@@ -546,4 +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

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

\ No newline at end of file

+** 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().

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

@@ -142,6 +142,11 @@ readIdatFiles <- function(sampleSheet=NULL,

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

        }

        storageMode(RG) = "lockedEnvironment"

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

+         close(RG@assayData$R)

+         close(RG@assayData$G)

+         close(RG@assayData$zero)         

+       }

        RG

 }

@@ -493,6 +498,12 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   XY@assayData$zero[infI,] = 0  

   gc()

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

+    close(XY@assayData$X)

+    close(XY@assayData$Y)

+    close(XY@assayData$zero)

+  }

+  

 #  storageMode(XY) = "lockedEnvironment"

   XY

 }

@@ -518,7 +529,12 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

   if(verbose){

     message("Quantile normalizing ", ncol(XY), " arrays by ", max(stripnum), " strips.")

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

-  } 

+  }

+  

+  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)

@@ -538,6 +554,11 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

     rm(subX, subY, tmp, sel)

     gc()

   }

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

+    close(XY@assayData$X)

+    close(XY@assayData$Y)

+  }

+  

   if(verbose)

     cat("\n")

   XY

@@ -673,12 +694,14 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

     t0 <- proc.time()-t0

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

   }

-  close(A)

-  close(B)

-  close(zero)

-  close(SKW)

-  close(mixtureParams)

-  close(SNR)

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

+    close(A)

+    close(B)

+    close(zero)

+    close(SKW)

+    close(mixtureParams)

+    close(SNR)

+  }

   return(res)

 }