@@ -1,6 +1,6 @@

 useDynLib("crlmm", .registration=TRUE)

 ## this is temporary

-## exportPattern("^[^\\.]")

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

 ##---------------------------------------------------------------------------

 ## Biobase

@@ -46,8 +46,7 @@ getFeatureData <- function(cdfName, copynumber=FALSE){

 		M[index, "chromosome"] <- chromosome2integer(cnProbes[, grep("chr", colnames(cnProbes))])

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

 	}

-	##A few of the snpProbes do not match -- I think it is chromosome Y.

-	M[is.na(M[, "isSnp"]), "isSnp"] <- 1L

+	M <- M[!is.na(M[, "chromosome"]), ]

 	M <- data.frame(M)

 	return(new("AnnotatedDataFrame", data=M))

 }

@@ -141,7 +141,7 @@ readIdatFiles = function(sampleSheet=NULL,

 	       protocolData(RG)[["ScanDate"]] = dates$scan

        }

        storageMode(RG) = "lockedEnvironment"

-       is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)       

+       is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

        if(is.lds) {

          close(RG@assayData$R)

          close(RG@assayData$G)

@@ -467,7 +467,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

 	     zero=initializeBigMatrix(name="zero", nr=nsnps, nc=narrays, vmode="integer"),

 	     annotation=chipType, phenoData=RG@phenoData,

 	     protocolData=RG@protocolData, storage.mode="environment")

-  featureNames(XY) = ids 

+  featureNames(XY) = ids

   sampleNames(XY) = sampleNames(RG)

   gc()

   # Need to initialize - matrices filled with NAs to begin with

@@ -476,7 +476,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   XY@assayData$zero[1:nsnps,] = 0

   is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

-  

+

   if(is.lds) {

     open(RG@assayData$G)

     open(RG@assayData$R)

@@ -513,7 +513,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   if(is.lds) {

     close(RG@assayData$G)

     close(RG@assayData$R)

-    close(RG@assayData$zero)    

+    close(RG@assayData$zero)

     close(XY@assayData$X)

     close(XY@assayData$Y)

     close(XY@assayData$zero)

@@ -544,7 +544,7 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

     if (getRversion() > '2.7.0') pb = txtProgressBar(min=0, max=max(stripnum), style=3)

   }

   is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

-  

+

   if(is.lds) {

     open(XY@assayData$X)

     open(XY@assayData$Y)

@@ -585,7 +585,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

 				cdfName,

 				sns,

 				stripNorm=TRUE,

-				useTarget=TRUE) { 

+				useTarget=TRUE) {

 #				save.it=FALSE,

 #				snpFile,

 #				cnFile) {

@@ -614,14 +614,14 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

   theKnots = getVarInEnv("theKnots")

   narrays = ncol(XY)

-  is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)    

-  

+  is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

+

 #  if(save.it & !missing(cnFile)) {

     # separate out copy number probes

     npIndex = getVarInEnv("npProbesFid")

     nprobes = length(npIndex)

     if(length(nprobes)>0) {

-      if(is.lds) {    

+      if(is.lds) {

         open(XY@assayData$X)

         open(XY@assayData$Y)

         open(XY@assayData$zero)

@@ -642,7 +642,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

 #      t0 <- proc.time()-t0

 #      if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")

        rm(A, B, zero)

-      if(is.lds) {    

+      if(is.lds) {

         close(XY@assayData$X)

         close(XY@assayData$Y)

         close(XY@assayData$zero)

@@ -686,7 +686,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

     open(XY@assayData$Y)

     open(XY@assayData$zero)

   }

-  

+

   for(i in 1:narrays){

      A[,i] = as.integer(exprs(channel(XY, "X"))[snpIndex,i])

      B[,i] = as.integer(exprs(channel(XY, "Y"))[snpIndex,i])

@@ -723,7 +723,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

   if(is.lds) {

     close(XY@assayData$X)

     close(XY@assayData$Y)

-    close(XY@assayData$zero)    

+    close(XY@assayData$zero)

     close(A)

     close(B)

     close(zero)

@@ -735,7 +735,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5,

   res = list(A=A, B=B,

              zero=zero, sns=sns, gns=names(snpIndex), SNR=SNR, SKW=SKW,

              mixtureParams=mixtureParams, cdfName=cdfName, cnAB=cnAB)

-  

+

 #  open(res[["A"]])

 #  open(res[["B"]])

 #  open(res[["zero"]])

@@ -796,7 +796,7 @@ crlmmIllumina = function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

       open(res[["SNR"]])

       open(res[["mixtureParams"]])

     }

-    

+

 #    fD = featureData(XY)

 #    phenD = XY@phenoData

 #    protD = XY@protocolData

@@ -859,7 +859,7 @@ crlmmIllumina = function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

                      verbose=verbose,

                      returnParams=returnParams,

                      badSNP=badSNP)

-    

+

 #  res2 <- crlmmGT2(A=res[["A"]], #as.matrix(A(callSet)[snp.index,]), # j]),

 #                  B=res[["B"]], # as.matrix(B(callSet)[snp.index,]),  # j]),

 #                  SNR=res[["SNR"]], # callSet$SNR, # [j],

@@ -923,7 +923,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

     if(missing(cdfName)) stop("must specify cdfName")

     if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")

-  

+

     is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

     RG = readIdatFiles(sampleSheet=sampleSheet, arrayNames=arrayNames,

@@ -937,9 +937,9 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

       delete(RG@assayData$R); delete(RG@assayData$G); delete(RG@assayData$zero)

     }

     rm(RG); gc()

-  

+

     if (missing(sns)) { sns = sampleNames(XY)

-    } 

+    }

     res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                                seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget) #,

 #                               save.it=save.it, snpFile=snpFile, cnFile=cnFile)

@@ -952,7 +952,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

     if(row.names) row.names=res$gns else row.names=NULL

     if(col.names) col.names=res$sns else col.names=NULL

-  

+

     FUN = ifelse(is.lds, "crlmmGT2", "crlmmGT")

     ## genotyping

     crlmmGTfxn = function(FUN,...){

@@ -977,7 +977,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

                      verbose=verbose,

                      returnParams=returnParams,

                      badSNP=badSNP)

-  

+

     if(is.lds) {

       open(res[["SNR"]]); open(res[["SKW"]])

     }

@@ -1078,7 +1078,7 @@ construct.Illumina = function(sampleSheet=NULL,

        }

        narrays = length(arrayNames)

-          

+

        if(!missing(batch)) {

 		stopifnot(length(batch) == narrays)

        }

@@ -1132,7 +1132,7 @@ construct.Illumina = function(sampleSheet=NULL,

 	protocolData(cnSet) = protocolData

 	featureData(cnSet) = featureData

 	featureNames(cnSet) = featureNames(featureData)

-	pd = data.frame(matrix(NA, nc, 3), row.names=sampleNames(cnSet)) 

+	pd = data.frame(matrix(NA, nc, 3), row.names=sampleNames(cnSet))

 	colnames(pd)=c("SKW", "SNR", "gender")

 	phenoData(cnSet) = new("AnnotatedDataFrame", data=pd)

 	return(cnSet)

@@ -1175,7 +1175,7 @@ genotype.Illumina = function(sampleSheet=NULL,

         pkgname = getCrlmmAnnotationName(cdfName)

 	callSet = construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,

 			     ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,

-                             highDensity=highDensity, sep=sep, fileExt=fileExt, 

+                             highDensity=highDensity, sep=sep, fileExt=fileExt,

 			     cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch,

                              fns=fns, saveDate=saveDate)

         if(missing(sns)) sns = sampleNames(callSet)

@@ -1183,14 +1183,13 @@ genotype.Illumina = function(sampleSheet=NULL,

 	is.snp = isSnp(callSet)

 	snp.index = which(is.snp)

         narrays = ncol(callSet)

-        

         if(is.lds) {

           sampleBatches = splitIndicesByNode(seq(along=sampleNames(callSet)))

           mixtureParams = initializeBigMatrix("crlmmMixt-", 4, narrays, "double")

           SNR = initializeBigVector("crlmmSNR-", narrays, "double")

           SKW = initializeBigVector("crlmmSKW-", narrays, "double")

-          

+

           ocLapply(sampleBatches, processIDAT, sampleSheet=sampleSheet, arrayNames=arrayNames,

                  ids=ids, path=path, arrayInfoColNames=arrayInfoColNames, highDensity=highDensity,

                  sep=sep, fileExt=fileExt, saveDate=saveDate, verbose=verbose, mixtureSampleSize=mixtureSampleSize,

@@ -1213,12 +1212,12 @@ genotype.Illumina = function(sampleSheet=NULL,

           XY = RGtoXY(RG, chipType=cdfName)

           rm(RG); gc()

-        

+

           res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                                seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget)

           rm(XY); gc()

           if(verbose) message("Finished preprocessing.")

-          np.index = which(!is.snp)        

+          np.index = which(!is.snp)

           A(callSet)[snp.index, ] = res[["A"]]

           B(callSet)[snp.index, ] = res[["B"]]

           if(length(np.index)>0) {

@@ -1257,7 +1256,7 @@ genotype.Illumina = function(sampleSheet=NULL,

           tmpA = A(callSet)[snp.index,]

           tmpB = B(callSet)[snp.index,]

         }

-        

+

 	tmp = crlmmGTfxn(FUN,

 			  A=tmpA,

 			  B=tmpB,

@@ -1308,7 +1307,7 @@ processIDAT =  function(sel, sampleSheet=NULL,

 			  highDensity=FALSE,

 			  sep="_",

 			  fileExt=list(green="Grn.idat", red="Red.idat"),

-			  saveDate=FALSE, 

+			  saveDate=FALSE,

                           verbose=TRUE,

                           mixtureSampleSize=10^5,

 			  fitMixture=TRUE,

@@ -1319,7 +1318,7 @@ processIDAT =  function(sel, sampleSheet=NULL,

 			  stripNorm=TRUE,

 			  useTarget=TRUE,

                           A, B, SKW, SNR, mixtureParams, is.snp) {

-  

+

         if(length(path)>= length(sel)) path = path[sel]

         RG = readIdatFiles(sampleSheet=sampleSheet[sel,], arrayNames=arrayNames[sel],

                        ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,

@@ -1330,7 +1329,7 @@ processIDAT =  function(sel, sampleSheet=NULL,

         delete(RG@assayData$R); delete(RG@assayData$G); delete(RG@assayData$zero); rm(RG)

         gc()

         if (missing(sns) || length(sns)!=ncol(XY)) sns = sampleNames(XY)

-        

+

         res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                                seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget)

         #                       save.it=save.it, snpFile=snpFile, cnFile=cnFile)

@@ -1339,7 +1338,7 @@ processIDAT =  function(sel, sampleSheet=NULL,

         gc()

 	if(verbose) message("Finished preprocessing.")

         snp.index = which(is.snp)

-	np.index = which(!is.snp)      

+	np.index = which(!is.snp)

         open(res[["A"]])

         open(res[["B"]])