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

Merge branch 'collab'

* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/07/2012 19:00:03
Showing 1 changed files
R/methods-AssayData.R
History View file @ 063b3d1
... ... 
@@ -50,6 +50,21 @@ setMethod("medians", signature(object="AssayData"),
50 50 
 		  return(res)
51 51 
 })
52 52
53 
+getMedians <- function(object){
54 
+	medianA.AA <- assayDataElement(object, "medianA.AA")
55 
+	medianA.AB <- assayDataElement(object, "medianA.AB")
56 
+	medianA.BB <- assayDataElement(object, "medianA.BB")
57 
+	medianB.AA <- assayDataElement(object, "medianB.AA")
58 
+	medianB.AB <- assayDataElement(object, "medianB.AB")
59 
+	medianB.BB <- assayDataElement(object, "medianB.BB")
60 
+	list(A.AA=medianA.AA,
61 
+	     A.AB=medianA.AB,
62 
+	     A.BB=medianA.BB,
63 
+	     B.AA=medianB.AA,
64 
+	     B.AB=medianB.AB,
65 
+	     B.BB=medianB.BB)
66 
+}
67 
+
53 68 
 setMethod("mads", signature(object="AssayData"),
54 69 
 	  function(object, ...){
55 70 
 		  batchnames <- sampleNames(object)
Browse code

Simplify accessors for batch summaries: Ns, corr, medians, mads

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58646 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:48:38
Showing 1 changed files
R/methods-AssayData.R
History View file @ 6dc7b94
... ... 
@@ -1,120 +1,74 @@
1 
+
1 2 
 setMethod("Ns", signature(object="AssayData"),
2 3 
 	  function(object, ...){
3 
-		  dotArgs <- names(list(...))
4 
-		  missing.i <- !("i" %in% dotArgs)
5 
-		  missing.j <- !("j" %in% dotArgs)
6 
-		  if(!missing.j) j <- list(...)[["j"]]
7 4 
 		  batchnames <- sampleNames(object)
8 
-		  if(!missing.j) batchnames <- batchnames[j]
9 
-		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
10 
-		  is.ff <- is(assayDataElement(object, "N.AA"), "ff") | is(assayDataElement(object, "N.AA"), "ffdf")
11 
-		  if(is.ff){
12 
-			  open(assayDataElement(object, "N.AA"))
13 
-			  open(assayDataElement(object, "N.AB"))
14 
-			  open(assayDataElement(object, "N.BB"))
15 
-		  }
16 
-		  N.AA <- as.matrix(assayDataElement(object, "N.AA")[...])
17 
-		  N.AB <- as.matrix(assayDataElement(object, "N.AB")[...])
18 
-		  N.BB <- as.matrix(assayDataElement(object, "N.BB")[...])
19 
-		  if(is.ff){
20 
-			  close(assayDataElement(object, "N.AA"))
21 
-			  close(assayDataElement(object, "N.AB"))
22 
-			  close(assayDataElement(object, "N.BB"))
23 
-		  }
5 
+		  N.AA <- assayDataElement(object, "N.AA")
6 
+		  N.AB <- assayDataElement(object, "N.AB")
7 
+		  N.BB <- assayDataElement(object, "N.BB")
24 8 
 		  res <- array(NA, dim=c(nrow(N.AA), 3, ncol(N.AA)))
25 9 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
26 10 
 		  dimnames(res)[[3]] <- batchnames
27 
-		  res[, "AA", ] <- N.AA
28 
-		  res[, "AB", ] <- N.AB
29 
-		  res[, "BB", ] <- N.BB
11 
+		  res[, "AA", ] <- N.AA[,]
12 
+		  res[, "AB", ] <- N.AB[,]
13 
+		  res[, "BB", ] <- N.BB[,]
30 14 
 		  return(res)
31 15 
 	  })
32 16 
 setMethod("corr", signature(object="AssayData"),
33 17 
 	  function(object, ...){
34 
-		  dotArgs <- names(list(...))
35 
-		  missing.i <- !("i" %in% dotArgs)
36 
-		  missing.j <- !("j" %in% dotArgs)
37 
-		  if(!missing.j) j <- list(...)[["j"]]
38 18 
 		  batchnames <- sampleNames(object)
39 
-		  if(!missing.j) batchnames <- batchnames[j]
40 
-
41 
-		  ##if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
42 
-		  is.ff <- is(assayDataElement(object, "corrAA"), "ff") | is(assayDataElement(object, "corrAA"), "ffdf")
43 
-		  if(is.ff){
44 
-			  open(assayDataElement(object, "corrAA"))
45 
-			  open(assayDataElement(object, "corrAB"))
46 
-			  open(assayDataElement(object, "corrBB"))
47 
-		  }
48 
-		  corrAA <- as.matrix(assayDataElement(object, "corrAA")[...])
49 
-		  corrAB <- as.matrix(assayDataElement(object, "corrAB")[...])
50 
-		  corrBB <- as.matrix(assayDataElement(object, "corrBB")[...])
51 
-		  if(is.ff){
52 
-			  close(assayDataElement(object, "corrAA"))
53 
-			  close(assayDataElement(object, "corrAB"))
54 
-			  close(assayDataElement(object, "corrBB"))
55 
-		  }
19 
+		  corrAA <- assayDataElement(object, "corrAA")
20 
+		  corrAB <- assayDataElement(object, "corrAB")
21 
+		  corrBB <- assayDataElement(object, "corrBB")
56 22 
 		  res <- array(NA, dim=c(nrow(corrAA), 3, ncol(corrAA)))
57 23 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
58 24 
 		  dimnames(res)[[3]] <- batchnames
59 
-		  res[, "AA", ] <- corrAA
60 
-		  res[, "AB", ] <- corrAB
61 
-		  res[, "BB", ] <- corrBB
25 
+		  res[, "AA", ] <- corrAA[,]
26 
+		  res[, "AB", ] <- corrAB[,]
27 
+		  res[, "BB", ] <- corrBB[,]
62 28 
 		  return(res)
63 29 
 	  })
64 30
65 31 
 setMethod("medians", signature(object="AssayData"),
66 32 
 	  function(object, ...){
67 
-		  dotArgs <- names(list(...))
68 
-		  missing.i <- !("i" %in% dotArgs)
69 
-		  missing.j <- !("j" %in% dotArgs)
70 
-		  if(!missing.j) j <- list(...)[["j"]]
71 33 
 		  batchnames <- sampleNames(object)
72 
-		  if(!missing.j) batchnames <- batchnames[j]
73 
-		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
74 
-		  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA")[...])
75 
-		  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB")[...])
76 
-		  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB")[...])
77 
-		  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA")[...])
78 
-		  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB")[...])
79 
-		  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB")[...])
34 
+		  medianA.AA <- assayDataElement(object, "medianA.AA")
35 
+		  medianA.AB <- assayDataElement(object, "medianA.AB")
36 
+		  medianA.BB <- assayDataElement(object, "medianA.BB")
37 
+		  medianB.AA <- assayDataElement(object, "medianB.AA")
38 
+		  medianB.AB <- assayDataElement(object, "medianB.AB")
39 
+		  medianB.BB <- assayDataElement(object, "medianB.BB")
80 40 
 		  res <- array(NA, dim=c(nrow(medianA.AA), 2, 3, ncol(medianA.AA)))
81 41 
 		  dimnames(res)[[2]] <- c("A", "B")
82 42 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
83 43 
 		  dimnames(res)[[4]] <- batchnames
84 
-		  res[, "A", "AA", ] <- medianA.AA
85 
-		  res[, "A", "AB", ] <- medianA.AB
86 
-		  res[, "A", "BB", ] <- medianA.BB
87 
-		  res[, "B", "AA", ] <- medianB.AA
88 
-		  res[, "B", "AB", ] <- medianB.AB
89 
-		  res[, "B", "BB", ] <- medianB.BB
44 
+		  res[, "A", "AA", ] <- medianA.AA[,]
45 
+		  res[, "A", "AB", ] <- medianA.AB[,]
46 
+		  res[, "A", "BB", ] <- medianA.BB[,]
47 
+		  res[, "B", "AA", ] <- medianB.AA[,]
48 
+		  res[, "B", "AB", ] <- medianB.AB[,]
49 
+		  res[, "B", "BB", ] <- medianB.BB[,]
90 50 
 		  return(res)
91 51 
 })
92 52
93 53 
 setMethod("mads", signature(object="AssayData"),
94 54 
 	  function(object, ...){
95 
-		  dotArgs <- names(list(...))
96 
-		  missing.i <- !("i" %in% dotArgs)
97 
-		  missing.j <- !("j" %in% dotArgs)
98 55 
 		  batchnames <- sampleNames(object)
99 
-		  if(!missing.j) j <- list(...)[["j"]]
100 
-		  if(!missing.j) batchnames <- batchnames[j]
101 
-		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
102 
-		  madA.AA <- as.matrix(assayDataElement(object, "madA.AA")[...])
103 
-		  madA.AB <- as.matrix(assayDataElement(object, "madA.AB")[...])
104 
-		  madA.BB <- as.matrix(assayDataElement(object, "madA.BB")[...])
105 
-		  madB.AA <- as.matrix(assayDataElement(object, "madB.AA")[...])
106 
-		  madB.AB <- as.matrix(assayDataElement(object, "madB.AB")[...])
107 
-		  madB.BB <- as.matrix(assayDataElement(object, "madB.BB")[...])
56 
+		  madA.AA <- assayDataElement(object, "madA.AA")
57 
+		  madA.AB <- assayDataElement(object, "madA.AB")
58 
+		  madA.BB <- assayDataElement(object, "madA.BB")
59 
+		  madB.AA <- assayDataElement(object, "madB.AA")
60 
+		  madB.AB <- assayDataElement(object, "madB.AB")
61 
+		  madB.BB <- assayDataElement(object, "madB.BB")
108 62 
 		  res <- array(NA, dim=c(nrow(madA.AA), 2, 3, ncol(madA.AA)))
109 63 
 		  dimnames(res)[[2]] <- c("A", "B")
110 64 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
111 65 
 		  dimnames(res)[[4]] <- batchnames
112 
-		  res[, "A", "AA", ] <- madA.AA
113 
-		  res[, "A", "AB", ] <- madA.AB
114 
-		  res[, "A", "BB", ] <- madA.BB
115 
-		  res[, "B", "AA", ] <- madB.AA
116 
-		  res[, "B", "AB", ] <- madB.AB
117 
-		  res[, "B", "BB", ] <- madB.BB
66 
+		  res[, "A", "AA", ] <- madA.AA[,]
67 
+		  res[, "A", "AB", ] <- madA.AB[,]
68 
+		  res[, "A", "BB", ] <- madA.BB[,]
69 
+		  res[, "B", "AA", ] <- madB.AA[,]
70 
+		  res[, "B", "AB", ] <- madB.AB[,]
71 
+		  res[, "B", "BB", ] <- madB.BB[,]
118 72 
 		  return(res)
119 73 
 })
120 74
... ... 
@@ -122,25 +76,19 @@ setMethod("mads", signature(object="AssayData"),
122 76
123 77 
 setMethod("tau2", signature(object="AssayData"),
124 78 
 	  function(object, ...){
125 
-		  dotArgs <- names(list(...))
126 
-		  missing.i <- !("i" %in% dotArgs)
127 
-		  missing.j <- !("j" %in% dotArgs)
128 79 
 		  batchnames <- sampleNames(object)
129 
-		  if(!missing.j) j <- list(...)[["j"]]
130 
-		  if(!missing.j) batchnames <- batchnames[j]
131 
-		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
132 
-		  tau2A.AA <- as.matrix(assayDataElement(object, "tau2A.AA")[...])
133 
-		  tau2A.BB <- as.matrix(assayDataElement(object, "tau2A.BB")[...])
134 
-		  tau2B.AA <- as.matrix(assayDataElement(object, "tau2B.AA")[...])
135 
-		  tau2B.BB <- as.matrix(assayDataElement(object, "tau2B.BB")[...])
80 
+		  tau2A.AA <- assayDataElement(object, "tau2A.AA")
81 
+		  tau2A.BB <- assayDataElement(object, "tau2A.BB")
82 
+		  tau2B.AA <- assayDataElement(object, "tau2B.AA")
83 
+		  tau2B.BB <- assayDataElement(object, "tau2B.BB")
136 84 
 		  res <- array(NA, dim=c(nrow(tau2A.AA), 2, 2, ncol(tau2A.AA)))
137 85 
 		  dimnames(res)[[2]] <- c("A", "B")
138 86 
 		  dimnames(res)[[3]] <- c("AA", "BB")
139 87 
 		  dimnames(res)[[4]] <- batchnames
140 
-		  res[, "A", "AA", ] <- tau2A.AA
141 
-		  res[, "A", "BB", ] <- tau2A.BB
142 
-		  res[, "B", "AA", ] <- tau2B.AA
143 
-		  res[, "B", "BB", ] <- tau2B.BB
88 
+		  res[, "A", "AA", ] <- tau2A.AA[,]
89 
+		  res[, "A", "BB", ] <- tau2A.BB[,]
90 
+		  res[, "B", "AA", ] <- tau2B.AA[,]
91 
+		  res[, "B", "BB", ] <- tau2B.BB[,]
144 92 
 		  return(res)
145 93 
 })
146 94
Browse code

Add generics and methods for predictionRegion, posteriorProbability, and calculatePosteriorMean.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58630 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:46:51
Showing 1 changed files
R/methods-AssayData.R
History View file @ e516fad
... ... 
@@ -37,7 +37,8 @@ setMethod("corr", signature(object="AssayData"),
37 37 
 		  if(!missing.j) j <- list(...)[["j"]]
38 38 
 		  batchnames <- sampleNames(object)
39 39 
 		  if(!missing.j) batchnames <- batchnames[j]
40 
-		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
40 
+
41 
+		  ##if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
41 42 
 		  is.ff <- is(assayDataElement(object, "corrAA"), "ff") | is(assayDataElement(object, "corrAA"), "ffdf")
42 43 
 		  if(is.ff){
43 44 
 			  open(assayDataElement(object, "corrAA"))
Browse code

Add illumina_copynumber.pdf to package.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49895 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2010 02:21:53
Showing 1 changed files
R/methods-AssayData.R
History View file @ fd0501a
... ... 
@@ -7,7 +7,7 @@ setMethod("Ns", signature(object="AssayData"),
7 7 
 		  batchnames <- sampleNames(object)
8 8 
 		  if(!missing.j) batchnames <- batchnames[j]
9 9 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
10 
-		  is.ff <- is(assayDataElement(object, "N.AA"), "ff")
10 
+		  is.ff <- is(assayDataElement(object, "N.AA"), "ff") | is(assayDataElement(object, "N.AA"), "ffdf")
11 11 
 		  if(is.ff){
12 12 
 			  open(assayDataElement(object, "N.AA"))
13 13 
 			  open(assayDataElement(object, "N.AB"))
... ... 
@@ -38,7 +38,7 @@ setMethod("corr", signature(object="AssayData"),
38 38 
 		  batchnames <- sampleNames(object)
39 39 
 		  if(!missing.j) batchnames <- batchnames[j]
40 40 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
41 
-		  is.ff <- is(assayDataElement(object, "corrAA"), "ff")
41 
+		  is.ff <- is(assayDataElement(object, "corrAA"), "ff") | is(assayDataElement(object, "corrAA"), "ffdf")
42 42 
 		  if(is.ff){
43 43 
 			  open(assayDataElement(object, "corrAA"))
44 44 
 			  open(assayDataElement(object, "corrAB"))
Browse code

Revised accesors in methods-AssayData -- some of the conflicts resolved by hand during rebase were incorrect

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49140 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:03
Showing 1 changed files
R/methods-AssayData.R
History View file @ 56b783e
... ... 
@@ -24,30 +24,6 @@ setMethod("Ns", signature(object="AssayData"),
24 24 
 		  res <- array(NA, dim=c(nrow(N.AA), 3, ncol(N.AA)))
25 25 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
26 26 
 		  dimnames(res)[[3]] <- batchnames
27 
-		  if(missing(i) & missing(j)){
28 
-			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))
29 
-			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))
30 
-			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))
31 
-		  }
32 
-		  if(missing(i) & !missing(j)){
33 
-			  J <- match(batchnames, batchNames(object))
34 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
35 
-			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[, J, ...]
36 
-			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[, J, ...]
37 
-			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[, J, ...]
38 
-		  }
39 
-		  if(!missing(i) & !missing(j)){
40 
-			  J <- match(batchnames, batchNames(object))
41 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
42 
-			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[i, J, ...]
43 
-			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[i, J, ...]
44 
-			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[i, J, ...]
45 
-		  }
46 
-		  if(!missing(i) & missing(j)){
47 
-			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[i, , ...]
48 
-			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[i, , ...]
49 
-			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[i, , ...]
50 
-		  }
51 27 
 		  res[, "AA", ] <- N.AA
52 28 
 		  res[, "AB", ] <- N.AB
53 29 
 		  res[, "BB", ] <- N.BB
... ... 
@@ -79,30 +55,6 @@ setMethod("corr", signature(object="AssayData"),
79 55 
 		  res <- array(NA, dim=c(nrow(corrAA), 3, ncol(corrAA)))
80 56 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
81 57 
 		  dimnames(res)[[3]] <- batchnames
82 
-		  if(missing(i) & missing(j)){
83 
-			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))
84 
-			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))
85 
-			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))
86 
-		  }
87 
-		  if(missing(i) & !missing(j)){
88 
-			  J <- match(batchnames, batchNames(object))
89 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
90 
-			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[, J, ...]
91 
-			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[, J, ...]
92 
-			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[, J, ...]
93 
-		  }
94 
-		  if(!missing(i) & !missing(j)){
95 
-			  J <- match(batchnames, batchNames(object))
96 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
97 
-			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[i, J, ...]
98 
-			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[i, J, ...]
99 
-			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[i, J, ...]
100 
-		  }
101 
-		  if(!missing(i) & missing(j)){
102 
-			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[i, , ...]
103 
-			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[i, , ...]
104 
-			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[i, , ...]
105 
-		  }
106 58 
 		  res[, "AA", ] <- corrAA
107 59 
 		  res[, "AB", ] <- corrAB
108 60 
 		  res[, "BB", ] <- corrBB
... ... 
@@ -128,43 +80,6 @@ setMethod("medians", signature(object="AssayData"),
128 80 
 		  dimnames(res)[[2]] <- c("A", "B")
129 81 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
130 82 
 		  dimnames(res)[[4]] <- batchnames
131 
-		  if(missing(i) & missing(j)){
132 
-			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))
133 
-			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))
134 
-			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))
135 
-			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))
136 
-			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))
137 
-			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))
138 
-		  }
139 
-		  if(missing(i) & !missing(j)){
140 
-			  J <- match(batchnames, batchNames(object))
141 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
142 
-			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[, J, ...]
143 
-			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[, J, ...]
144 
-			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[, J, ...]
145 
-			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[, J, ...]
146 
-			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[, J, ...]
147 
-			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[, J, ...]
148 
-
149 
-		  }
150 
-		  if(!missing(i) & !missing(j)){
151 
-			  J <- match(batchnames, batchNames(object))
152 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
153 
-			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[i, J, ...]
154 
-			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[i, J, ...]
155 
-			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[i, J, ...]
156 
-			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[i, J, ...]
157 
-			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[i, J, ...]
158 
-			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[i, J, ...]
159 
-		  }
160 
-		  if(!missing(i) & missing(j)){
161 
-			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[i, ...]
162 
-			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[i, ...]
163 
-			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[i, ...]
164 
-			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[i, ...]
165 
-			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[i, ...]
166 
-			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[i, ...]
167 
-		  }
168 83 
 		  res[, "A", "AA", ] <- medianA.AA
169 84 
 		  res[, "A", "AB", ] <- medianA.AB
170 85 
 		  res[, "A", "BB", ] <- medianA.BB
... ... 
@@ -193,43 +108,6 @@ setMethod("mads", signature(object="AssayData"),
193 108 
 		  dimnames(res)[[2]] <- c("A", "B")
194 109 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
195 110 
 		  dimnames(res)[[4]] <- batchnames
196 
-		  if(missing(i) & missing(j)){
197 
-			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))
198 
-			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))
199 
-			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))
200 
-			  madB.AA <- as.matrix(assayDataElement(object, "madB.AA"))
201 
-			  madB.AB <- as.matrix(assayDataElement(object, "madB.AB"))
202 
-			  madB.BB <- as.matrix(assayDataElement(object, "madB.BB"))
203 
-		  }
204 
-		  if(missing(i) & !missing(j)){
205 
-			  J <- match(batchnames, batchNames(object))
206 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
207 
-			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[, J, ...]
208 
-			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[, J, ...]
209 
-			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))[, J, ...]
210 
-			  madB.AA <- as.matrix(assayDataElement(object, "madB.AA"))[, J, ...]
211 
-			  madB.AB <- as.matrix(assayDataElement(object, "madB.AB"))[, J, ...]
212 
-			  madB.BB <- as.matrix(assayDataElement(object, "madB.BB"))[, J, ...]
213 
-
214 
-		  }
215 
-		  if(!missing(i) & !missing(j)){
216 
-			  J <- match(batchnames, batchNames(object))
217 
-			  stopifnot(length(J) > 0 & !all(is.na(J)))
218 
-			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[i, J, ...]
219 
-			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[i, J, ...]
220 
-			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))[i, J, ...]
221 
-			  madB.AA <- as.matrix(assayDataElement(object, "madB.AA"))[i, J, ...]
222 
-			  madB.AB <- as.matrix(assayDataElement(object, "madB.AB"))[i, J, ...]
223 
-			  madB.BB <- as.matrix(assayDataElement(object, "madB.BB"))[i, J, ...]
224 
-		  }
225 
-		  if(!missing(i) & missing(j)){
226 
-			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[i, ...]
227 
-			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[i, ...]
228 
-			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))[i, ...]
229 
-			  madB.AA <- as.matrix(assayDataElement(object, "madB.AA"))[i, ...]
230 
-			  madB.AB <- as.matrix(assayDataElement(object, "madB.AB"))[i, ...]
231 
-			  madB.BB <- as.matrix(assayDataElement(object, "madB.BB"))[i, ...]
232 
-		  }
233 111 
 		  res[, "A", "AA", ] <- madA.AA
234 112 
 		  res[, "A", "AB", ] <- madA.AB
235 113 
 		  res[, "A", "BB", ] <- madA.BB
Browse code

added open and close statements in Ns and corr accessors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49137 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:57
Showing 1 changed files
R/methods-AssayData.R
History View file @ 1b3b1c3
... ... 
@@ -7,9 +7,20 @@ setMethod("Ns", signature(object="AssayData"),
7 7 
 		  batchnames <- sampleNames(object)
8 8 
 		  if(!missing.j) batchnames <- batchnames[j]
9 9 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
10 
+		  is.ff <- is(assayDataElement(object, "N.AA"), "ff")
11 
+		  if(is.ff){
12 
+			  open(assayDataElement(object, "N.AA"))
13 
+			  open(assayDataElement(object, "N.AB"))
14 
+			  open(assayDataElement(object, "N.BB"))
15 
+		  }
10 16 
 		  N.AA <- as.matrix(assayDataElement(object, "N.AA")[...])
11 17 
 		  N.AB <- as.matrix(assayDataElement(object, "N.AB")[...])
12 18 
 		  N.BB <- as.matrix(assayDataElement(object, "N.BB")[...])
19 
+		  if(is.ff){
20 
+			  close(assayDataElement(object, "N.AA"))
21 
+			  close(assayDataElement(object, "N.AB"))
22 
+			  close(assayDataElement(object, "N.BB"))
23 
+		  }
13 24 
 		  res <- array(NA, dim=c(nrow(N.AA), 3, ncol(N.AA)))
14 25 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
15 26 
 		  dimnames(res)[[3]] <- batchnames
... ... 
@@ -51,9 +62,20 @@ setMethod("corr", signature(object="AssayData"),
51 62 
 		  batchnames <- sampleNames(object)
52 63 
 		  if(!missing.j) batchnames <- batchnames[j]
53 64 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
65 
+		  is.ff <- is(assayDataElement(object, "corrAA"), "ff")
66 
+		  if(is.ff){
67 
+			  open(assayDataElement(object, "corrAA"))
68 
+			  open(assayDataElement(object, "corrAB"))
69 
+			  open(assayDataElement(object, "corrBB"))
70 
+		  }
54 71 
 		  corrAA <- as.matrix(assayDataElement(object, "corrAA")[...])
55 72 
 		  corrAB <- as.matrix(assayDataElement(object, "corrAB")[...])
56 73 
 		  corrBB <- as.matrix(assayDataElement(object, "corrBB")[...])
74 
+		  if(is.ff){
75 
+			  close(assayDataElement(object, "corrAA"))
76 
+			  close(assayDataElement(object, "corrAB"))
77 
+			  close(assayDataElement(object, "corrBB"))
78 
+		  }
57 79 
 		  res <- array(NA, dim=c(nrow(corrAA), 3, ncol(corrAA)))
58 80 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
59 81 
 		  dimnames(res)[[3]] <- batchnames
Browse code

CB estimates were NA for SNP indices were mixed with NP indices. Bug was fixed in the ACN function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49136 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:54
Showing 1 changed files
R/methods-AssayData.R
History View file @ d5b39e2
... ... 
@@ -43,7 +43,7 @@ setMethod("Ns", signature(object="AssayData"),
43 43 
 		  return(res)
44 44 
 	  })
45 45 
 setMethod("corr", signature(object="AssayData"),
46 
-	  function(object, i, j, ...){
46 
+	  function(object, ...){
47 47 
 		  dotArgs <- names(list(...))
48 48 
 		  missing.i <- !("i" %in% dotArgs)
49 49 
 		  missing.j <- !("j" %in% dotArgs)
Browse code

Fixed several bugs in the CA, CB, ACN functions. Updated the copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49132 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:42
Showing 1 changed files
R/methods-AssayData.R
History View file @ 0198a9a
... ... 
@@ -3,7 +3,8 @@ setMethod("Ns", signature(object="AssayData"),
3 3 
 		  dotArgs <- names(list(...))
4 4 
 		  missing.i <- !("i" %in% dotArgs)
5 5 
 		  missing.j <- !("j" %in% dotArgs)
6 
-		  batchnames <- batchNames(object)
6 
+		  if(!missing.j) j <- list(...)[["j"]]
7 
+		  batchnames <- sampleNames(object)
7 8 
 		  if(!missing.j) batchnames <- batchnames[j]
8 9 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
9 10 
 		  N.AA <- as.matrix(assayDataElement(object, "N.AA")[...])
... ... 
@@ -46,7 +47,8 @@ setMethod("corr", signature(object="AssayData"),
46 47 
 		  dotArgs <- names(list(...))
47 48 
 		  missing.i <- !("i" %in% dotArgs)
48 49 
 		  missing.j <- !("j" %in% dotArgs)
49 
-		  batchnames <- batchNames(object)
50 
+		  if(!missing.j) j <- list(...)[["j"]]
51 
+		  batchnames <- sampleNames(object)
50 52 
 		  if(!missing.j) batchnames <- batchnames[j]
51 53 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
52 54 
 		  corrAA <- as.matrix(assayDataElement(object, "corrAA")[...])
... ... 
@@ -90,7 +92,8 @@ setMethod("medians", signature(object="AssayData"),
90 92 
 		  dotArgs <- names(list(...))
91 93 
 		  missing.i <- !("i" %in% dotArgs)
92 94 
 		  missing.j <- !("j" %in% dotArgs)
93 
-		  batchnames <- batchNames(object)
95 
+		  if(!missing.j) j <- list(...)[["j"]]
96 
+		  batchnames <- sampleNames(object)
94 97 
 		  if(!missing.j) batchnames <- batchnames[j]
95 98 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
96 99 
 		  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA")[...])
... ... 
@@ -154,7 +157,8 @@ setMethod("mads", signature(object="AssayData"),
154 157 
 		  dotArgs <- names(list(...))
155 158 
 		  missing.i <- !("i" %in% dotArgs)
156 159 
 		  missing.j <- !("j" %in% dotArgs)
157 
-		  batchnames <- batchNames(object)
160 
+		  batchnames <- sampleNames(object)
161 
+		  if(!missing.j) j <- list(...)[["j"]]
158 162 
 		  if(!missing.j) batchnames <- batchnames[j]
159 163 
 		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
160 164 
 		  madA.AA <- as.matrix(assayDataElement(object, "madA.AA")[...])
... ... 
@@ -216,26 +220,27 @@ setMethod("mads", signature(object="AssayData"),
216 220
217 221
218 222 
 setMethod("tau2", signature(object="AssayData"),
219 
-	  function(object, allele, batchname){
220 
-		  stopifnot(!missing(allele))
221 
-		  if(missing(batchname) & length(sampleNames(object)) > 1)
222 
-			  stop("must supply batchname")
223 
-		  if(!missing(batchname)){
224 
-			  stopifnot(batchname %in% batchNames(object))
225 
-			  j <- match(batchname, sampleNames(object))
226 
-		  } else j <- 1
227 
-		  getTaus <- function(allele){
228 
-			  switch(allele,
229 
-				 A=cbind(assayDataElement(object, "tau2A.AA")[, j],
230 
-				         assayDataElement(object, "tau2A.AB")[, j],
231 
-         			         assayDataElement(object, "tau2A.BB")[, j]),
232 
-				 B=cbind(assayDataElement(object, "tau2B.AA")[, j],
233 
-				         assayDataElement(object, "tau2B.AB")[, j],
234 
-				         assayDataElement(object, "tau2B.BB")[, j]),
235 
-				 stop("allele must be 'A' or 'B'")
236 
-				 )
237 
-		  }
238 
-		  getTaus(allele)
223 
+	  function(object, ...){
224 
+		  dotArgs <- names(list(...))
225 
+		  missing.i <- !("i" %in% dotArgs)
226 
+		  missing.j <- !("j" %in% dotArgs)
227 
+		  batchnames <- sampleNames(object)
228 
+		  if(!missing.j) j <- list(...)[["j"]]
229 
+		  if(!missing.j) batchnames <- batchnames[j]
230 
+		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
231 
+		  tau2A.AA <- as.matrix(assayDataElement(object, "tau2A.AA")[...])
232 
+		  tau2A.BB <- as.matrix(assayDataElement(object, "tau2A.BB")[...])
233 
+		  tau2B.AA <- as.matrix(assayDataElement(object, "tau2B.AA")[...])
234 
+		  tau2B.BB <- as.matrix(assayDataElement(object, "tau2B.BB")[...])
235 
+		  res <- array(NA, dim=c(nrow(tau2A.AA), 2, 2, ncol(tau2A.AA)))
236 
+		  dimnames(res)[[2]] <- c("A", "B")
237 
+		  dimnames(res)[[3]] <- c("AA", "BB")
238 
+		  dimnames(res)[[4]] <- batchnames
239 
+		  res[, "A", "AA", ] <- tau2A.AA
240 
+		  res[, "A", "BB", ] <- tau2A.BB
241 
+		  res[, "B", "AA", ] <- tau2B.AA
242 
+		  res[, "B", "BB", ] <- tau2B.BB
243 
+		  return(res)
239 244 
 })
240 245
241 246
Browse code

constructIlluminaAssayData allows for either ff or matrices. Fixed bug in accessors for medians, mads, ...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49131 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:33
Showing 1 changed files
R/methods-AssayData.R
History View file @ 3e4db4b
... ... 
@@ -1,11 +1,15 @@
1 1 
 setMethod("Ns", signature(object="AssayData"),
2 
-	  function(object, i, j, ...){
3 
-		  if(!missing(j)){
4 
-			  batchnames <- unique(as.character(batch(object)[j]))
5 
-		  } else batchnames <- batchNames(object)
6 
-		  nc <- length(batchnames)
7 
-		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
8 
-		  res <- array(NA, dim=c(nr, 3, nc))
2 
+	  function(object, ...){
3 
+		  dotArgs <- names(list(...))
4 
+		  missing.i <- !("i" %in% dotArgs)
5 
+		  missing.j <- !("j" %in% dotArgs)
6 
+		  batchnames <- batchNames(object)
7 
+		  if(!missing.j) batchnames <- batchnames[j]
8 
+		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
9 
+		  N.AA <- as.matrix(assayDataElement(object, "N.AA")[...])
10 
+		  N.AB <- as.matrix(assayDataElement(object, "N.AB")[...])
11 
+		  N.BB <- as.matrix(assayDataElement(object, "N.BB")[...])
12 
+		  res <- array(NA, dim=c(nrow(N.AA), 3, ncol(N.AA)))
9 13 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
10 14 
 		  dimnames(res)[[3]] <- batchnames
11 15 
 		  if(missing(i) & missing(j)){
... ... 
@@ -39,12 +43,16 @@ setMethod("Ns", signature(object="AssayData"),
39 43 
 	  })
40 44 
 setMethod("corr", signature(object="AssayData"),
41 45 
 	  function(object, i, j, ...){
42 
-		  if(!missing(j)){
43 
-			  batchnames <- unique(as.character(batch(object)[j]))
44 
-		  } else batchnames <- batchNames(object)
45 
-		  nc <- length(batchnames)
46 
-		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
47 
-		  res <- array(NA, dim=c(nr, 3, nc))
46 
+		  dotArgs <- names(list(...))
47 
+		  missing.i <- !("i" %in% dotArgs)
48 
+		  missing.j <- !("j" %in% dotArgs)
49 
+		  batchnames <- batchNames(object)
50 
+		  if(!missing.j) batchnames <- batchnames[j]
51 
+		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
52 
+		  corrAA <- as.matrix(assayDataElement(object, "corrAA")[...])
53 
+		  corrAB <- as.matrix(assayDataElement(object, "corrAB")[...])
54 
+		  corrBB <- as.matrix(assayDataElement(object, "corrBB")[...])
55 
+		  res <- array(NA, dim=c(nrow(corrAA), 3, ncol(corrAA)))
48 56 
 		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
49 57 
 		  dimnames(res)[[3]] <- batchnames
50 58 
 		  if(missing(i) & missing(j)){
... ... 
@@ -78,13 +86,20 @@ setMethod("corr", signature(object="AssayData"),
78 86 
 	  })
79 87
80 88 
 setMethod("medians", signature(object="AssayData"),
81 
-	  function(object, i, j, ...){
82 
-		  if(!missing(j)){
83 
-			  batchnames <- unique(as.character(batch(object)[j]))
84 
-		  } else batchnames <- batchNames(object)
85 
-		  nc <- length(batchnames)
86 
-		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
87 
-		  res <- array(NA, dim=c(nr, 2, 3, nc))
89 
+	  function(object, ...){
90 
+		  dotArgs <- names(list(...))
91 
+		  missing.i <- !("i" %in% dotArgs)
92 
+		  missing.j <- !("j" %in% dotArgs)
93 
+		  batchnames <- batchNames(object)
94 
+		  if(!missing.j) batchnames <- batchnames[j]
95 
+		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
96 
+		  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA")[...])
97 
+		  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB")[...])
98 
+		  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB")[...])
99 
+		  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA")[...])
100 
+		  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB")[...])
101 
+		  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB")[...])
102 
+		  res <- array(NA, dim=c(nrow(medianA.AA), 2, 3, ncol(medianA.AA)))
88 103 
 		  dimnames(res)[[2]] <- c("A", "B")
89 104 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
90 105 
 		  dimnames(res)[[4]] <- batchnames
... ... 
@@ -134,14 +149,21 @@ setMethod("medians", signature(object="AssayData"),
134 149 
 		  return(res)
135 150 
 })
136 151
137 
-setMethod("medians", signature(object="AssayData"),
138 
-	  function(object, i, j, ...){
139 
-		  if(!missing(j)){
140 
-			  batchnames <- unique(as.character(batch(object)[j]))
141 
-		  } else batchnames <- batchNames(object)
142 
-		  nc <- length(batchnames)
143 
-		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
144 
-		  res <- array(NA, dim=c(nr, 2, 3, nc))
152 
+setMethod("mads", signature(object="AssayData"),
153 
+	  function(object, ...){
154 
+		  dotArgs <- names(list(...))
155 
+		  missing.i <- !("i" %in% dotArgs)
156 
+		  missing.j <- !("j" %in% dotArgs)
157 
+		  batchnames <- batchNames(object)
158 
+		  if(!missing.j) batchnames <- batchnames[j]
159 
+		  if(missing.i & missing.j) stop("Must specify either the rows i or batches j")
160 
+		  madA.AA <- as.matrix(assayDataElement(object, "madA.AA")[...])
161 
+		  madA.AB <- as.matrix(assayDataElement(object, "madA.AB")[...])
162 
+		  madA.BB <- as.matrix(assayDataElement(object, "madA.BB")[...])
163 
+		  madB.AA <- as.matrix(assayDataElement(object, "madB.AA")[...])
164 
+		  madB.AB <- as.matrix(assayDataElement(object, "madB.AB")[...])
165 
+		  madB.BB <- as.matrix(assayDataElement(object, "madB.BB")[...])
166 
+		  res <- array(NA, dim=c(nrow(madA.AA), 2, 3, ncol(madA.AA)))
145 167 
 		  dimnames(res)[[2]] <- c("A", "B")
146 168 
 		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
147 169 
 		  dimnames(res)[[4]] <- batchnames
Browse code

methods Ns, medians, corr, and mads return arrays.

Ns and corr return an array with dimension: features x genotype x batch

medians and mads return an array with dimension: features x allele x genotype x batch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48964 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:19
Showing 1 changed files
R/methods-AssayData.R
History View file @ fda1107
... ... 
@@ -1,99 +1,198 @@
1 1 
 setMethod("Ns", signature(object="AssayData"),
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-	  function(object, genotype, batchname){
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-		  if(missing(batchname) & length(sampleNames(object)) > 1)
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-			  stop("must supply batchname")
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-		  if(!missing(batchname)){
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-			  stopifnot(batchname %in% batchNames(object))
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-			  j <- match(batchname, sampleNames(object))
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-		  } else j <- 1
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-		  if(missing(genotype)){
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-			  res <- cbind(assayDataElement(object, "N.AA")[, j],
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-				       assayDataElement(object, "N.AB")[, j],
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-				       assayDataElement(object, "N.BB")[, j])
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-			  return(res)
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-		  } else{
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-			  getValue <- function(genotype){
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-				  switch(genotype,
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-					 AA="N.AA",
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-					 AB="N.AB",
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-					 BB="N.BB",
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-					 stop("allele must be 'AA', 'AB', or 'BB'"))
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-			  }
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-			  val <- getValue(genotype)
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-			  return(assayDataElement(object, val)[, j])
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+	  function(object, i, j, ...){
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+		  if(!missing(j)){
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+			  batchnames <- unique(as.character(batch(object)[j]))
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+		  } else batchnames <- batchNames(object)
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+		  nc <- length(batchnames)
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+		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
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+		  res <- array(NA, dim=c(nr, 3, nc))
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+		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
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+		  dimnames(res)[[3]] <- batchnames
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+		  if(missing(i) & missing(j)){
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+			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))
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+			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))
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+			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))
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+		  }
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+		  if(missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[, J, ...]
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+			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[, J, ...]
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+			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[, J, ...]
24 22 
 		  }
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+		  if(!missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[i, J, ...]
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+			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[i, J, ...]
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+			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[i, J, ...]
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+		  }
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+		  if(!missing(i) & missing(j)){
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+			  N.AA <- as.matrix(assayDataElement(object, "N.AA"))[i, , ...]
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+			  N.AB <- as.matrix(assayDataElement(object, "N.AB"))[i, , ...]
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+			  N.BB <- as.matrix(assayDataElement(object, "N.BB"))[i, , ...]
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+		  }
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+		  res[, "AA", ] <- N.AA
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+		  res[, "AB", ] <- N.AB
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+		  res[, "BB", ] <- N.BB
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+		  return(res)
25 39 
 	  })
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 setMethod("corr", signature(object="AssayData"),
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-	  function(object, genotype, batchname){
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-		  if(missing(batchname) & length(sampleNames(object)) > 1)
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-			  stop("must supply batchname")
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-		  if(!missing(batchname)){
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-			  stopifnot(batchname %in% batchNames(object))
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-			  j <- match(batchname, sampleNames(object))
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-		  } else j <- 1
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-		  if(missing(genotype)){
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-			  res <- cbind(assayDataElement(object, "corrAA")[, j],
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-				       assayDataElement(object, "corrAB")[, j],
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-				       assayDataElement(object, "corrBB")[, j])
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-			  return(res)
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-		  } else{
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-			  getValue <- function(genotype){
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-				  switch(genotype,
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-					 AA="corrAA",
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-					 AB="corrAB",
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-					 BB="corrBB",
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-					 stop("allele must be 'AA', 'AB', or 'BB'"))
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-			  }
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-			  val <- getValue(genotype)
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-			  return(assayDataElement(object, val)[, j])
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+	  function(object, i, j, ...){
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+		  if(!missing(j)){
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+			  batchnames <- unique(as.character(batch(object)[j]))
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+		  } else batchnames <- batchNames(object)
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+		  nc <- length(batchnames)
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+		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
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+		  res <- array(NA, dim=c(nr, 3, nc))
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+		  dimnames(res)[[2]] <- c("AA", "AB", "BB")
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+		  dimnames(res)[[3]] <- batchnames
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+		  if(missing(i) & missing(j)){
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+			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))
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+			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))
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+			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))
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+		  }
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+		  if(missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[, J, ...]
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+			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[, J, ...]
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+			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[, J, ...]
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+		  }
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+		  if(!missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[i, J, ...]
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+			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[i, J, ...]
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+			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[i, J, ...]
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 		  }
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+		  if(!missing(i) & missing(j)){
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+			  corrAA <- as.matrix(assayDataElement(object, "corrAA"))[i, , ...]
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+			  corrAB <- as.matrix(assayDataElement(object, "corrAB"))[i, , ...]
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+			  corrBB <- as.matrix(assayDataElement(object, "corrBB"))[i, , ...]
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+		  }
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+		  res[, "AA", ] <- corrAA
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+		  res[, "AB", ] <- corrAB
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+		  res[, "BB", ] <- corrBB
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+		  return(res)
50 78 
 	  })
51 79
52 80 
 setMethod("medians", signature(object="AssayData"),
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-	  function(object, allele, batchname){
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-		  stopifnot(!missing(allele))
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-		  if(missing(batchname) & length(sampleNames(object)) > 1)
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-			  stop("must supply batchname")
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-		  if(!missing(batchname)){
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-			  stopifnot(batchname %in% batchNames(object))
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-			  j <- match(batchname, sampleNames(object))
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-		  } else j <- 1
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-		  getMedians <- function(allele){
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-			  switch(allele,
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-				 A=cbind(assayDataElement(object, "medianA.AA")[, j],
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-				         assayDataElement(object, "medianA.AB")[, j],
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-         			         assayDataElement(object, "medianA.BB")[, j]),
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-				 B=cbind(assayDataElement(object, "medianB.AA")[, j],
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-				         assayDataElement(object, "medianB.AB")[, j],
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-				         assayDataElement(object, "medianB.BB")[, j]),
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-				 stop("allele must be 'A' or 'B'")
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-				 )
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+	  function(object, i, j, ...){
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+		  if(!missing(j)){
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+			  batchnames <- unique(as.character(batch(object)[j]))
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+		  } else batchnames <- batchNames(object)
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+		  nc <- length(batchnames)
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+		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
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+		  res <- array(NA, dim=c(nr, 2, 3, nc))
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+		  dimnames(res)[[2]] <- c("A", "B")
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+		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
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+		  dimnames(res)[[4]] <- batchnames
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+		  if(missing(i) & missing(j)){
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+			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))
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+			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))
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+			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))
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+			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))
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+			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))
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+			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))
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+		  }
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+		  if(missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[, J, ...]
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+			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[, J, ...]
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+			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[, J, ...]
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+			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[, J, ...]
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+			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[, J, ...]
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+			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[, J, ...]
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+
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+		  }
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+		  if(!missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[i, J, ...]
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+			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[i, J, ...]
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+			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[i, J, ...]
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+			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[i, J, ...]
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+			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[i, J, ...]
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+			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[i, J, ...]
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+		  }
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+		  if(!missing(i) & missing(j)){
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+			  medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[i, ...]
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+			  medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[i, ...]
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+			  medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB"))[i, ...]
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+			  medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA"))[i, ...]
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+			  medianB.AB <- as.matrix(assayDataElement(object, "medianB.AB"))[i, ...]
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+			  medianB.BB <- as.matrix(assayDataElement(object, "medianB.BB"))[i, ...]
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 		  }
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-		  getMedians(allele)
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+		  res[, "A", "AA", ] <- medianA.AA
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+		  res[, "A", "AB", ] <- medianA.AB
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+		  res[, "A", "BB", ] <- medianA.BB
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+		  res[, "B", "AA", ] <- medianB.AA
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+		  res[, "B", "AB", ] <- medianB.AB
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+		  res[, "B", "BB", ] <- medianB.BB
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+		  return(res)
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 })
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-setMethod("mads", signature(object="AssayData"),
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-	  function(object, allele, batchname){
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-		  stopifnot(!missing(allele))
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-		  if(missing(batchname) & length(sampleNames(object)) > 1)
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-			  stop("must supply batchname")
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-		  if(!missing(batchname)){
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-			  stopifnot(batchname %in% batchNames(object))
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-			  j <- match(batchname, sampleNames(object))
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-		  } else j <- 1
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-		  getMads <- function(allele){
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-			  switch(allele,
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-				 A=cbind(assayDataElement(object, "madA.AA")[, j],
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-				         assayDataElement(object, "madA.AB")[, j],
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-         			         assayDataElement(object, "madA.BB")[, j]),
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-				 B=cbind(assayDataElement(object, "madB.AA")[, j],
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-				         assayDataElement(object, "madB.AB")[, j],
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-				         assayDataElement(object, "madB.BB")[, j]),
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-				 stop("allele must be 'A' or 'B'")
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-				 )
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+
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+setMethod("medians", signature(object="AssayData"),
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+	  function(object, i, j, ...){
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+		  if(!missing(j)){
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+			  batchnames <- unique(as.character(batch(object)[j]))
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+		  } else batchnames <- batchNames(object)
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+		  nc <- length(batchnames)
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+		  if(!missing(i)) nr <- length(i) else nr <- nrow(object)
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+		  res <- array(NA, dim=c(nr, 2, 3, nc))
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+		  dimnames(res)[[2]] <- c("A", "B")
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+		  dimnames(res)[[3]] <- c("AA", "AB", "BB")
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+		  dimnames(res)[[4]] <- batchnames
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+		  if(missing(i) & missing(j)){
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+			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))
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+			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))
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+			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))
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+			  madB.AA <- as.matrix(assayDataElement(object, "madB.AA"))
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+			  madB.AB <- as.matrix(assayDataElement(object, "madB.AB"))
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+			  madB.BB <- as.matrix(assayDataElement(object, "madB.BB"))
93 155 
 		  }
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-		  getMads(allele)
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+		  if(missing(i) & !missing(j)){
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+			  J <- match(batchnames, batchNames(object))
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+			  stopifnot(length(J) > 0 & !all(is.na(J)))
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+			  madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[, J, ...]
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+			  madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[, J, ...]
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+			  madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))[, J, ...]
162