Browse code

removed old code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45686 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/04/2010 16:21:15
Showing1 changed files

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@@ -419,30 +419,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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                              cIndexes=cIndexes, SMEDIAN=SMEDIAN,
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                              theKnots=theKnots, DF=DF, probs=probs,
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                              batchSize=ocProbesets())
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-##   last <- 0
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-##   for (idxBatch in seq(along=snpBatches)){
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-##     snps <- snpBatches[[idxBatch]]
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-##     rSnps <- range(snps)
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-##     IndexesBatch <- list(autosomeIndex[autosomeIndex %in% snps]-last,
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-##                          XIndex[XIndex %in% snps]-last,
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-##                          YIndex[YIndex %in% snps]-last)
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-##     IndexesBatch <- lapply(IndexesBatch, as.integer)
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-##     tmpA <- A[snps,]
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-##     tmpB <- B[snps,]
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-##     newparamsBatch[[idxBatch]] <- gtypeCallerR(tmpA, tmpB, fIndex, mIndex,
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-##                                                params[["centers"]][snps,],
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-##                                                params[["scales"]][snps,],
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-##                                                params[["N"]][snps,],
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-##                                                IndexesBatch, cIndexes,
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-##                                                sapply(IndexesBatch, length),
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-##                                                sapply(cIndexes, length),
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-##                                                SMEDIAN, theKnots,
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-##                                                mixtureParams[], DF, probs, 0.025)
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-##     last <- rSnps[2]
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-##     rm(snps, rSnps, IndexesBatch, tmpA, tmpB)
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-##   }
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-##   rm(last)
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-  
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   newparams <- vector("list", 3)
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   names(newparams) <- c("centers", "scales", "N")
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   newparams[["centers"]] <- do.call("rbind", lapply(newparamsBatch, "[[", 1))
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@@ -525,8 +501,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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   ## ## MOVE TO C#######
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   ## running in batches
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-  ## snpBatches <- splitIndicesByLength(1:nrow(A), ocProbesets())
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-
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   process2 <- function(idxBatch, snpBatches, autosomeIndex, XIndex,
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                        YIndex, A, B, mixtureParams, fIndex, mIndex,
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                        params, cIndexes, SMEDIAN, theKnots, DF, probs,
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@@ -569,35 +543,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,
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            mIndex=mIndex, params=params, cIndexes=cIndexes,
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            SMEDIAN=SMEDIAN, theKnots=theKnots, DF=DF, probs=probs,
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            regionInfo=regionInfo, batchSize=ocProbesets())
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-  
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-##   last <- 0
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-##   for (idxBatch in seq(along=snpBatches)){
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-##     snps <- snpBatches[[idxBatch]]
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-##     tmpA <- A[snps,]
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-##     tmpB <- B[snps,]
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-##     rSnps <- range(snps)
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-##     IndexesBatch <- list(autosomeIndex[autosomeIndex %in% snps]-last,
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-##                          XIndex[XIndex %in% snps]-last,
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-##                          YIndex[YIndex %in% snps]-last)
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-##     IndexesBatch <- lapply(IndexesBatch, as.integer)
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-##     ImNull <- gtypeCallerR2(tmpA, tmpB, fIndex, mIndex,
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-##                             params[["centers"]][snps,],
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-##                             params[["scales"]][snps,],
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-##                             params[["N"]][snps,],
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-##                             IndexesBatch, cIndexes,
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-##                             sapply(IndexesBatch, length),
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-##                             sapply(cIndexes, length),
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-##                             SMEDIAN, theKnots, mixtureParams[],
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-##                             DF, probs, 0.025,
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-##                             which(regionInfo[snps, 2]),
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-##                             which(regionInfo[snps, 1]))
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-##     A[snps,] <- tmpA
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-##     B[snps,] <- tmpB
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-##     last <- rSnps[2]
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-##     rm(tmpA, tmpB, snps, rSnps, IndexesBatch, ImNull)
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-##   }
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-##   
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-##   gc(verbose=FALSE)
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   ##  END MOVE TO C#######
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   ## ##################
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