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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49035 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 23:53:32
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@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)
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 2010-08-25 M. Ritchie 1.7.12
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 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
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 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
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-** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().
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+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()
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 ** tidied up crlmm-illumina.R, removing commented out code.
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@@ -684,6 +684,16 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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   }
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   if (!fitMixture) SNR <- mixtureParams <- NA
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   ## gns comes from preprocStuff.rda
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+
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+#  if(class(A)[1]=="ff_matrix") {
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+    close(A)
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+    close(B)
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+    close(zero)
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+    close(SKW)
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+    close(mixtureParams)
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+    close(SNR)
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+#  }  
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+  
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   res = list(A=A, B=B,
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              zero=zero, sns=sns, gns=names(snpIndex), SNR=SNR, SKW=SKW,
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              mixtureParams=mixtureParams, cdfName=cdfName)
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@@ -694,14 +704,7 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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     t0 <- proc.time()-t0
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     if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".")
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   }
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-#  if(class(A)[1]=="ff_matrix") {
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-    close(A)
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-    close(B)
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-    close(zero)
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-    close(SKW)
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-    close(mixtureParams)
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-    close(SNR)
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-#  }
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+
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   return(res)
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 }
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@@ -735,6 +738,10 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,
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     res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,
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                         seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget,
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                         save.it=save.it, snpFile=snpFile, cnFile=cnFile)
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+    open(res[["A"]])  # this should perhaps go below }else{ below
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+    open(res[["B"]])
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+    open(res[["SNR"]])
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+    open(res[["mixtureParams"]])    
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 #    fD = featureData(XY)
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 #    phenD = XY@phenoData
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@@ -762,7 +769,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,
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           stop("Object in ", snpFile, " seems to be invalid.")
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   }
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- #   rm(phenD, protD , fD)
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+#    rm(phenD, protD , fD)
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 #    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))                
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 #    suppressWarnings(A(callSet) <- res[["A"]])