@@ -377,3 +377,7 @@ in the one function to reduce memory usage (not exported as yet)

 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 

 is stored in the assayData slot.

  * now store 'zero' with copy number AB intensities in preprocessInfinium2()

+

+2010-02-05 M. Ritchie - committed version 1.5.24

+ * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina().  The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.

+ * updated man page for crlmmIllumina()

\ No newline at end of file

@@ -1,8 +1,8 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.5.23

-Date: 2010-02-04

+Version: 1.5.24

+Date: 2010-02-05

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

@@ -612,7 +612,8 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

 				stripNorm=TRUE,

 				useTarget=TRUE,

 				save.it=FALSE,

-				intensityFile) {

+				snpFile,

+				cnFile) {

   if(stripNorm)

     XY = stripNormalize(XY, useTarget=useTarget, verbose=verbose)

@@ -660,7 +661,13 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)

   cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)

-  rm(A, B, zero)

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

+    t0 <- proc.time() 

+    save(cnAB, file=cnFile) 

+    t0 <- proc.time()-t0

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

+  }

+  rm(cnAB, B, zero)

   # next process snp probes

   snpIndex = getVarInEnv("snpProbesFid")

@@ -723,11 +730,11 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   ## gns comes from preprocStuff.rda

   res = list(A=A, B=B, zero=zero, sns=sns, gns=gns, SNR=SNR, SKW=SKW, mixtureParams=mixtureParams, cdfName=cdfName)

-  if(save.it & !missing(intensityFile)) {

+  if(save.it & !missing(snpFile)) {

     t0 <- proc.time() 

-    save(cnAB, res, file=intensityFile)

+    save(res, file=snpFile) 

     t0 <- proc.time()-t0

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

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

   }

   return(res)

 }

@@ -738,17 +745,19 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

 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, snpFile, cnFile,

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

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

                   returnParams=FALSE, badSNP=.7) {

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

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

-  if (!missing(intensityFile))

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

+  if (save.it & (missing(snpFile) | missing(cnFile)))

+    stop("'snpFile' and/or 'cnFile' is missing and you chose to save.it")

+  if (load.it & missing(snpFile))

+    stop("'snpFile' is missing and you chose to load.it")

+  if (!missing(snpFile))

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

       load.it <- FALSE

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

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

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

+      stop("Cannot load SNP data.")

   }

   if (!load.it){

     if(!missing(RG)) {

@@ -761,13 +770,13 @@ 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, intensityFile=intensityFile)

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

   }else{

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

-        obj <- load(intensityFile)

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

+        obj <- load(snpFile)

         if(verbose) message("Done.")

         if(!any(obj == "res"))

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

+          stop("Object in ", snpFile, " 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

@@ -804,15 +813,15 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

           	  row.names=TRUE, 

 			  col.names=TRUE,

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

-              seed=1, save.ab=FALSE, abFile,

+              seed=1, save.ab=FALSE, snpFile, cnFile,

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

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

               returnParams=FALSE, badSNP=.7) {

   if (save.rg & missing(rgFile))

     stop("'rgFile' is missing, and you chose save.rg")

-  if (save.ab & missing(abFile))

-    stop("'abFile' is missing, and you chose save.ab")

+  if (save.ab & (missing(snpFile) | missing(cnFile)))

+    stop("'snpFile' or 'cnFile' is missing and you chose save.ab")

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

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

@@ -827,7 +836,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

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

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

-                        save.it=save.ab, intensityFile=abFile)

+                        save.it=save.ab, snpFile=snpFile, cnFile=cnFile)

   rm(XY)

   gc()

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

@@ -11,7 +11,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, method="quantile",

       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, mixtureSampleSize=10^5,

+      snpFile, cnFile, mixtureSampleSize=10^5,

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

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

 }

@@ -33,10 +33,12 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, method="quantile",

     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

+  \item{save.it}{'logical'. Save preprocessed SNP and copy number data?}

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

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

     be saved/loaded.}

+  \item{cnFile}{'character' with filename of preprocessed copy number 

+    data to be saved.}

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

     when fitting the mixture model.}

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