git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58739 bc3139a8-67e5-0310-9ffc-ced21a209358
Benilton Carvalho authored on 04/10/2011 11:02:32
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| 4 |
-Version: 1.11.46 |
|
| 4 |
+Version: 1.11.47 |
|
| 5 | 5 |
Date: 2010-12-10 |
| 6 | 6 |
Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry |
| 7 | 7 |
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| ... | ... |
@@ -151,6 +151,7 @@ readIdatFiles = function(sampleSheet=NULL, |
| 151 | 151 |
|
| 152 | 152 |
|
| 153 | 153 |
## the readIDAT() and readBPM() functions below were provided by Keith Baggerly, 27/8/2008 |
| 154 |
+## edits provided by Kasper Daniel Hansen, 4/10/2011 |
|
| 154 | 155 |
readIDAT <- function(idatFile){
|
| 155 | 156 |
fileSize <- file.info(idatFile)$size |
| 156 | 157 |
|
| ... | ... |
@@ -160,14 +161,12 @@ readIDAT <- function(idatFile){
|
| 160 | 161 |
|
| 161 | 162 |
} |
| 162 | 163 |
|
| 163 |
- versionNumber <- readBin(tempCon, "integer", n=1, size=8, |
|
| 164 |
- endian="little") |
|
| 164 |
+ versionNumber <- readBin(tempCon, "integer", n=1, size=8, endian="little") |
|
| 165 | 165 |
|
| 166 | 166 |
if(versionNumber<3) |
| 167 | 167 |
stop("Older style IDAT files not supported: consider updating your scanner settings")
|
| 168 | 168 |
|
| 169 |
- nFields <- readBin(tempCon, "integer", n=1, size=4, |
|
| 170 |
- endian="little") |
|
| 169 |
+ nFields <- readBin(tempCon, "integer", n=1, size=4, endian="little") |
|
| 171 | 170 |
|
| 172 | 171 |
fields <- matrix(0,nFields,3); |
| 173 | 172 |
colnames(fields) <- c("Field Code", "Byte Offset", "Bytes")
|
| ... | ... |
@@ -178,26 +177,26 @@ readIDAT <- function(idatFile){
|
| 178 | 177 |
readBin(tempCon, "integer", n=1, size=8, endian="little") |
| 179 | 178 |
} |
| 180 | 179 |
|
| 181 |
- knownCodes <- c(1000, 102, 103, 104, 107, 200, 300, 400, |
|
| 182 |
- 401, 402, 403, 404, 405, 406, 407, 408, 409) |
|
| 183 |
- names(knownCodes) <- |
|
| 184 |
- c("nSNPsRead", # 1000
|
|
| 185 |
- "IlluminaID", # 102 |
|
| 186 |
- "SD", # 103 |
|
| 187 |
- "Mean", # 104 |
|
| 188 |
- "NBeads", # 107 |
|
| 189 |
- "MidBlock", # 200 |
|
| 190 |
- "RunInfo", # 300 |
|
| 191 |
- "RedGreen", # 400 |
|
| 192 |
- "MostlyNull", # 401 |
|
| 193 |
- "Barcode", # 402 |
|
| 194 |
- "ChipType", # 403 |
|
| 195 |
- "MostlyA", # 404 |
|
| 196 |
- "Unknown.1", # 405 |
|
| 197 |
- "Unknown.2", # 406 |
|
| 198 |
- "Unknown.3", # 407 |
|
| 199 |
- "Unknown.4", # 408 |
|
| 200 |
- "Unknown.5" # 409 |
|
| 180 |
+ knownCodes <- |
|
| 181 |
+ c("nSNPsRead" = 1000,
|
|
| 182 |
+ "IlluminaID" = 102, |
|
| 183 |
+ "SD" = 103, |
|
| 184 |
+ "Mean" = 104, |
|
| 185 |
+ "NBeads" = 107, |
|
| 186 |
+ "MidBlock" = 200, |
|
| 187 |
+ "RunInfo" = 300, |
|
| 188 |
+ "RedGreen" = 400, |
|
| 189 |
+ "MostlyNull" = 401, |
|
| 190 |
+ "Barcode" = 402, |
|
| 191 |
+ "ChipType" = 403, |
|
| 192 |
+ "MostlyA" = 404, |
|
| 193 |
+ "Unknown.1" = 405, |
|
| 194 |
+ "Unknown.2" = 406, |
|
| 195 |
+ "Unknown.3" = 407, |
|
| 196 |
+ "Unknown.4" = 408, |
|
| 197 |
+ "Unknown.5" = 409, |
|
| 198 |
+ "Unknown.6" = 410, |
|
| 199 |
+ "Unknown.7" = 510 |
|
| 201 | 200 |
) |
| 202 | 201 |
|
| 203 | 202 |
nNewFields <- 1 |
| ... | ... |
@@ -212,123 +211,158 @@ readIDAT <- function(idatFile){
|
| 212 | 211 |
} |
| 213 | 212 |
} |
| 214 | 213 |
|
| 215 |
- seek(tempCon, fields["nSNPsRead", "Byte Offset"]) |
|
| 216 |
- nSNPsRead <- readBin(tempCon, "integer", n=1, size=4, |
|
| 217 |
- endian="little") |
|
| 218 |
- |
|
| 219 |
- seek(tempCon, fields["IlluminaID", "Byte Offset"]) |
|
| 220 |
- IlluminaID <- readBin(tempCon, "integer", n=nSNPsRead, size=4, |
|
| 221 |
- endian="little") |
|
| 222 |
- |
|
| 223 |
- seek(tempCon, fields["SD", "Byte Offset"]) |
|
| 224 |
- SD <- readBin(tempCon, "integer", n=nSNPsRead, size=2, |
|
| 225 |
- endian="little", signed=FALSE) |
|
| 226 |
- |
|
| 227 |
- seek(tempCon, fields["Mean", "Byte Offset"]) |
|
| 228 |
- Mean <- readBin(tempCon, "integer", n=nSNPsRead, size=2, |
|
| 229 |
- endian="little", signed=FALSE) |
|
| 214 |
+ fields <- fields[order(fields[, "Byte Offset"]),] |
|
| 230 | 215 |
|
| 231 |
- seek(tempCon, fields["NBeads", "Byte Offset"]) |
|
| 232 |
- NBeads <- readBin(tempCon, "integer", n=nSNPsRead, size=1, signed=FALSE) |
|
| 233 |
- |
|
| 234 |
- seek(tempCon, fields["MidBlock", "Byte Offset"]) |
|
| 235 |
- nMidBlockEntries <- readBin(tempCon, "integer", n=1, size=4, |
|
| 236 |
- endian="little") |
|
| 237 |
- MidBlock <- readBin(tempCon, "integer", n=nMidBlockEntries, size=4, |
|
| 238 |
- endian="little") |
|
| 239 |
- |
|
| 240 |
- seek(tempCon, fields["RunInfo", "Byte Offset"]) |
|
| 241 |
- nRunInfoBlocks <- readBin(tempCon, "integer", n=1, size=4, |
|
| 242 |
- endian="little") |
|
| 243 |
- RunInfo <- matrix(NA, nRunInfoBlocks, 5) |
|
| 244 |
- colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars",
|
|
| 245 |
- "BlockCode", "CodeVersion") |
|
| 246 |
- for(i1 in 1:2) { #nRunInfoBlocks){ ## MR edit
|
|
| 247 |
- for(i2 in 1:5){
|
|
| 248 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 249 |
- RunInfo[i1,i2] <- readChar(tempCon, nChars) |
|
| 250 |
- } |
|
| 216 |
+ seek(tempCon, fields["nSNPsRead", "Byte Offset"]) |
|
| 217 |
+ nSNPsRead <- readBin(tempCon, "integer", n=1, size=4, endian="little") |
|
| 218 |
+ |
|
| 219 |
+ readBlock <- function(nam) {
|
|
| 220 |
+ switch(nam, |
|
| 221 |
+ "IlluminaID" = {
|
|
| 222 |
+ seek(tempCon, fields["IlluminaID", "Byte Offset"]) |
|
| 223 |
+ IlluminaID <- readBin(tempCon, "integer", n=nSNPsRead, size=4, endian="little") |
|
| 224 |
+ IlluminaID |
|
| 225 |
+ }, |
|
| 226 |
+ "SD" = {
|
|
| 227 |
+ seek(tempCon, fields["SD", "Byte Offset"]) |
|
| 228 |
+ SD <- readBin(tempCon, "integer", n=nSNPsRead, size=2, endian="little", signed=FALSE) |
|
| 229 |
+ SD |
|
| 230 |
+ }, |
|
| 231 |
+ "Mean" = {
|
|
| 232 |
+ seek(tempCon, fields["Mean", "Byte Offset"]) |
|
| 233 |
+ Mean <- readBin(tempCon, "integer", n=nSNPsRead, size=2, endian="little", signed=FALSE) |
|
| 234 |
+ Mean |
|
| 235 |
+ }, |
|
| 236 |
+ "NBeads" = {
|
|
| 237 |
+ seek(tempCon, fields["NBeads", "Byte Offset"]) |
|
| 238 |
+ NBeads <- readBin(tempCon, "integer", n=nSNPsRead, size=1, signed=FALSE) |
|
| 239 |
+ NBeads |
|
| 240 |
+ }, |
|
| 241 |
+ "MidBlock" = {
|
|
| 242 |
+ seek(tempCon, fields["MidBlock", "Byte Offset"]) |
|
| 243 |
+ nMidBlockEntries <- readBin(tempCon, "integer", n=1, size=4, endian="little") |
|
| 244 |
+ MidBlock <- readBin(tempCon, "integer", n=nMidBlockEntries, size=4, |
|
| 245 |
+ endian="little") |
|
| 246 |
+ MidBlock |
|
| 247 |
+ }, |
|
| 248 |
+ "RunInfo" = {
|
|
| 249 |
+ seek(tempCon, fields["RunInfo", "Byte Offset"]) |
|
| 250 |
+ nRunInfoBlocks <- readBin(tempCon, "integer", n=1, size=4, endian="little") |
|
| 251 |
+ RunInfo <- matrix(NA, nRunInfoBlocks, 5) |
|
| 252 |
+ colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars",
|
|
| 253 |
+ "BlockCode", "CodeVersion") |
|
| 254 |
+ for(i1 in 1:2) { #nRunInfoBlocks){ ## MR edit
|
|
| 255 |
+ for(i2 in 1:5){
|
|
| 256 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 257 |
+ RunInfo[i1,i2] <- readChar(tempCon, nChars) |
|
| 258 |
+ } |
|
| 259 |
+ } |
|
| 260 |
+ RunInfo |
|
| 261 |
+ }, |
|
| 262 |
+ "RedGreen" = {
|
|
| 263 |
+ seek(tempCon, fields["RedGreen", "Byte Offset"]) |
|
| 264 |
+ RedGreen <- readBin(tempCon, "numeric", n=1, size=4, |
|
| 265 |
+ endian="little") |
|
| 266 |
+ RedGreen |
|
| 267 |
+ }, |
|
| 268 |
+ "MostlyNull" = {
|
|
| 269 |
+ seek(tempCon, fields["MostlyNull", "Byte Offset"]) |
|
| 270 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 271 |
+ MostlyNull <- readChar(tempCon, nChars) |
|
| 272 |
+ MostlyNull |
|
| 273 |
+ }, |
|
| 274 |
+ "Barcode" = {
|
|
| 275 |
+ seek(tempCon, fields["Barcode", "Byte Offset"]) |
|
| 276 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 277 |
+ Barcode <- readChar(tempCon, nChars) |
|
| 278 |
+ Barcode |
|
| 279 |
+ }, |
|
| 280 |
+ "ChipType" = {
|
|
| 281 |
+ seek(tempCon, fields["ChipType", "Byte Offset"]) |
|
| 282 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 283 |
+ ChipType <- readChar(tempCon, nChars) |
|
| 284 |
+ ChipType |
|
| 285 |
+ }, |
|
| 286 |
+ "MostlyA" = {
|
|
| 287 |
+ seek(tempCon, fields["MostlyA", "Byte Offset"]) |
|
| 288 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 289 |
+ MostlyA <- readChar(tempCon, nChars) |
|
| 290 |
+ }, |
|
| 291 |
+ "Unknown.1" = {
|
|
| 292 |
+ seek(tempCon, fields["Unknown.1", "Byte Offset"]) |
|
| 293 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 294 |
+ Unknown.1 <- readChar(tempCon, nChars) |
|
| 295 |
+ Unknown.1 |
|
| 296 |
+ }, |
|
| 297 |
+ "Unknown.2" = {
|
|
| 298 |
+ seek(tempCon, fields["Unknown.2", "Byte Offset"]) |
|
| 299 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 300 |
+ Unknown.2 <- readChar(tempCon, nChars) |
|
| 301 |
+ Unknown.2 |
|
| 302 |
+ }, |
|
| 303 |
+ "Unknown.3" = {
|
|
| 304 |
+ seek(tempCon, fields["Unknown.3", "Byte Offset"]) |
|
| 305 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 306 |
+ Unknown.3 <- readChar(tempCon, nChars) |
|
| 307 |
+ Unknown.3 |
|
| 308 |
+ }, |
|
| 309 |
+ "Unknown.4" = {
|
|
| 310 |
+ seek(tempCon, fields["Unknown.4", "Byte Offset"]) |
|
| 311 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 312 |
+ Unknown.4 <- readChar(tempCon, nChars) |
|
| 313 |
+ Unknown.4 |
|
| 314 |
+ }, |
|
| 315 |
+ "Unknown.5" = {
|
|
| 316 |
+ seek(tempCon, fields["Unknown.5", "Byte Offset"]) |
|
| 317 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 318 |
+ Unknown.5 <- readChar(tempCon, nChars) |
|
| 319 |
+ Unknown.5 |
|
| 320 |
+ }, |
|
| 321 |
+ "Unknown.6" = {
|
|
| 322 |
+ seek(tempCon, fields["Unknown.6", "Byte Offset"]) |
|
| 323 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 324 |
+ Unknown.6 <- readChar(tempCon, nChars) |
|
| 325 |
+ Unknown.6 |
|
| 326 |
+ }, |
|
| 327 |
+ "Unknown.7" = {
|
|
| 328 |
+ seek(tempCon, fields["Unknown.7", "Byte Offset"]) |
|
| 329 |
+ nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 330 |
+ Unknown.7 <- readChar(tempCon, nChars) |
|
| 331 |
+ Unknown.7 |
|
| 332 |
+ }) |
|
| 251 | 333 |
} |
| 252 | 334 |
|
| 253 |
- seek(tempCon, fields["RedGreen", "Byte Offset"]) |
|
| 254 |
- RedGreen <- readBin(tempCon, "numeric", n=1, size=4, |
|
| 255 |
- endian="little") |
|
| 256 |
- #RedGreen <- readBin(tempCon, "integer", n=4, size=1, |
|
| 257 |
- # endian="little") |
|
| 258 |
- |
|
| 259 |
- seek(tempCon, fields["MostlyNull", "Byte Offset"]) |
|
| 260 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 261 |
- MostlyNull <- readChar(tempCon, nChars) |
|
| 262 |
- |
|
| 263 |
- seek(tempCon, fields["Barcode", "Byte Offset"]) |
|
| 264 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 265 |
- Barcode <- readChar(tempCon, nChars) |
|
| 266 |
- |
|
| 267 |
- seek(tempCon, fields["ChipType", "Byte Offset"]) |
|
| 268 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 269 |
- ChipType <- readChar(tempCon, nChars) |
|
| 270 |
- |
|
| 271 |
- seek(tempCon, fields["MostlyA", "Byte Offset"]) |
|
| 272 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 273 |
- MostlyA <- readChar(tempCon, nChars) |
|
| 274 |
- |
|
| 275 |
- seek(tempCon, fields["Unknown.1", "Byte Offset"]) |
|
| 276 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 277 |
- Unknown.1 <- readChar(tempCon, nChars) |
|
| 278 |
- |
|
| 279 |
- seek(tempCon, fields["Unknown.2", "Byte Offset"]) |
|
| 280 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 281 |
- Unknown.2 <- readChar(tempCon, nChars) |
|
| 282 |
- |
|
| 283 |
- seek(tempCon, fields["Unknown.3", "Byte Offset"]) |
|
| 284 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 285 |
- Unknown.3 <- readChar(tempCon, nChars) |
|
| 286 |
- |
|
| 287 |
- seek(tempCon, fields["Unknown.4", "Byte Offset"]) |
|
| 288 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 289 |
- Unknown.4 <- readChar(tempCon, nChars) |
|
| 290 |
- |
|
| 291 |
- seek(tempCon, fields["Unknown.5", "Byte Offset"]) |
|
| 292 |
- nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE) |
|
| 293 |
- Unknown.5 <- readChar(tempCon, nChars) |
|
| 335 |
+ readFields <- setdiff(rownames(fields), "nSNPsRead") |
|
| 336 |
+ names(readFields) <- readFields |
|
| 337 |
+ |
|
| 338 |
+ allFields <- lapply(readFields, readBlock) |
|
| 294 | 339 |
|
| 295 | 340 |
close(tempCon) |
| 296 | 341 |
|
| 297 |
- Unknowns <- |
|
| 298 |
- list(MostlyNull=MostlyNull, |
|
| 299 |
- MostlyA=MostlyA, |
|
| 300 |
- Unknown.1=Unknown.1, |
|
| 301 |
- Unknown.2=Unknown.2, |
|
| 302 |
- Unknown.3=Unknown.3, |
|
| 303 |
- Unknown.4=Unknown.4, |
|
| 304 |
- Unknown.5=Unknown.5) |
|
| 342 |
+ UnknownNames <- c("MostlyNull", "MostlyA", "Unknown.1",
|
|
| 343 |
+ "Unknown.2", "Unknown.3", "Unknown.4", |
|
| 344 |
+ "Unknown.5", "Unknown.6", "Unknown.7") |
|
| 345 |
+ Unknowns <- allFields[intersect(names(allFields), UnknownNames)] |
|
| 305 | 346 |
|
| 306 |
- Quants <- cbind(Mean, SD, NBeads) |
|
| 347 |
+ Quants <- cbind(allFields$Mean, allFields$SD, allFields$NBeads) |
|
| 307 | 348 |
colnames(Quants) <- c("Mean", "SD", "NBeads")
|
| 308 |
- rownames(Quants) <- as.character(IlluminaID) |
|
| 349 |
+ rownames(Quants) <- as.character(allFields$IlluminaID) |
|
| 309 | 350 |
|
| 351 |
+ InfoNames <- c("MidBlock", "RunInfo", "RedGreen", "Barcode", "ChipType")
|
|
| 352 |
+ Info <- allFields[intersect(names(allFields), InfoNames)] |
|
| 353 |
+ |
|
| 310 | 354 |
idatValues <- |
| 311 | 355 |
list(fileSize=fileSize, |
| 312 | 356 |
versionNumber=versionNumber, |
| 313 | 357 |
nFields=nFields, |
| 314 | 358 |
fields=fields, |
| 315 | 359 |
nSNPsRead=nSNPsRead, |
| 316 |
- #IlluminaID=IlluminaID, |
|
| 317 |
- #SD=SD, |
|
| 318 |
- #Mean=Mean, |
|
| 319 |
- #NBeads=NBeads, |
|
| 320 |
- Quants=Quants, |
|
| 321 |
- MidBlock=MidBlock, |
|
| 322 |
- RunInfo=RunInfo, |
|
| 323 |
- RedGreen=RedGreen, |
|
| 324 |
- Barcode=Barcode, |
|
| 325 |
- ChipType=ChipType, |
|
| 326 |
- Unknowns=Unknowns) |
|
| 327 |
- |
|
| 360 |
+ Quants=Quants) |
|
| 361 |
+ idatValues <- c(idatValues, Info, list(Unknowns = Unknowns)) |
|
| 328 | 362 |
idatValues |
| 329 |
- |
|
| 330 | 363 |
} |
| 331 | 364 |
|
| 365 |
+ |
|
| 332 | 366 |
readBPM <- function(bpmFile){
|
| 333 | 367 |
|
| 334 | 368 |
## Reads and parses Illumina BPM files |