@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)

 2010-08-25 M. Ritchie 1.7.12

 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

-** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().

+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

@@ -684,6 +684,16 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   }

   if (!fitMixture) SNR <- mixtureParams <- NA

   ## gns comes from preprocStuff.rda

+

+#  if(class(A)[1]=="ff_matrix") {

+    close(A)

+    close(B)

+    close(zero)

+    close(SKW)

+    close(mixtureParams)

+    close(SNR)

+#  }  

+  

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

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

              mixtureParams=mixtureParams, cdfName=cdfName)

@@ -694,14 +704,7 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

     t0 <- proc.time()-t0

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

   }

-#  if(class(A)[1]=="ff_matrix") {

-    close(A)

-    close(B)

-    close(zero)

-    close(SKW)

-    close(mixtureParams)

-    close(SNR)

-#  }

+

   return(res)

 }

@@ -735,6 +738,10 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

     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)

+    open(res[["A"]])  # this should perhaps go below }else{ below

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

+    open(res[["SNR"]])

+    open(res[["mixtureParams"]])    

 #    fD = featureData(XY)

 #    phenD = XY@phenoData

@@ -762,7 +769,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

           stop("Object in ", snpFile, " seems to be invalid.")

   }

- #   rm(phenD, protD , fD)

+#    rm(phenD, protD , fD)

 #    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))                

 #    suppressWarnings(A(callSet) <- res[["A"]])