@@ -76,7 +76,7 @@ export(constructIlluminaCNSet)

 export(linesCNSetLM)

 export(computeCN, fit.lm1, fit.lm2, fit.lm3, fit.lm4, construct,

        dqrlsWrapper, nuphiAllele)

-export(computeCopynumber)

+export(computeCopynumber, ACN)

@@ -237,36 +237,59 @@ setMethod("corr", c("CNSetLM", "character"), function(object, allele){

 	return(res)

 })

-setMethod("CB", 

-	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

-	  function(object, i, j){

-		  ##assayDataElement(object, "CB")

-		  browser()

-	  })

+ACN <- function(object, allele, i , j){

+	if(missing(i) & missing(j)){

+		if(inherits(A(object), "ff") | inherits(A(object), "ffdf")) stop("Must specify i and/or j for ff objects")

+	}

+	if(missing(i) & !missing(j)){

+		## calculate ca only for batches indexed by j

+		ubatch <- unique(batch(object))

+		batches <- unique(batch(object)[j])

+		for(k in seq_along(batches)){

+			l <- match(batches[k], ubatch)

+			bg <- nu(object, allele)[, l]

+			sl <- phi(object, allele)[, l]

+			I <- allele(object, allele)[, j]

+			acn <- 1/sl*(I - bg)				  

+		}

+	}

+	if(!missing(i) & missing(j)){

+		## calculate ca, cb for all batches

+		batches <- unique(batch(object))

+		for(k in seq_along(batches)){

+			##bb <- batches[k]

+			bg <- nu(object, allele)[i, k]

+			sl <- phi(object, allele)[i, k]

+			I <- allele(object, allele)[i, j]

+			acn <- 1/sl*(I - bg)

+		}

+	}

+	if(!missing(i) & !missing(j)){

+		ubatch <- unique(batch(object))

+		batches <- unique(batch(object)[j])

+		for(k in seq_along(batches)){

+			l <- match(batches[k], ubatch)

+			bg <- nu(object, allele)[i, l]

+			sl <- phi(object, allele)[i, l]

+			I <- allele(object, allele)[i, j]

+			acn <- 1/bg*(I - sl)				  

+		}			  

+	}

+	return(acn)

+}

 setMethod("CA",

 	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

 	  function(object, i, j) {

-		  browser()

-		  if(missing(i) & missing(j)){

-			  if(inherits(A(object), "ff") | inherits(A(object), "ffdf")) stop("Must specify i and/or j for ff objects")

-		  }

-		  if(missing(i) & !missing(j)){

-			  ## calculate ca only for batches indexed by j

-			  batches <- unique(batch(object))[j]

-			  for(k in seq_along(batches)){

-				  bb <- batches[k]

-			  }

-		  }

-		  if(!missing(i) & missing(j)){

-			  ## calculate ca, cb for all batches

-			  batches <- unique(batch(object))

-		  }

-		  if(!missing(i) & !missing(j)){

-

-		  }

+		  ca <- ACN(object, allele="A", i, j)

 		  return(ca)

 	  })

+setMethod("CB",

+	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

+	  function(object, i, j) {

+		  cb <- ACN(object, allele="B", i, j)

+		  return(cb)

+	  })

 setMethod("totalCopyNumber",

 	  signature=signature(object="CNSet", i="integerOrMissing", j="integerOrMissing"),

@@ -301,7 +324,7 @@ setMethod("totalCopyNumber",

 			cn.total[snps, ] <- cn.total[snps, ] + cb

 		}

 	}

-	cn.total <- cn.total/100

+	##cn.total <- cn.total/100

 	dimnames(cn.total) <- NULL

 	return(cn.total)

 })

@@ -130,7 +130,6 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){

 	class(calls(gtSet.assayData_matrix))

 }

 ##q("no")

-stop()

 @ 

 Next, we estimate copy number for the 20 CEL files.  The copy number

@@ -147,9 +146,9 @@ cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",

 				      .FUN=crlmmCopynumber,

 				      object=gtSet.assayData_matrix,

 				      chromosome=22)

-Rprof(interval=0.1)

-obj <- crlmmCopynumber(gtSet.assayData_matrix, chromosome=22)

-Rprof(NULL)

+##Rprof(interval=0.1)

+##obj <- crlmmCopynumber(gtSet.assayData_matrix, chromosome=22)

+##Rprof(NULL)

 if(file.exists(file.path(outdir, "gtSet.assayData_matrix.rda")))

 	unlink(file.path(outdir, "gtSet.assayData_matrix.rda"))

 @ 

@@ -181,13 +180,14 @@ so that subsequent calls to \verb@Sweave@ can be run interactively.

 <<LDS_genotype>>=

 if(!file.exists(file.path(outdir, "cnSet.assayData_ff.rda"))){

-	library(ff)

+	Rprof(filename="Rprof_genotypeff.out", interval=0.1)

 	gtSet.assayData_ff <- checkExists("gtSet.assayData_ff",

 					  .path=outdir,

 					  .FUN=genotypeLD,

 					  filenames=celFiles,

 					  cdfName=cdfName,

 					  batch=batch)

+	Rprof(NULL)

 	class(calls(gtSet.assayData_ff))

 }

 @ 

@@ -198,12 +198,14 @@ practice, once the object \Robject{cnSet.assayData_ff} is created the

 from the \Robject{outdir}.

 <<LDS_copynumber>>=

+Rprof(filename="Rprof_cnff.out", interval=0.1)

 cnSet.assayData_ff <- checkExists("cnSet.assayData_ff",

 				  .path=outdir,

 				  .FUN=crlmmCopynumberLD,

 				  filenames=celFiles,

 				  cdfName=cdfName,

 				  batch=batch)

+Rprof(NULL)

 if(file.exists(file.path(outdir, "gtSet.assayData_ff.rda")))

 	unlink(file.path(outdir, "gtSet.assayData_ff.rda"))

 gc()

@@ -373,7 +375,11 @@ genotypeConf <- integerScoreToProbability(snpCallProbability(x)[snp.index[1:10],

 Allele-specific copy number at polymorphic loci:

 <<ca>>=

-ca <- CA(x[snp.index, ])/100

+##ca <- CA(x[snp.index, ])/100

+snp.index <- which(isSnp(obj))

+ca <- CA(obj, i=snp.index)

+##or

+ca <- ACN(obj, "A", i=snp.index)

 @ 

 Total copy number at nonpolymorphic loci: