@@ -441,3 +441,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-08 R.Scharpf committed version 1.5.33

 **	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)

+

+2010-03-10 R.Scharpf committed version 1.5.34

+

+**	  updated DESCRIPTION to import ff

+**        added AllClasses.R with defitions for ff-derived classes

+**        temporarily exporting everything in the NAMESPACE

@@ -7,10 +7,27 @@ Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scha

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

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

 License: Artistic-2.0

-Depends: methods, Biobase (>= 2.7.2), R (>= 2.11.0), oligoClasses (>= 1.9.21)

-Imports: affyio (>= 1.15.2), preprocessCore, utils, stats, genefilter, splines, mvtnorm, ellipse, SNPchip

-Suggests: hapmapsnp5, hapmapsnp6, genomewidesnp5Crlmm (>= 1.0.2),genomewidesnp6Crlmm (>= 1.0.2), snpMatrix

+Depends: R (>= 2.11.0),

+         methods,

+         Biobase (>= 2.7.2),

+         oligoClasses (>= 1.9.28)

+Imports: affyio (>= 1.15.2),

+         preprocessCore,

+         utils,

+         stats,

+         genefilter,

+         splines,

+         mvtnorm,

+         ellipse,

+         SNPchip,ff

+Suggests: hapmapsnp5,

+          hapmapsnp6,

+          genomewidesnp5Crlmm (>= 1.0.2),

+          genomewidesnp6Crlmm (>= 1.0.2),

+          snpMatrix,

+          metaArray

 Collate: AllGenerics.R

+	 AllClasses.R

 	 methods-CNSet.R

 	 methods-eSet.R

          methods-SnpSuperSet.R

@@ -1,5 +1,8 @@

 useDynLib("crlmm", .registration=TRUE)

+## this is temporary

+exportPattern("^[^\\.]")

+

 ## Biobase

 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,

 		  NChannelSet, MIAME, Versioned, VersionedBiobase,

@@ -23,7 +26,7 @@ importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)

 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,

 		  "confs<-", cnConfidence, "cnConfidence<-", 

-		  isSnp, chromosome, position, CA, "CA<-", CB, "CB<-")

+		  isSnp, chromosome, position, CA, "CA<-", CB, "CB<-", A, B)

 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles)

@@ -1,5 +1,3 @@

-setGeneric("A", function(object) standardGeneric("A"))

-setGeneric("B", function(object) standardGeneric("B"))

 ##setGeneric("A<-", function(object, value) standardGeneric("A<-"))

 ##setGeneric("B<-", function(object, value) standardGeneric("B<-"))

@@ -1,3 +1,80 @@

+##---------------------------------------------------------------------------

+##---------------------------------------------------------------------------

+getProtocolData.Affy <- function(filenames){

+	scanDates <- data.frame(ScanDate=sapply(filenames, celfileDate))

+	rownames(scanDates) <- basename(rownames(scanDates))

+	protocoldata <- new("AnnotatedDataFrame",

+			    data=scanDates,

+			    varMetadata=data.frame(labelDescription=colnames(scanDates),

+			                           row.names=colnames(scanDates)))

+	return(protocoldata)

+}

+getFeatureData.Affy <- function(cdfName, copynumber=FALSE){

+	pkgname <- getCrlmmAnnotationName(cdfName)

+	if(!require(pkgname, character.only=TRUE)){

+		suggCall <- paste("library(", pkgname, ", lib.loc='/Altern/Lib/Loc')", sep="")

+		msg <- paste("If", pkgname, "is installed on an alternative location, please load it manually by using", suggCall)

+		message(strwrap(msg))

+		stop("Package ", pkgname, " could not be found.")

+		rm(suggCall, msg)

+	}

+	loader("preprocStuff.rda", .crlmmPkgEnv, pkgname)

+	loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+	loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+	gns <- getVarInEnv("gns")

+	path <- system.file("extdata", package=paste(cdfName, "Crlmm", sep=""))

+	load(file.path(path, "snpProbes.rda"))

+

+	if(copynumber){

+		load(file.path(path, "cnProbes.rda"))

+		cnProbes <- get("cnProbes")

+		snpIndex <- seq(along=gns)

+		npIndex <- seq(along=rownames(cnProbes)) + max(snpIndex) 

+		featurenames <- c(gns, rownames(cnProbes))

+	} else featurenames <- gns

+	fvarlabels=c("chromosome", "position", "isSnp")

+	M <- matrix(NA, length(featurenames), 3, dimnames=list(featurenames, fvarlabels))

+	index <- match(rownames(snpProbes), rownames(M)) #only snp probes in M get assigned position

+	M[index, "position"] <- snpProbes[, grep("pos", colnames(snpProbes))]

+	M[index, "chromosome"] <- snpProbes[, grep("chr", colnames(snpProbes))]

+	M[index, "isSnp"] <- 1L

+	index <- which(is.na(M[, "isSnp"]))

+	M[index, "isSnp"] <- 1L

+

+	if(copynumber){

+		index <- match(rownames(cnProbes), rownames(M)) #only snp probes in M get assigned position

+		M[index, "position"] <- cnProbes[, grep("pos", colnames(cnProbes))]

+		M[index, "chromosome"] <- cnProbes[, grep("chr", colnames(cnProbes))]

+		M[index, "isSnp"] <- 0L

+	}

+	return(new("AnnotatedDataFrame", data=data.frame(M)))

+	##list(snpIndex, npIndex, fns)

+	##crlmmOpts$snpRange <- range(snpIndex)

+	##crlmmOpts$npRange <- range(npIndex)

+}

+construct <- function(filenames, cdfName){

+	protocolData <- getProtocolData.Affy(filenames)

+	M <- getFeatureData.Affy(cdfName)

+	dns <- list(rownames(M), basename(filenames))

+	nr <- nrow(M)

+	alleleSet <- new("AffymetrixAlleleSet", 

+			 alleleA=initializeBigMatrix(dns),

+			 alleleB=initializeBigMatrix(dns),

+			 genomeAnnotation=M,

+			 options=crlmmOptions(object),

+			 annotation=annotation(object))

+	protocolData(alleleSet) <- protocolData

+	sampleNames(alleleSet) <- basename(filenames)

+	featureNames(alleleSet) <- dns[[1]]

+	return(alleleSet)

+}

+

+

+

+

+

+##---------------------------------------------------------------------------

+##---------------------------------------------------------------------------

 rowCovs <- function(x, y, ...){

 	notna <- !is.na(x)

 	N <- rowSums(notna)