@@ -631,7 +631,7 @@ preprocessInfinium2 = function(XY, mixtureSampleSize=10^5, fitMixture=TRUE, eps=

 crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

                   row.names=TRUE, col.names=TRUE,

                   probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5, gender=NULL,

-                  seed=1, # save.it=FALSE, load.it=FALSE, intensityFile,

+                  seed=1, save.it=FALSE, load.it=FALSE, intensityFile,

                   mixtureSampleSize=10^5, eps=0.1, verbose=TRUE,

                   cdfName, sns, recallMin=10, recallRegMin=1000,

                   returnParams=FALSE, badSNP=.7) {

@@ -641,34 +641,34 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

     else

       stop("Both RG and XY specified - please use one or the other")

   }

-#  if ((load.it | save.it) & missing(intensityFile))

-#    stop("'intensityFile' is missing, and you chose either load.it or save.it")

+  if ((load.it | save.it) & missing(intensityFile))

+    stop("'intensityFile' is missing, and you chose either load.it or save.it")

   if (missing(sns)) sns <- sampleNames(XY) #basename(filenames)

-#  if (!missing(intensityFile))

-#    if (load.it & !file.exists(intensityFile)){

-#      load.it <- FALSE

-#      message("File ", intensityFile, " does not exist.")

-#      message("Not loading it, but running SNPRMA from scratch.")

-# }

-#  if (!load.it){

+  if (!missing(intensityFile))

+    if (load.it & !file.exists(intensityFile)){

+      load.it <- FALSE

+      message("File ", intensityFile, " does not exist.")

+      message("Not loading it, but running SNPRMA from scratch.")

+  }

+  if (!load.it){

 #    res <- snprma(filenames, fitMixture=TRUE,

 #                    mixtureSampleSize=mixtureSampleSize, verbose=verbose,

 #                    eps=eps, cdfName=cdfName, sns=sns)

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

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

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

-#    if(save.it){

-#      t0 <- proc.time()

-#      save(res, file=intensityFile)

-#      t0 <- proc.time()-t0

-#      if (verbose) message("Used ", t0[3], " seconds to save ", intensityFile, ".")

-#    }

-#      }else{

-#            if (verbose) message("Loading ", intensityFile, ".")

-#                obj <- load(intensityFile)

-#                if (verbose) message("Done.")

-#                if (obj != "res")

-#                        stop("Object in ", intensityFile, " seems to be invalid.")

-#          }

+    if(save.it){

+      t0 <- proc.time()

+      save(res, file=intensityFile)

+      t0 <- proc.time()-t0

+      if(verbose) message("Used ", t0[3], " seconds to save ", intensityFile, ".")

+    }

+  }else{

+      if(verbose) message("Loading ", intensityFile, ".")

+        obj <- load(intensityFile)

+        if(verbose) message("Done.")

+        if(obj != "res")

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

+  }

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

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

@@ -680,13 +680,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

                   returnParams=returnParams, badSNP=badSNP,

                   verbose=verbose)

-  res2[["A"]] <- res[["A"]]  # added for copy number analysis

-  res2[["B"]] <- res[["B"]]  # added for copy number analysis

   res2[["SNR"]] <- res[["SNR"]]

   res2[["SKW"]] <- res[["SKW"]]

-  res2[["zero"]] <- res[["zero"]]

-  rm(res)

-  gc()

-  # MR: FIXME - for consistency with crlmm, need to save results in a 'SnpSet' object

-  return(res2)

+  return(res2) # return(list2SnpSet(res2, returnParams=returnParams))

 }

@@ -10,7 +10,8 @@

 crlmmIllumina(RG, XY, stripNorm=TRUE, useTarget=TRUE,

       row.names=TRUE, col.names=TRUE,

       probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5,

-      gender=NULL, seed=1, mixtureSampleSize=10^5,

+      gender=NULL, seed=1, save.it=FALSE, load.it=FALSE,

+      intensityFile, mixtureSampleSize=10^5,

       eps=0.1, verbose=TRUE, cdfName, sns, recallMin=10,

       recallRegMin=1000, returnParams=FALSE, badSNP=0.7)

 }

@@ -31,6 +32,10 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, useTarget=TRUE,

     defining sex. (1 - male; 2 - female)}

   \item{seed}{'integer' scalar for random number generator (used to

     sample \code{mixtureSampleSize} SNPs for mixture model.}

+  \item{save.it}{'logical'. Save preprocessed data?}

+  \item{load.it}{'logical'. Load preprocessed data to speed up analysis?}

+  \item{intensityFile}{'character' with filename of preprocessed data to

+    be saved/loaded.}

   \item{mixtureSampleSize}{'integer'. The number of SNP's to be used

     when fitting the mixture model.}

   \item{eps}{Minimum change for mixture model.}