@@ -332,3 +332,7 @@ is decoded and scanned

  * added CNSet class

  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)

+2009-11-19 R. Scharpf - committed version 1.5.6

+

+ * fixed bug in initialization of SnpCallSetPlus

+

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.5.5

+Version: 1.5.6

 Date: 2009-11-15

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -148,34 +148,33 @@ setMethod("computeHmm", "CNSet", function(object, hmmOptions){

 ## Genotype everything to get callSetPlus objects

 ## Go from callSets to Segments sets, writing only the segment set to file

 ## Safe, but very inefficient. Writes the quantile normalized data to file several times...

-setMethod("computeHmm", "character", function(object, hmmOptions){

-	outdir <- cnOptions[["outdir"]]

-	hmmOptions <- hmmOptions[["hmmOpts"]]

-	filenames <- object

-	for(i in seq(along=filenames)){

-		chrom <- gsub(".rda", "", strsplit(filenames[i], "_")[[1]][[2]])

-		if(hmmOptions[["verbose"]])

-			message("Fitting HMM to chromosome ", chrom)

-		if(file.exists(filenames[i])){

-			message("Loading ", filenames[i])

-			load(filenames[i])

-			cnSet <- get("cnSet")

-		} else {

-			stop("File ", filenames[i], " does not exist.")

-		}

-		hmmOptions$emission <- computeEmission(filenames[i], hmmOptions)

-		cnSet <- computeHmm(cnSet, hmmOptions)

-		##MIN.MARKERS <- hmmOptions[["MIN.MARKERS"]]

-		##segmentSet <- segments[segments$nprobes >= MIN.MARKERS, ]

-		message("Saving ", file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

-		save(cnSet,

-		     file=file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

-		unlink(file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

-	}

-	fns <- list.files(outdir, pattern="cnSet", full.names=TRUE)

-	return(fns)	

-})

-

+##setMethod("computeHmm", "character", function(object, hmmOptions){

+##	outdir <- cnOptions[["outdir"]]

+##	hmmOptions <- hmmOptions[["hmmOpts"]]

+##	filenames <- object

+##	for(i in seq(along=filenames)){

+##		chrom <- gsub(".rda", "", strsplit(filenames[i], "_")[[1]][[2]])

+##		if(hmmOptions[["verbose"]])

+##			message("Fitting HMM to chromosome ", chrom)

+##		if(file.exists(filenames[i])){

+##			message("Loading ", filenames[i])

+##			load(filenames[i])

+##			cnSet <- get("cnSet")

+##		} else {

+##			stop("File ", filenames[i], " does not exist.")

+##		}

+##		hmmOptions$emission <- computeEmission(filenames[i], hmmOptions)

+##		cnSet <- computeHmm(cnSet, hmmOptions)

+##		##MIN.MARKERS <- hmmOptions[["MIN.MARKERS"]]

+##		##segmentSet <- segments[segments$nprobes >= MIN.MARKERS, ]

+##		message("Saving ", file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

+##		save(cnSet,

+##		     file=file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

+##		unlink(file.path(outdir, paste("cnSet_", chrom, ".rda", sep="")))

+##	}

+##	fns <- list.files(outdir, pattern="cnSet", full.names=TRUE)

+##	return(fns)	

+##})

 setValidity("CNSet", function(object) {

@@ -32,7 +32,7 @@ setMethod("initialize", "SnpCallSetPlus",

 		  ## Do after annotation has been assigned

 		  if(!(all(c("chromosome", "position", "isSnp")  %in% colnames(.Object@featureData)))){

 			  ##update the featureData

-			  .Object@featureData <- addFeatureAnnotation.SnpCallSetPlus(object)

+			  .Object@featureData <- addFeatureAnnotation.SnpCallSetPlus(.Object)

 		  }

 		  .Object

           })