
fData <- data.frame(row.names=seq_len(nrow(exprs)))
}
new("ExpressionSet", exprs=exprs,
phenoData=new("AnnotatedDataFrame", data=maInfo(maTargets(from))),
featureData=new("AnnotatedDataFrame", data=fData),
experimentData=nM)
})
setAs("MAList", "marrayNorm", function(from, to)
# Gordon Smyth
# 20 Dec 2003. Last modified 7 March 2004.
{
y <- new(to)
if(!is.null(from$A)) y@maA <- from$A
if(!is.null(from$M)) y@maM <- from$M
if(!is.null(from$weights)) y@maW <- from$weights
if(!is.null(from$printer$ngrid.r)) y@maLayout@maNgr <- from$printer$ngrid.r
if(!is.null(from$printer$ngrid.c)) y@maLayout@maNgc <- from$printer$ngrid.c
if(!is.null(from$printer$nspot.r)) y@maLayout@maNsr <- from$printer$nspot.r
if(!is.null(from$printer$nspot.c)) y@maLayout@maNsc <- from$printer$nspot.c
if(!is.null(from$genes)) y@maGnames@maInfo <- from$genes
if(!is.null(from$targets)) y@maTargets@maInfo <- from$targets
y@maNotes <- "Converted from MAList object"
y
})
setAs("MAList", "ExpressionSet", function(from)
# Robert Gentleman
# 22 November 2006
{
theExperimentData <- new("MIAME")
notes(theExperimentData) <- list("Converted from MAList object, exprs are M-values")
theExprs <- as.matrix(from$M)
thePhenoData <- from$targets
rownames(thePhenoData) <- colnames(theExprs)
new("ExpressionSet", exprs = theExprs,
phenoData = new("AnnotatedDataFrame", data=thePhenoData),
experimentData = theExperimentData)
})
setAs("RGList", "marrayRaw", function(from, to) {
# Gordon Smyth
# 20 Dec 2003
# Last modified by Jean Yang, June 30, 2004. Add conversation of control status
y <- new(to)
if(!is.null(from$G)) y@maGf <- from$G
if(!is.null(from$R)) y@maRf <- from$R
if(!is.null(from$Gb)) y@maGb <- from$Gb
if(!is.null(from$Rb)) y@maRb <- from$Rb
if(!is.null(from$weights)) y@maW <- from$weights
if(!is.null(from$printer$ngrid.r)) y@maLayout@maNgr <- from$printer$ngrid.r
if(!is.null(from$printer$ngrid.c)) y@maLayout@maNgc <- from$printer$ngrid.c
if(!is.null(from$printer$nspot.r)) y@maLayout@maNsr <- from$printer$nspot.r
if(!is.null(from$printer$nspot.c)) y@maLayout@maNsc <- from$printer$nspot.c
if(!is.null(from$genes)) y@maGnames@maInfo <- from$genes
if(!is.null(from$genes$Status)) y@maLayout@maControls <- as.factor(from$genes$Status)
if(!is.null(from$targets)) y@maTargets@maInfo <- from$targets
if(!is.null(from$notes)) y@maNotes <- "Converted from RGList object"
y
})
##there is intentionally no setAs function of this type
##setAs("RGList", "ExpressionSet", function(from)
##Robert Gentleman
##Nov 22, 2006
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