1. crlmm
  2. R
  3. methods-CopyNumberSet.R
Browse code

cleaned up a few of the classes. defined new class called CNSet to take the place of CrlmmSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2009 14:59:04
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ 96d10c6
1 1 
deleted file mode 100644
... ... 
@@ -1,79 +0,0 @@
1 
-setValidity("CopyNumberSet", function(object) {
2 
-	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
3 
-	if (is.null(msg)) TRUE else msg
4 
-})
5 
-##may want to allow thresholding here (... arg)
6 
-setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]]/100)
7 
-setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]]/100)
8 
-
9 
-setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
10 
-		 function(object, value){
11 
-			 assayDataElementReplace(object, "CA", value)
12 
-		 })
13 
-
14 
-setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
15 
-		 function(object, value){
16 
-			 assayDataElementReplace(object, "CB", value)
17 
-		 })
18 
-
19 
-setMethod("copyNumber", "CopyNumberSet", function(object){
20 
-	I <- isSnp(object)
21 
-	CA <- CA(object)
22 
-	CB <- CB(object)
23 
-	CN <- CA + CB
24 
-	##For nonpolymorphic probes, CA is the total copy number
25 
-	CN[!I, ] <- CA(object)[!I, ]
26 
-	CN
27 
-})
28 
-
29 
-
30 
-
31 
-##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
32 
-ellipse.CopyNumberSet <- function(x, copynumber, ...){
33 
-##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
34 
-	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
35 
-	##index <- match(plates, fittedOrder)
36 
-	if(nrow(x) > 1) stop("only 1 snp at a time")
37 
-	##batch <- unique(x$batch)
38 
-	args <- list(...)
39 
-	if(!"batch" %in% names(args)){
40 
-		jj <- match("batch", varLabels(x))
41 
-		if(length(jj) < 1) stop("batch not in varLabels")
42 
-		batch <- unique(pData(x)[, jj])
43 
-	} else{
44 
-		batch <- unique(args$batch)
45 
-	}
46 
-	if(length(batch) > 1) stop("batch variable not unique")
47 
-	nuA <- as.numeric(fData(x)[, match(paste("nuA", batch, sep="_"), fvarLabels(x))])
48 
-	nuB <- as.numeric(fData(x)[, match(paste("nuB", batch, sep="_"), fvarLabels(x))])
49 
-	phiA <- as.numeric(fData(x)[, match(paste("phiA", batch, sep="_"), fvarLabels(x))])
50 
-	phiB <- as.numeric(fData(x)[, match(paste("phiB", batch, sep="_"), fvarLabels(x))])
51 
-	tau2A <- as.numeric(fData(x)[, match(paste("tau2A", batch, sep="_"), fvarLabels(x))])
52 
-	tau2B <- as.numeric(fData(x)[, match(paste("tau2B", batch, sep="_"), fvarLabels(x))])
53 
-	sig2A <- as.numeric(fData(x)[, match(paste("sig2A", batch, sep="_"), fvarLabels(x))])
54 
-	sig2B <- as.numeric(fData(x)[, match(paste("sig2B", batch, sep="_"), fvarLabels(x))])
55 
-	corrA.BB <- as.numeric(fData(x)[, match(paste("corrA.BB", batch, sep="_"), fvarLabels(x))])
56 
-	corrB.AA <- as.numeric(fData(x)[, match(paste("corrB.AA", batch, sep="_"), fvarLabels(x))])
57 
-	corr <- as.numeric(fData(x)[, match(paste("corr", batch, sep="_"), fvarLabels(x))])
58 
-	for(CN in copynumber){
59 
-		for(CA in 0:CN){
60 
-			CB <- CN-CA
61 
-			A.scale <- sqrt(tau2A*(CA==0) + sig2A*(CA > 0))
62 
-			B.scale <- sqrt(tau2B*(CB==0) + sig2B*(CB > 0))
63 
-			scale <- c(A.scale, B.scale)
64 
-			if(CA == 0 & CB > 0) rho <- corrA.BB
65 
-			if(CA > 0 & CB == 0) rho <- corrB.AA
66 
-			if(CA > 0 & CB > 0) rho <- corr
67 
-			if(CA == 0 & CB == 0) rho <- 0
68 
-			lines(ellipse(x=rho, centre=c(log2(nuA+CA*phiA),
69 
-					     log2(nuB+CB*phiB)),
70 
-				      scale=scale), ...)
71 
-		}
72 
-	}
73 
-}
74 
-
75 
-
76 
-
77 
-
78 
-
79 
-
Browse code

numerous changes to the code and class definitions used for copy number estimation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43010 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2009 10:46:23
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ bf8acd0
... ... 
@@ -3,49 +3,26 @@ setValidity("CopyNumberSet", function(object) {
3 3 
 	if (is.null(msg)) TRUE else msg
4 4 
 })
5 5 
 ##may want to allow thresholding here (... arg)
6 
-setMethod("CA", "CopyNumberSet", function(object, ...) assayData(object)[["CA"]]/100)
7 
-setMethod("CB", "CopyNumberSet", function(object, ...) assayData(object)[["CB"]]/100)
8 
-
9 
-setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"), function(object, value){
10 
-	dns <- dimnames(value)
11 
-	value <- matrix(as.integer(value*100), nrow(value), ncol(value))
12 
-	dimnames(value) <- dns
13 
-	assayDataElementReplace(object, "CA", value)
14 
-})
15 
-
16 
-setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"), function(object, value){
17 
-	dns <- dimnames(value)
18 
-	value <- matrix(as.integer(value*100), nrow(value), ncol(value))
19 
-	dimnames(value) <- dns
20 
-	assayDataElementReplace(object, "CB", value)
21 
-})
22 
-
6 
+setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]]/100)
7 
+setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]]/100)
23 8
9 
+setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
10 
+		 function(object, value){
11 
+			 assayDataElementReplace(object, "CA", value)
12 
+		 })
24 13
25 
-
26 
-setMethod("batch", "CopyNumberSet", function(object){
27 
-	if("batch" %in% varLabels(object)){
28 
-		result <- object$batch
29 
-	} else {
30 
-		stop("batch not in varLabels of CopyNumberSet")
31 
-	}
32 
-	return(result)
33 
-})
14 
+setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
15 
+		 function(object, value){
16 
+			 assayDataElementReplace(object, "CB", value)
17 
+		 })
34 18
35 19 
 setMethod("copyNumber", "CopyNumberSet", function(object){
36 
-	require(paste(annotation(object), "Crlmm", sep=""), character.only=TRUE) || stop(paste("Annotation package ", annotation(object), "Crlmm not available", sep=""))
37 
-	##ensure that 2 + NA = 2 by replacing NA's with zero
38 
-	##the above results in copy number 0, 1, or 2 depending on the genotype....safer just to drop
20 
+	I <- isSnp(object)
39 21 
 	CA <- CA(object)
40 22 
 	CB <- CB(object)
41 
-	##nas <- is.na(CA) & is.na(CB)
42 
-	##CA[is.na(CA)] <- 0
43 
-	##CB[is.na(CB)] <- 0
44 23 
 	CN <- CA + CB
45 24 
 	##For nonpolymorphic probes, CA is the total copy number
46 
-	CN[cnIndex(object, annotation(object)), ] <- CA(object)[cnIndex(object, annotation(object)), ]
47 
-	##if both CA and CB are NA, report NA
48 
-	##CN[nas] <- NA
25 
+	CN[!I, ] <- CA(object)[!I, ]
49 26 
 	CN
50 27 
 })
51 28
... ... 
@@ -98,3 +75,5 @@ ellipse.CopyNumberSet <- function(x, copynumber, ...){
98 75
99 76
100 77
78 
+
79 
+
Browse code

updated vignettes for illumina and affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42431 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/10/2009 12:08:21
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ 3ddde61
... ... 
@@ -6,10 +6,19 @@ setValidity("CopyNumberSet", function(object) {
6 6 
 setMethod("CA", "CopyNumberSet", function(object, ...) assayData(object)[["CA"]]/100)
7 7 
 setMethod("CB", "CopyNumberSet", function(object, ...) assayData(object)[["CB"]]/100)
8 8
9 
-setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
10 
-		 function(object, value) assayDataElementReplace(object, "CA", value*100))
11 
-setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
12 
-		 function(object, value) assayDataElementReplace(object, "CB", value*100))
9 
+setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"), function(object, value){
10 
+	dns <- dimnames(value)
11 
+	value <- matrix(as.integer(value*100), nrow(value), ncol(value))
12 
+	dimnames(value) <- dns
13 
+	assayDataElementReplace(object, "CA", value)
14 
+})
15 
+
16 
+setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"), function(object, value){
17 
+	dns <- dimnames(value)
18 
+	value <- matrix(as.integer(value*100), nrow(value), ncol(value))
19 
+	dimnames(value) <- dns
20 
+	assayDataElementReplace(object, "CB", value)
21 
+})
13 22
14 23
15 24
Browse code

bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42271 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 09/10/2009 12:47:42
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ e4e0b21
... ... 
@@ -1,5 +1,4 @@
1 1 
 setValidity("CopyNumberSet", function(object) {
2 
-	##msg <- validMsg(NULL, Biobase:::isValidVersion(object, "CopyNumberSet"))
3 2 
 	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
4 3 
 	if (is.null(msg)) TRUE else msg
5 4 
 })
Browse code

changes to crlmmWrapper. updated vignettes in inst/scripts.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2009 02:37:32
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ 2ae7850
... ... 
@@ -6,12 +6,14 @@ setValidity("CopyNumberSet", function(object) {
6 6 
 ##may want to allow thresholding here (... arg)
7 7 
 setMethod("CA", "CopyNumberSet", function(object, ...) assayData(object)[["CA"]]/100)
8 8 
 setMethod("CB", "CopyNumberSet", function(object, ...) assayData(object)[["CB"]]/100)
9 
-setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
10 
-		 function(object, value) assayDataElementReplace(object, "CB", value))
9 
+
11 10 
 setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
12 
-		 function(object, value) assayDataElementReplace(object, "CA", value))
11 
+		 function(object, value) assayDataElementReplace(object, "CA", value*100))
12 
+setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
13 
+		 function(object, value) assayDataElementReplace(object, "CB", value*100))
14 
+
15 
+
13 16
14 
-setMethod("chromosome", "CopyNumberSet", function(object) fData(object)$chromosome)
15 17
16 18 
 setMethod("batch", "CopyNumberSet", function(object){
17 19 
 	if("batch" %in% varLabels(object)){
... ... 
@@ -23,19 +25,23 @@ setMethod("batch", "CopyNumberSet", function(object){
23 25 
 })
24 26
25 27 
 setMethod("copyNumber", "CopyNumberSet", function(object){
28 
+	require(paste(annotation(object), "Crlmm", sep=""), character.only=TRUE) || stop(paste("Annotation package ", annotation(object), "Crlmm not available", sep=""))
26 29 
 	##ensure that 2 + NA = 2 by replacing NA's with zero
30 
+	##the above results in copy number 0, 1, or 2 depending on the genotype....safer just to drop
27 31 
 	CA <- CA(object)
28 32 
 	CB <- CB(object)
29 
-	nas <- is.na(CA) & is.na(CB)
30 
-	CA[is.na(CA)] <- 0
31 
-	CB[is.na(CB)] <- 0
33 
+	##nas <- is.na(CA) & is.na(CB)
34 
+	##CA[is.na(CA)] <- 0
35 
+	##CB[is.na(CB)] <- 0
32 36 
 	CN <- CA + CB
37 
+	##For nonpolymorphic probes, CA is the total copy number
38 
+	CN[cnIndex(object, annotation(object)), ] <- CA(object)[cnIndex(object, annotation(object)), ]
33 39 
 	##if both CA and CB are NA, report NA
34 
-	CN[nas] <- NA
40 
+	##CN[nas] <- NA
35 41 
 	CN
36 42 
 })
37 43
38 
-setMethod("position", "CopyNumberSet", function(object) fData(object)$position)
44 
+
39 45
40 46 
 ##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
41 47 
 ellipse.CopyNumberSet <- function(x, copynumber, ...){
... ... 
@@ -43,7 +49,15 @@ ellipse.CopyNumberSet <- function(x, copynumber, ...){
43 49 
 	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
44 50 
 	##index <- match(plates, fittedOrder)
45 51 
 	if(nrow(x) > 1) stop("only 1 snp at a time")
46 
-	batch <- unique(x$batch)
52 
+	##batch <- unique(x$batch)
53 
+	args <- list(...)
54 
+	if(!"batch" %in% names(args)){
55 
+		jj <- match("batch", varLabels(x))
56 
+		if(length(jj) < 1) stop("batch not in varLabels")
57 
+		batch <- unique(pData(x)[, jj])
58 
+	} else{
59 
+		batch <- unique(args$batch)
60 
+	}
47 61 
 	if(length(batch) > 1) stop("batch variable not unique")
48 62 
 	nuA <- as.numeric(fData(x)[, match(paste("nuA", batch, sep="_"), fvarLabels(x))])
49 63 
 	nuB <- as.numeric(fData(x)[, match(paste("nuB", batch, sep="_"), fvarLabels(x))])
... ... 
@@ -65,6 +79,7 @@ ellipse.CopyNumberSet <- function(x, copynumber, ...){
65 79 
 			if(CA == 0 & CB > 0) rho <- corrA.BB
66 80 
 			if(CA > 0 & CB == 0) rho <- corrB.AA
67 81 
 			if(CA > 0 & CB > 0) rho <- corr
82 
+			if(CA == 0 & CB == 0) rho <- 0
68 83 
 			lines(ellipse(x=rho, centre=c(log2(nuA+CA*phiA),
69 84 
 					     log2(nuB+CB*phiB)),
70 85 
 				      scale=scale), ...)
Browse code

computeCopynumber returns CrlmmSetList object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40618 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/07/2009 17:22:19
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ b9c7172
... ... 
@@ -3,8 +3,9 @@ setValidity("CopyNumberSet", function(object) {
3 3 
 	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
4 4 
 	if (is.null(msg)) TRUE else msg
5 5 
 })
6 
-setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]]/100)
7 
-setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]]/100)
6 
+##may want to allow thresholding here (... arg)
7 
+setMethod("CA", "CopyNumberSet", function(object, ...) assayData(object)[["CA"]]/100)
8 
+setMethod("CB", "CopyNumberSet", function(object, ...) assayData(object)[["CB"]]/100)
8 9 
 setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
9 10 
 		 function(object, value) assayDataElementReplace(object, "CB", value))
10 11 
 setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
... ... 
@@ -12,6 +13,14 @@ setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
12 13
13 14 
 setMethod("chromosome", "CopyNumberSet", function(object) fData(object)$chromosome)
14 15
16 
+setMethod("batch", "CopyNumberSet", function(object){
17 
+	if("batch" %in% varLabels(object)){
18 
+		result <- object$batch
19 
+	} else {
20 
+		stop("batch not in varLabels of CopyNumberSet")
21 
+	}
22 
+	return(result)
23 
+})
15 24
16 25 
 setMethod("copyNumber", "CopyNumberSet", function(object){
17 26 
 	##ensure that 2 + NA = 2 by replacing NA's with zero
... ... 
@@ -29,8 +38,8 @@ setMethod("copyNumber", "CopyNumberSet", function(object){
29 38 
 setMethod("position", "CopyNumberSet", function(object) fData(object)$position)
30 39
31 40 
 ##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
32 
-##ellipse.CopyNumberSet <- function(x, copynumber, ...){
33 
-setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
41 
+ellipse.CopyNumberSet <- function(x, copynumber, ...){
42 
+##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
34 43 
 	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
35 44 
 	##index <- match(plates, fittedOrder)
36 45 
 	if(nrow(x) > 1) stop("only 1 snp at a time")
... ... 
@@ -61,7 +70,7 @@ setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
61 70 
 				      scale=scale), ...)
62 71 
 		}
63 72 
 	}
64 
-})
73 
+}
65 74
66 75
67 76
Browse code

beginning of copy number methods for illumina. some work on copy number estimation for chromosome X

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40527 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 06/07/2009 19:24:27
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ 6446394
... ... 
@@ -3,15 +3,15 @@ setValidity("CopyNumberSet", function(object) {
3 3 
 	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
4 4 
 	if (is.null(msg)) TRUE else msg
5 5 
 })
6 
-setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]])
7 
-setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]])
6 
+setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]]/100)
7 
+setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]]/100)
8 8 
 setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
9 9 
 		 function(object, value) assayDataElementReplace(object, "CB", value))
10 10 
 setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
11 11 
 		 function(object, value) assayDataElementReplace(object, "CA", value))
12 12
13 13 
 setMethod("chromosome", "CopyNumberSet", function(object) fData(object)$chromosome)
14 
-setMethod("position", "CopyNumberSet", function(object) fData(object)$position)
14 
+
15 15
16 16 
 setMethod("copyNumber", "CopyNumberSet", function(object){
17 17 
 	##ensure that 2 + NA = 2 by replacing NA's with zero
... ... 
@@ -20,14 +20,17 @@ setMethod("copyNumber", "CopyNumberSet", function(object){
20 20 
 	nas <- is.na(CA) & is.na(CB)
21 21 
 	CA[is.na(CA)] <- 0
22 22 
 	CB[is.na(CB)] <- 0
23 
-	CN <- CA/100 + CB/100
23 
+	CN <- CA + CB
24 24 
 	##if both CA and CB are NA, report NA
25 25 
 	CN[nas] <- NA
26 26 
 	CN
27 27 
 })
28 28
29 
+setMethod("position", "CopyNumberSet", function(object) fData(object)$position)
30 
+
29 31 
 ##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
30 
-ellipse.CopyNumberSet <- function(x, copynumber, ...){
32 
+##ellipse.CopyNumberSet <- function(x, copynumber, ...){
33 
+setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
31 34 
 	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
32 35 
 	##index <- match(plates, fittedOrder)
33 36 
 	if(nrow(x) > 1) stop("only 1 snp at a time")
... ... 
@@ -58,7 +61,7 @@ ellipse.CopyNumberSet <- function(x, copynumber, ...){
58 61 
 				      scale=scale), ...)
59 62 
 		}
60 63 
 	}
61 
-}
64 
+})
62 65
63 66
64 67
Browse code

update computeCopynumber, added .R files for new classes/methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40371 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 29/06/2009 12:29:11
Showing 1 changed files
R/methods-CopyNumberSet.R
History View file @ 45dab54
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,65 @@
1 
+setValidity("CopyNumberSet", function(object) {
2 
+	##msg <- validMsg(NULL, Biobase:::isValidVersion(object, "CopyNumberSet"))
3 
+	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
4 
+	if (is.null(msg)) TRUE else msg
5 
+})
6 
+setMethod("CA", "CopyNumberSet", function(object) assayData(object)[["CA"]])
7 
+setMethod("CB", "CopyNumberSet", function(object) assayData(object)[["CB"]])
8 
+setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
9 
+		 function(object, value) assayDataElementReplace(object, "CB", value))
10 
+setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),
11 
+		 function(object, value) assayDataElementReplace(object, "CA", value))
12 
+
13 
+setMethod("chromosome", "CopyNumberSet", function(object) fData(object)$chromosome)
14 
+setMethod("position", "CopyNumberSet", function(object) fData(object)$position)
15 
+
16 
+setMethod("copyNumber", "CopyNumberSet", function(object){
17 
+	##ensure that 2 + NA = 2 by replacing NA's with zero
18 
+	CA <- CA(object)
19 
+	CB <- CB(object)
20 
+	nas <- is.na(CA) & is.na(CB)
21 
+	CA[is.na(CA)] <- 0
22 
+	CB[is.na(CB)] <- 0
23 
+	CN <- CA/100 + CB/100
24 
+	##if both CA and CB are NA, report NA
25 
+	CN[nas] <- NA
26 
+	CN
27 
+})
28 
+
29 
+##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){
30 
+ellipse.CopyNumberSet <- function(x, copynumber, ...){
31 
+	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
32 
+	##index <- match(plates, fittedOrder)
33 
+	if(nrow(x) > 1) stop("only 1 snp at a time")
34 
+	batch <- unique(x$batch)
35 
+	if(length(batch) > 1) stop("batch variable not unique")
36 
+	nuA <- as.numeric(fData(x)[, match(paste("nuA", batch, sep="_"), fvarLabels(x))])
37 
+	nuB <- as.numeric(fData(x)[, match(paste("nuB", batch, sep="_"), fvarLabels(x))])
38 
+	phiA <- as.numeric(fData(x)[, match(paste("phiA", batch, sep="_"), fvarLabels(x))])
39 
+	phiB <- as.numeric(fData(x)[, match(paste("phiB", batch, sep="_"), fvarLabels(x))])
40 
+	tau2A <- as.numeric(fData(x)[, match(paste("tau2A", batch, sep="_"), fvarLabels(x))])
41 
+	tau2B <- as.numeric(fData(x)[, match(paste("tau2B", batch, sep="_"), fvarLabels(x))])
42 
+	sig2A <- as.numeric(fData(x)[, match(paste("sig2A", batch, sep="_"), fvarLabels(x))])
43 
+	sig2B <- as.numeric(fData(x)[, match(paste("sig2B", batch, sep="_"), fvarLabels(x))])
44 
+	corrA.BB <- as.numeric(fData(x)[, match(paste("corrA.BB", batch, sep="_"), fvarLabels(x))])
45 
+	corrB.AA <- as.numeric(fData(x)[, match(paste("corrB.AA", batch, sep="_"), fvarLabels(x))])
46 
+	corr <- as.numeric(fData(x)[, match(paste("corr", batch, sep="_"), fvarLabels(x))])
47 
+	for(CN in copynumber){
48 
+		for(CA in 0:CN){
49 
+			CB <- CN-CA
50 
+			A.scale <- sqrt(tau2A*(CA==0) + sig2A*(CA > 0))
51 
+			B.scale <- sqrt(tau2B*(CB==0) + sig2B*(CB > 0))
52 
+			scale <- c(A.scale, B.scale)
53 
+			if(CA == 0 & CB > 0) rho <- corrA.BB
54 
+			if(CA > 0 & CB == 0) rho <- corrB.AA
55 
+			if(CA > 0 & CB > 0) rho <- corr
56 
+			lines(ellipse(x=rho, centre=c(log2(nuA+CA*phiA),
57 
+					     log2(nuB+CB*phiB)),
58 
+				      scale=scale), ...)
59 
+		}
60 
+	}
61 
+}
62 
+
63 
+
64 
+
65 
+