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## Define methods for coerce (as) generic function
##
## Gustavo H. Esteves
## 11/05/07
##
##
## Convert maigesRaw into RGList object
setAs("maigesRaw", "RGList", function(from, to) {
y <- new(to)
tmpf <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
tmpb <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
idxR1 <- (tolower(from@Sdye) == "red")
idxR2 <- (tolower(from@Rdye) == "red")
tmpf[, idxR1] <- from@Sf[, idxR1]
tmpb[, idxR1] <- from@Sb[, idxR1]
tmpf[, idxR2] <- from@Rf[, idxR2]
tmpb[, idxR2] <- from@Rb[, idxR2]
y$R <- tmpf
y$Rb <- tmpb
tmpf <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
tmpb <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
idxG1 <- (tolower(from@Sdye) == "green")
idxG2 <- (tolower(from@Rdye) == "green")
tmpf[, idxG1] <- from@Sf[, idxG1]
tmpb[, idxG1] <- from@Sb[, idxG1]
tmpf[, idxG2] <- from@Rf[, idxG2]
tmpb[, idxG2] <- from@Rb[, idxG2]
y$G <- tmpf
y$Gb <- tmpb
y$weights <- from@Flag
y$printer$ngrid.r <- from@Layout$gridR
y$printer$ngrid.c <- from@Layout$gridC
y$printer$nspot.r <- from@Layout$spotR
y$printer$nspot.c <- from@Layout$spotC
y$printer$notes <- from@Layout$Nspots
y$genes <- from@Glabels
y$genes$Labels <- from@Glabels[[1]]
attr(y$genes,"notes") <- NULL
y$genes$Sub <- NULL
y$genes$Plate <- NULL
y$genes$Controls <- NULL
y$targets <- from@Slabels
y$targets$Labels <- from@Slabels[[1]]
y$notes <- "Converted from maigesRaw class"
return(y)
})
## Convert RGList into maigesRaw object
setAs("RGList", "maigesRaw", function(from, to) {
y <- new(to)
y@Sf <- from$R
y@Sb <- from$Rb
y@Sdye <- rep("red", dim(from)[2])
y@Rf <- from$G
y@Rb <- from$Gb
y@Rdye <- rep("green", dim(from)[2])
y@Flag <- from$weights
y@Layout$gridR <- from$printer$ngrid.r
y@Layout$gridC <- from$printer$ngrid.c
y@Layout$spotR <- from$printer$nspot.r
y@Layout$spotC <- from$printer$nspot.c
y@Layout$Nspots <- (from$printer$ngrid.r*from$printer$ngrid.c*
from$printer$nspot.r*from$printer$nspot.c)
y@Glabels <- from$genes
y@Slabels <- from$targets
y@BadSpots <- rep(FALSE, dim(from)[2])
y@UseSpots <- matrix(TRUE, dim(from)[1], dim(from)[2])
y@Notes <- "Converted from RGList class"
return(y)
})
## Convert maigesRaw into marrayRaw object
setAs("maigesRaw", "marrayRaw", function(from, to) {
y <- new(to)
tmpf <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
tmpb <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
idxR1 <- (tolower(from@Sdye) == "red")
idxR2 <- (tolower(from@Rdye) == "red")
tmpf[, idxR1] <- from@Sf[, idxR1]
tmpb[, idxR1] <- from@Sb[, idxR1]
tmpf[, idxR2] <- from@Rf[, idxR2]
tmpb[, idxR2] <- from@Rb[, idxR2]
y@maRf <- tmpf
y@maRb <- tmpb
tmpf <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
tmpb <- matrix(NA, nrow=dim(from)[1], ncol=dim(from)[2])
idxG1 <- (tolower(from@Sdye) == "green")
idxG2 <- (tolower(from@Rdye) == "green")
tmpf[, idxG1] <- from@Sf[, idxG1]
tmpb[, idxG1] <- from@Sb[, idxG1]
tmpf[, idxG2] <- from@Rf[, idxG2]
tmpb[, idxG2] <- from@Rb[, idxG2]
y@maGf <- tmpf
y@maGb <- tmpb
y@maW <- from@Flag
y@maLayout@maNgr <- from@Layout$gridR
y@maLayout@maNgc <- from@Layout$gridC
y@maLayout@maNsr <- from@Layout$spotR
y@maLayout@maNsc <- from@Layout$spotC
y@maLayout@maNspots <- from@Layout$Nspots
y@maLayout@maSub <- rep(TRUE, dim(from)[1])
y@maLayout@maPlate <- factor(NA)
y@maLayout@maControls <- factor(NA)
y@maGnames@maInfo <- from@Glabels
y@maGnames@maLabels <- as.character(from@Glabels[[1]])
y@maTargets@maInfo <- from@Slabels
y@maTargets@maLabels <- as.character(from@Slabels[[1]])
y@maNotes <- "Converted from maigesRaw object"
return(y)
})
## Convert marrayRaw into maigesRaw object
setAs("marrayRaw", "maigesRaw", function(from, to) {
y <- new(to)
y@Sf <- from@maRf
y@Sb <- from@maRb
y@Sdye <- rep("red", dim(from)[2])
y@Rf <- from@maGf
y@Rb <- from@maGb
y@Rdye <- rep("green", dim(from)[2])
y@Flag <- from@maW
y@Layout$gridR <- from@maLayout@maNgr
y@Layout$gridC <- from@maLayout@maNgc
y@Layout$spotR <- from@maLayout@maNsr
y@Layout$spotC <- from@maLayout@maNsc
y@Layout$Nspots <- from@maLayout@maNspots
y@Glabels <- from@maGnames@maInfo
y@Slabels <- from@maTargets@maInfo
y@BadSpots <- rep(FALSE, dim(from)[2])
y@UseSpots <- matrix(TRUE, dim(from)[1], dim(from)[2])
y@Notes <- "Converted from marrayRaw class"
return(y)
})
## Convert maiges into MAList object
setAs("maiges", "MAList", function(from, to) {
y <- new(to)
y$M <- from@W
## indexing ref labelled with green
idx <- tolower(getLabels(from, "Ref")) == "red"
if(sum(idx) > 0)
y$M[, idx] <- (-1)*y$M[, idx]
y$A <- from@A
y$weights <- matrix(numeric())
y$printer$ngrid.r <- from@Layout$gridR
y$printer$ngrid.c <- from@Layout$gridC
y$printer$nspot.r <- from@Layout$spotR
y$printer$nspot.c <- from@Layout$spotC
y$printer$notes <- from@Layout$Nspots
y$genes <- from@Glabels
y$genes$Labels <- from@Glabels[[1]]
attr(y$genes,"notes") <- NULL
y$genes$Sub <- NULL
y$genes$Plate <- NULL
y$genes$Controls <- NULL
y$targets <- from@Slabels
y$targets$Labels <- from@Slabels[[1]]
y$notes <- "Converted from maiges class"
return(y)
})
## Convert MAList into maiges object
setAs("MAList", "maiges", function(from, to) {
y <- new(to)
y@W <- from$M
y@A <- from$A
y@Layout$gridR <- from$printer$ngrid.r
y@Layout$gridC <- from$printer$ngrid.c
y@Layout$spotR <- from$printer$nspot.r
y@Layout$spotC <- from$printer$nspot.c
y@Layout$Nspots <- (from$printer$ngrid.r*from$printer$ngrid.c*
from$printer$nspot.r*from$printer$nspot.c)
y@Glabels <- from$genes
y@Slabels <- from$targets
y@BadSpots <- rep(FALSE, dim(from)[2])
y@Notes <- "Converted from MAList class"
return(y)
})
## Convert maiges into marrayNorm
setAs("maiges", "marrayNorm", function(from, to) {
y <- new(to)
y@maM <- from@W
## indexing ref labelled with green
idx <- tolower(getLabels(from, "Ref")) == "red"
if(sum(idx) > 0)
y@maM[, idx] <- (-1)*y@maM[, idx]
y@maA <- from@A
y@maW <- matrix(numeric())
y@maLayout@maNgr <- from@Layout$gridR
y@maLayout@maNgc <- from@Layout$gridC
y@maLayout@maNsr <- from@Layout$spotR
y@maLayout@maNsc <- from@Layout$spotC
y@maLayout@maNspots <- from@Layout$Nspots
y@maLayout@maSub <- rep(TRUE, dim(from)[1])
y@maLayout@maPlate <- factor(NA)
y@maLayout@maControls <- factor(NA)
y@maGnames@maInfo <- from@Glabels
y@maGnames@maLabels <- as.character(from@Glabels[[1]])
y@maTargets@maInfo <- from@Slabels
y@maTargets@maLabels <- as.character(from@Slabels[[1]])
y@maNotes <- "Converted from maiges object"
return(y)
})
## Convert marrayNorm into maiges object
setAs("marrayNorm", "maiges", function(from, to) {
y <- new(to)
y@W <- from@maM
y@A <- from@maA
y@Layout$gridR <- from@maLayout@maNgr
y@Layout$gridC <- from@maLayout@maNgc
y@Layout$spotR <- from@maLayout@maNsr
y@Layout$spotC <- from@maLayout@maNsc
y@Layout$Nspots <- from@maLayout@maNspots
y@Glabels <- from@maGnames@maInfo
y@Slabels <- from@maTargets@maInfo
y@BadSpots <- rep(FALSE, dim(from)[2])
y@Notes <- "Converted from marrayNorm class"
return(y)
})
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