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 | ... | ... |
@@ -56,7 +56,7 @@ importFrom(mvtnorm, dmvnorm) |
| 56 | 56 |
|
| 57 | 57 |
importFrom(ellipse, ellipse) |
| 58 | 58 |
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| 59 |
-importFrom(ff, ffdf, physical.ff, physical.ffdf) |
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| 59 |
+importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply) |
|
| 60 | 60 |
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| 61 | 61 |
## It is important not to import these classes from oligoClasses |
| 62 | 62 |
## Doing so causes the following errors: |
| ... | ... |
@@ -66,7 +66,8 @@ importFrom(ff, ffdf, physical.ff, physical.ffdf) |
| 66 | 66 |
##importClassesFrom(oligoClasses, ffdf, ff_matrix) |
| 67 | 67 |
|
| 68 | 68 |
## Important to export these classes |
| 69 |
-exportClasses(ff_or_matrix, ff_matrix, ffdf) |
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| 69 |
+##exportClasses(ff_or_matrix, ff_matrix, ffdf) |
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| 70 |
+exportClasses(ff_or_matrix) |
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| 70 | 71 |
exportMethods(lines) |
| 71 | 72 |
exportMethods(CA, CB) |
| 72 | 73 |
export(crlmm, |
| ... | ... |
@@ -1887,7 +1887,7 @@ estimateCnParameters <- function(object, |
| 1887 | 1887 |
index.list=list(marker.index), |
| 1888 | 1888 |
marker.index=marker.index, |
| 1889 | 1889 |
object=object, |
| 1890 |
- batchSize=batchSize, |
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| 1890 |
+ batchSize=ocProbesets(), |
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| 1891 | 1891 |
SNRMin=SNRMin, |
| 1892 | 1892 |
MIN.SAMPLES=MIN.SAMPLES, |
| 1893 | 1893 |
MIN.OBS=MIN.OBS, |
| ... | ... |
@@ -24,30 +24,6 @@ setMethod("Ns", signature(object="AssayData"),
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| 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)){
|
|
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- N.AA <- as.matrix(assayDataElement(object, "N.AA")) |
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| 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)){
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|
| 33 |
- J <- match(batchnames, batchNames(object)) |
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| 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, ...] |
|
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- N.BB <- as.matrix(assayDataElement(object, "N.BB"))[, 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))) |
|
| 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 |
- } |
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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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| 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"),
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| 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)){
|
|
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- corrAA <- as.matrix(assayDataElement(object, "corrAA")) |
|
| 84 |
- corrAB <- as.matrix(assayDataElement(object, "corrAB")) |
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| 85 |
- corrBB <- as.matrix(assayDataElement(object, "corrBB")) |
|
| 86 |
- } |
|
| 87 |
- 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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- } |
|
| 106 | 58 |
res[, "AA", ] <- corrAA |
| 107 | 59 |
res[, "AB", ] <- corrAB |
| 108 | 60 |
res[, "BB", ] <- corrBB |
| ... | ... |
@@ -128,43 +80,6 @@ setMethod("medians", signature(object="AssayData"),
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| 128 | 80 |
dimnames(res)[[2]] <- c("A", "B")
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| 129 | 81 |
dimnames(res)[[3]] <- c("AA", "AB", "BB")
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| 130 | 82 |
dimnames(res)[[4]] <- batchnames |
| 131 |
- if(missing(i) & missing(j)){
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| 132 |
- medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA")) |
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| 133 |
- medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB")) |
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| 134 |
- medianA.BB <- as.matrix(assayDataElement(object, "medianA.BB")) |
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| 135 |
- medianB.AA <- as.matrix(assayDataElement(object, "medianB.AA")) |
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| 136 |
- 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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| 139 |
- if(missing(i) & !missing(j)){
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| 140 |
- J <- match(batchnames, batchNames(object)) |
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| 141 |
- stopifnot(length(J) > 0 & !all(is.na(J))) |
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| 142 |
- medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[, J, ...] |
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| 143 |
- medianA.AB <- as.matrix(assayDataElement(object, "medianA.AB"))[, J, ...] |
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| 144 |
- 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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| 150 |
- if(!missing(i) & !missing(j)){
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| 151 |
- J <- match(batchnames, batchNames(object)) |
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| 152 |
- 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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| 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)){
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| 161 |
- medianA.AA <- as.matrix(assayDataElement(object, "medianA.AA"))[i, ...] |
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| 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, ...] |
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| 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"),
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| 193 | 108 |
dimnames(res)[[2]] <- c("A", "B")
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| 194 | 109 |
dimnames(res)[[3]] <- c("AA", "AB", "BB")
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| 195 | 110 |
dimnames(res)[[4]] <- batchnames |
| 196 |
- if(missing(i) & missing(j)){
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| 197 |
- madA.AA <- as.matrix(assayDataElement(object, "madA.AA")) |
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| 198 |
- madA.AB <- as.matrix(assayDataElement(object, "madA.AB")) |
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| 199 |
- madA.BB <- as.matrix(assayDataElement(object, "madA.BB")) |
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| 200 |
- madB.AA <- as.matrix(assayDataElement(object, "madB.AA")) |
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| 201 |
- madB.AB <- as.matrix(assayDataElement(object, "madB.AB")) |
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| 202 |
- madB.BB <- as.matrix(assayDataElement(object, "madB.BB")) |
|
| 203 |
- } |
|
| 204 |
- if(missing(i) & !missing(j)){
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| 205 |
- J <- match(batchnames, batchNames(object)) |
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| 206 |
- stopifnot(length(J) > 0 & !all(is.na(J))) |
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| 207 |
- madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[, J, ...] |
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| 208 |
- madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[, J, ...] |
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| 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)){
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| 216 |
- J <- match(batchnames, batchNames(object)) |
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| 217 |
- stopifnot(length(J) > 0 & !all(is.na(J))) |
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- madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[i, J, ...] |
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| 219 |
- madA.AB <- as.matrix(assayDataElement(object, "madA.AB"))[i, J, ...] |
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| 220 |
- madA.BB <- as.matrix(assayDataElement(object, "madA.BB"))[i, J, ...] |
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| 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)){
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| 226 |
- madA.AA <- as.matrix(assayDataElement(object, "madA.AA"))[i, ...] |
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| 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 |