@@ -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 a check for whether an object is an 'ff_matrix' before running open() or close() to several functions.  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().

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

@@ -142,11 +142,11 @@ readIdatFiles <- function(sampleSheet=NULL,

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

        }

        storageMode(RG) = "lockedEnvironment"

-       if(class(RG@assayData$R)[1]=="ff_matrix") {

+#       if(class(RG@assayData$R)[1]=="ff_matrix") {

          close(RG@assayData$R)

          close(RG@assayData$G)

          close(RG@assayData$zero)         

-       }

+#       }

        RG

 }

@@ -498,11 +498,11 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   XY@assayData$zero[infI,] = 0  

   gc()

-  if(class(XY@assayData$X)[1]=="ff_matrix") {

+#  if(class(XY@assayData$X)[1]=="ff_matrix") {

     close(XY@assayData$X)

     close(XY@assayData$Y)

     close(XY@assayData$zero)

-  }

+#  }

 #  storageMode(XY) = "lockedEnvironment"

   XY

@@ -531,10 +531,10 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

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

   }

-  if(class(XY@assayData$X)[1]=="ff_matrix") {

+#  if(class(XY@assayData$X)[1]=="ff_matrix") {

     open(XY@assayData$X)

     open(XY@assayData$Y)

-  }

+#  }

   for(s in 1:max(stripnum)) {

     if(verbose) {

       if (getRversion() > '2.7.0') setTxtProgressBar(pb, s)

@@ -554,10 +554,10 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

     rm(subX, subY, tmp, sel)

     gc()

   }

-  if(class(XY@assayData$X)[1]=="ff_matrix") {

+#  if(class(XY@assayData$X)[1]=="ff_matrix") {

     close(XY@assayData$X)

     close(XY@assayData$Y)

-  }

+#  }

   if(verbose)

     cat("\n")

@@ -694,14 +694,14 @@ 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") {

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

     close(A)

     close(B)

     close(zero)

     close(SKW)

     close(mixtureParams)

     close(SNR)

-  }

+#  }

   return(res)

 }