@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.11.16

+Version: 1.11.18

 Date: 2010-12-10

 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -10,7 +10,7 @@ License: Artistic-2.0

 Depends: R (>= 2.13.0),

          methods,

          Biobase (>= 2.11.9),

-         oligoClasses (>= 1.13.22)

+         oligoClasses (>= 1.15.31)

 Imports: affyio (>= 1.19.2),

          ellipse,

          ff (>= 2.2-1),

@@ -2702,24 +2702,16 @@ dbvn <- function(x, mu, Sigma){

 ABpanel <- function(x, y, predictRegion,

 		    copyNumber=0:4,

-		    object,

-##		    x.axis,

-##		    line.col,

-##		    line.lwd,

-##		    shades,

+		    fill,

 		    ...,

 		    subscripts){

-##		    data.last=FALSE,

-##		    highlight.index=NULL){

-	##if(length(scale.sd)==1) scale.sd <- rep(scale.sd,3)

 	panel.grid(h=5, v=5)

-	panel.xyplot(x, y, ...)

-##	if(!is.null(highlight.index)){

-##		##ii <- subscripts[highlight.index]

-##		ii <- highlight.index

-##		lpoints(x[ii], y[ii], pch="X", cex=1.5, col="black")

-##	}

-	i <- panel.number()

+	if(!missing(fill)){

+		panel.xyplot(x, y, fill=fill[subscripts], ...)

+	} else {

+		panel.xyplot(x, y, ...)

+	}

+	pn <- panel.number()

 	for(CN in copyNumber){

 		gts <- genotypes(CN)

 		index <- match(gts, names(predictRegion))

@@ -2727,65 +2719,15 @@ ABpanel <- function(x, y, predictRegion,

 		for(i in seq_along(pr)){

 			## scale?

 			pr2 <- pr[[i]]

-			mu <- pr2$mu

-			Sigma <- pr2$cov

+			mu <- pr2$mu[pn, , , drop=FALSE] ## pn=panel number

+			Sigma <- pr2$cov[pn, , ,drop=FALSE]

 			for(j in seq_len(dim(mu)[3])){

 				dat.ellipse <- ellipse(x=Sigma[, 2, j],

-						       centre=mu[, , j],

-						       scale=c(sqrt(Sigma[,1,j]),

+						       centre=mu[ , , j],

+						       scale=c(sqrt(Sigma[ , 1, j]),

 						       sqrt(Sigma[, 3, j])))

 				lpolygon(dat.ellipse[,1], dat.ellipse[,2], ...)

 			}

-##			} else {

-##				dat.ellipse <- ellipse(x=rho, centre=c(log2(nuB+CB*phB), log2(nuA+CA*phA)), scale=rev(scale))

-##			}

-##			lpolygon(dat.ellipse[, 1], dat.ellipse[, 2], border=line.col[k], col=shades[k], ...)

 		}

 	}

-##	nuB <- as.numeric(nu(object, "B"))[i]

-##	phB <- as.numeric(phi(object, "B"))[i]

-##	nuA <- as.numeric(nu(object, "A"))[i]

-##	phA <- as.numeric(phi(object, "A"))[i]

-##	taus <- tau2(object, i=i)[, , , 1]

-##	cors <- corr(object, i=i)[, , 1]

-##	t2A <- taus["A", "BB"]

-##	t2B <- taus["B", "AA"]

-##	s2A <- taus["A", "AA"]

-##	s2B <- taus["B", "BB"]

-##	corrAB <- cors["AB"]

-##	corrAA <- cors["AA"]

-##	corrBB <- cors["BB"]

-##	k <- 1

-##	for(CN in copynumber){

-##		for(CA in 0:CN){

-##			CB <- CN-CA

-##			A.scale <- sqrt(t2A*(CA==0) + s2A*(CA > 0))

-##			B.scale <- sqrt(t2B*(CB==0) + s2B*(CB > 0))

-##			if(CA == 0 | CB == 0){

-##				A.scale <- A.scale*scale.sd[1]

-##				B.scale <- B.scale*scale.sd[1]

-##			} else { ## both greater than zero

-##				A.scale <- A.scale*scale.sd[2]

-##				B.scale <- B.scale*scale.sd[2]

-##			}

-##			scale <- c(A.scale, B.scale)

-##			if(CA == 0 & CB > 0) rho <- corrBB

-##			if(CA > 0 & CB == 0) rho <- corrAA

-##			if(CA > 0 & CB > 0) rho <- corrAB

-##			if(CA == 0 & CB == 0) rho <- 0

-##			if(x.axis=="A"){

-##				dat.ellipse <- ellipse(x=rho, centre=c(log2(nuA+CA*phA), log2(nuB+CB*phB)), scale=scale)

-##			} else {

-##				dat.ellipse <- ellipse(x=rho, centre=c(log2(nuB+CB*phB), log2(nuA+CA*phA)), scale=rev(scale))

-##			}

-##			lpolygon(dat.ellipse[, 1], dat.ellipse[, 2], border=line.col[k], col=shades[k], ...)

-##		}

-##		k <- k+1

-##	}

-##	if(data.last) {

-##		panel.xyplot(x, y, ...)

-##		if(!is.null(highlight.index)){

-##			lpoints(x[ii], y[ii], pch="X", cex=1.5, col="black")

-##		}

-##	}

 }

new file mode 100644

@@ -0,0 +1,64 @@

+\name{ABpanel}

+\alias{ABpanel}

+\title{A panel function for plotting prediction regions and

+  log-normalized intensities

+}

+\description{

+  A panel function for plotting prediction regions and

+  log-normalized intensities

+}

+\usage{

+ABpanel(x, y, predictRegion, copyNumber = 0:4, fill, ..., subscripts)

+}

+%- maybe also 'usage' for other objects documented here.

+\arguments{

+  \item{x}{

+    log-normalized intensities for the A or B allele

+}

+\item{y}{

+      log-normalized intensities for the A or B allele

+}

+  \item{predictRegion}{

+    A \code{list}. See \code{predictionRegion}.

+}

+  \item{copyNumber}{

+    Integer vector.  Indicates which prediction regions are drawn.

+}

+  \item{fill}{

+    Character or integer vector for coloring the points.  Only valid for

+    certain point symbols.  See \code{points}.

+}

+  \item{\dots}{

+    Additional arguments to \code{panel.xyplot} and \code{\lpolygon}.

+}

+  \item{subscripts}{

+    See \code{xyplot} in the \pkg{lattice} package.

+}

+}

+\details{

+%%  ~~ If necessary, more details than the description above ~~

+}

+\value{

+  Not applicable

+}

+

+\note{

+

+  \code{ABpanel} can be passed as the argument to panel in the

+  \code{xyplot} method for \code{CNSet} objects.  See the examples in

+  \code{xyplot}.

+

+}

+

+\author{

+R. Scharpf

+}

+

+\seealso{

+  \code{\link[lattice]{xyplot}},   \code{\link[lattice]{panel.xyplot}}

+  \code{\link[lattice]{lpolygon}}

+}

+

+% Add one or more standard keywords, see file 'KEYWORDS' in the

+% R documentation directory.

+\keyword{aplot}

\ No newline at end of file