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@@ -693,6 +693,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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close(mixtureParams)
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close(SNR)
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# }
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+
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+ open(res[["A"]])
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+ open(res[["B"]])
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+ open(res[["zero"]])
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+ open(res[["SNR"]])
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+ open(res[["mixtureParams"]])
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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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@@ -705,6 +711,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".")
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}
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+ close(res[["A"]])
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+ close(res[["B"]])
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+ close(res[["zero"]])
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+ close(res[["SNR"]])
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+ close(res[["mixtureParams"]])
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+
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return(res)
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721 |
}
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722 |
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@@ -738,10 +750,6 @@ 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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753 |
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# fD = featureData(XY)
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# phenD = XY@phenoData
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@@ -769,8 +777,13 @@ 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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771 |
779 |
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+ open(res[["A"]])
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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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784 |
+
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# rm(phenD, protD , fD)
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|
-
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786 |
+
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# snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))
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788 |
# suppressWarnings(A(callSet) <- res[["A"]])
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# suppressWarnings(B(callSet) <- res[["B"]])
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... |
... |
@@ -873,6 +886,11 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,
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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, #) # sns=subsns
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save.it=save.it, snpFile=snpFile, cnFile=cnFile)
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889 |
+ open(res[["A"]])
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+ open(res[["B"]])
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+ open(res[["SNR"]])
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|
892 |
+ open(res[["mixtureParams"]])
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893 |
+
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876 |
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# fD = featureData(XY)
|
877 |
895 |
# phenD = XY@phenoData
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# protD = XY@protocolData
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