...
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...
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@@ -693,6 +693,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
|
693
|
693
|
close(mixtureParams)
|
694
|
694
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close(SNR)
|
695
|
695
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# }
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|
696
|
+
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|
697
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+ open(res[["A"]])
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|
698
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+ open(res[["B"]])
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|
699
|
+ open(res[["zero"]])
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|
700
|
+ open(res[["SNR"]])
|
|
701
|
+ open(res[["mixtureParams"]])
|
696
|
702
|
|
697
|
703
|
res = list(A=A, B=B,
|
698
|
704
|
zero=zero, sns=sns, gns=names(snpIndex), SNR=SNR, SKW=SKW,
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...
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...
|
@@ -705,6 +711,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
|
705
|
711
|
if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".")
|
706
|
712
|
}
|
707
|
713
|
|
|
714
|
+ close(res[["A"]])
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|
715
|
+ close(res[["B"]])
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|
716
|
+ close(res[["zero"]])
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|
717
|
+ close(res[["SNR"]])
|
|
718
|
+ close(res[["mixtureParams"]])
|
|
719
|
+
|
708
|
720
|
return(res)
|
709
|
721
|
}
|
710
|
722
|
|
...
|
...
|
@@ -738,10 +750,6 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,
|
738
|
750
|
res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,
|
739
|
751
|
seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget,
|
740
|
752
|
save.it=save.it, snpFile=snpFile, cnFile=cnFile)
|
741
|
|
- open(res[["A"]]) # this should perhaps go below }else{ below
|
742
|
|
- open(res[["B"]])
|
743
|
|
- open(res[["SNR"]])
|
744
|
|
- open(res[["mixtureParams"]])
|
745
|
753
|
|
746
|
754
|
# fD = featureData(XY)
|
747
|
755
|
# phenD = XY@phenoData
|
...
|
...
|
@@ -769,8 +777,13 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,
|
769
|
777
|
stop("Object in ", snpFile, " seems to be invalid.")
|
770
|
778
|
}
|
771
|
779
|
|
|
780
|
+ open(res[["A"]])
|
|
781
|
+ open(res[["B"]])
|
|
782
|
+ open(res[["SNR"]])
|
|
783
|
+ open(res[["mixtureParams"]])
|
|
784
|
+
|
772
|
785
|
# rm(phenD, protD , fD)
|
773
|
|
-
|
|
786
|
+
|
774
|
787
|
# snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))
|
775
|
788
|
# suppressWarnings(A(callSet) <- res[["A"]])
|
776
|
789
|
# suppressWarnings(B(callSet) <- res[["B"]])
|
...
|
...
|
@@ -873,6 +886,11 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,
|
873
|
886
|
res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,
|
874
|
887
|
seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget, #) # sns=subsns
|
875
|
888
|
save.it=save.it, snpFile=snpFile, cnFile=cnFile)
|
|
889
|
+ open(res[["A"]])
|
|
890
|
+ open(res[["B"]])
|
|
891
|
+ open(res[["SNR"]])
|
|
892
|
+ open(res[["mixtureParams"]])
|
|
893
|
+
|
876
|
894
|
# fD = featureData(XY)
|
877
|
895
|
# phenD = XY@phenoData
|
878
|
896
|
# protD = XY@protocolData
|