Error in re-building vignettes:
  ...
Segmenting by CBS...
 Chromosome: 1
 Segmenting multiple segments on current chromosome...
  Number of segments: 3
  Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG")
  Produced 3 seeds from this stream for future usage
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
 Segmenting multiple segments on current chromosome...done
Segmenting by CBS...done
Warning in plotTracks.CBS(fit) :
  Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning.
Prune segments by hierarchical clustering...
 Clustering arguments:
 List of 4
  $ size        : NULL
  $ distMethod  : chr "euclidean"
  $ hclustMethod: chr "ward.D"
  $ h           : num 0.25
 Clustering...
  Hierarchical clustering of segmented copy numbers...
   Extracting/sampling CNs...
     num [1:9, 1] 1.38 3.19 1.39 NA 2.07 ...
     - attr(*, "dimnames")=List of 2
      ..$ : chr [1:9] "1" "2" "3" "4" ...
      ..$ : chr "mean"
     num [1:8, 1] 1.38 3.19 1.39 2.07 2.71 ...
     - attr(*, "dimnames")=List of 2
      ..$ : chr [1:8] "1" "2" "3" "5" ...
      ..$ : chr "mean"
   Extracting/sampling CNs...done
   Calculating distance matrix...
    Class 'dist'  atomic [1:28] 1.8055 0.0115 0.6858 1.3278 1.2065 ...
      ..- attr(*, "Size")= int 8
      ..- attr(*, "Labels")= chr [1:8] "1" "2" "3" "5" ...
      ..- attr(*, "Diag")= logi FALSE
      ..- attr(*, "Upper")= logi FALSE
      ..- attr(*, "method")= chr "euclidean"
      ..- attr(*, "call")= language stats::dist(x = C, method = distMethod)
   Calculating distance matrix...done
   Clustering...
    List of 7
     $ merge      : int [1:7, 1:2] -1 -6 -5 -2 -4 4 1 -3 -8 2 ...
     $ height     : num [1:7] 0.0115 0.0514 0.1103 0.6868 0.827 ...
     $ order      : int [1:8] 1 3 2 7 4 5 6 8
     $ labels     : chr [1:8] "1" "2" "3" "5" ...
     $ method     : chr "ward.D"
     $ call       : language stats::hclust(d = D, method = hclustMethod)
     $ dist.method: chr "euclidean"
     - attr(*, "class")= chr "hclust"
   Clustering...done
  Hierarchical clustering of segmented copy numbers...done
  
  Call:
  stats::hclust(d = D, method = hclustMethod)
  
  Cluster method   : ward.D 
  Distance         : euclidean 
  Number of objects: 8 
  
 Clustering...done
 Cutting tree...
  Cutting arguments:
  List of 2
   $ tree:List of 7
    ..$ merge      : int [1:7, 1:2] -1 -6 -5 -2 -4 4 1 -3 -8 2 ...
    ..$ height     : num [1:7] 0.0115 0.0514 0.1103 0.6868 0.827 ...
    ..$ order      : int [1:8] 1 3 2 7 4 5 6 8
    ..$ labels     : chr [1:8] "1" "2" "3" "5" ...
    ..$ method     : chr "ward.D"
    ..$ call       : language stats::hclust(d = D, method = hclustMethod)
    ..$ dist.method: chr "euclidean"
    ..- attr(*, "class")= chr "hclust"
   $ h   : num 0.25
   Named int [1:8] 1 2 1 3 4 4 5 4
   - attr(*, "names")= chr [1:8] "1" "2" "3" "5" ...
  List of 5
   $ 1: int [1:2] 1 3
   $ 2: int 2
   $ 3: int 5
   $ 4: int [1:3] 6 7 9
   $ 5: int 8
   - attr(*, "call")= language by.default(data = names(p), INDICES = p, FUN = functio..
   - attr(*, "class")= chr "by"
 Cutting tree...done
 Merging mean levels of clustered segments...
 Merging mean levels of clustered segments...done
 Merging neighboring segments within each cluster...
  Cluster #1 of 5...
   Segments in cluster:
    int [1:2] 1 3
   Left indices of neighboring segments:
    int(0) 
  Cluster #1 of 5...done
  Cluster #2 of 5...
   Segments in cluster:
    int 2
   Left indices of neighboring segments:
    int(0) 
  Cluster #2 of 5...done
  Cluster #3 of 5...
   Segments in cluster:
    int 5
   Left indices of neighboring segments:
    int(0) 
  Cluster #3 of 5...done
  Cluster #4 of 5...
   Segments in cluster:
    int [1:3] 6 7 9
   Left indices of neighboring segments:
    int 6
  Cluster #4 of 5...done
  Cluster #5 of 5...
   Segments in cluster:
    int 8
   Left indices of neighboring segments:
    int(0) 
  Cluster #5 of 5...done
  Left indices of segments to be merged:
   int 6
 Merging neighboring segments within each cluster...done
 Merging segments...
 Merging segments...done
 Updating segment means...
 Updating segment means...done
Prune segments by hierarchical clustering...done
Warning in plotTracks.CBS(fitP) :
  Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fitP) is unknown ('NA'). Use signalType(fitP) <- 'ratio' to avoid this warning.
Warning: Argument 'preserveScale' for segmentByPairedPSCBS() is deprecated and ignored; as of PSCBS 0.64.0 (Mar 2018) it is effectively fixed to FALSE, which has been the default since PSCBS 0.50.0 (Oct 2015). To avoid this warning, do not specify 'preserveScale' when calling segmentByPairedPSCBS().
Segmenting paired tumor-normal signals using Paired PSCBS...
 Calling genotypes from normal allele B fractions...
   num [1:73346] 0.827 0.875 0.887 0.884 0.103 ...
  Called genotypes:
   atomic [1:73346] 1 1 1 1 0 0.5 0.5 0 0.5 0 ...
   - attr(*, "modelFit")=List of 1
    ..$ :List of 7
    .. ..$ flavor             : chr "density"
    .. ..$ cn                 : int 2
    .. ..$ nbrOfGenotypeGroups: int 3
    .. ..$ tau                : num [1:2] 0.316 0.679
    .. ..$ n                  : int 73181
    .. ..$ fit                :Classes 'PeaksAndValleys' and 'data.frame':	5 obs. of ..
    .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 1 2 1 2 1
    .. .. ..$ x      : num [1:5] 0.096 0.316 0.496 0.679 0.894
    .. .. ..$ density: num [1:5] 1.709 0.437 1.12 0.466 1.673
    .. ..$ fitValleys         :Classes 'PeaksAndValleys' and 'data.frame':	2 obs. of ..
    .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 2 2
    .. .. ..$ x      : num [1:2] 0.316 0.679
    .. .. ..$ density: num [1:2] 0.437 0.466
    ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list"
  muN
      0   0.5     1 
  26499 20487 26360 
 Calling genotypes from normal allele B fractions...done
 Normalizing betaT using betaN (TumorBoost)...
  Normalized BAFs:
   atomic [1:73346] 0.93 0.896 0.947 0.894 0.126 ...
   - attr(*, "modelFit")=List of 5
    ..$ method       : chr "normalizeTumorBoost"
    ..$ flavor       : chr "v4"
    ..$ delta        : atomic [1:73346] -0.173 -0.125 -0.113 -0.116 0.103 ...
    .. ..- attr(*, "modelFit")=List of 1
    .. .. ..$ :List of 7
    .. .. .. ..$ flavor             : chr "density"
    .. .. .. ..$ cn                 : int 2
    .. .. .. ..$ nbrOfGenotypeGroups: int 3
    .. .. .. ..$ tau                : num [1:2] 0.316 0.679
    .. .. .. ..$ n                  : int 73181
    .. .. .. ..$ fit                :Classes 'PeaksAndValleys' and 'data.frame':	5 ob..
    .. .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 1 2 1 2 1
    .. .. .. .. ..$ x      : num [1:5] 0.096 0.316 0.496 0.679 0.894
    .. .. .. .. ..$ density: num [1:5] 1.709 0.437 1.12 0.466 1.673
    .. .. .. ..$ fitValleys         :Classes 'PeaksAndValleys' and 'data.frame':	2 ob..
    .. .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 2 2
    .. .. .. .. ..$ x      : num [1:2] 0.316 0.679
    .. .. .. .. ..$ density: num [1:2] 0.437 0.466
    .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list"
    ..$ preserveScale: logi FALSE
    ..$ scaleFactor  : num NA
 Normalizing betaT using betaN (TumorBoost)...done
 Setup up data...
  'data.frame':	73346 obs. of  7 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  1145994 2224111 2319424 2543484 2926730 ...
   $ CT        : num  1.625 1.071 1.406 1.18 0.856 ...
   $ betaT     : num  0.757 0.771 0.834 0.778 0.229 ...
   $ betaTN    : atomic  0.93 0.896 0.947 0.894 0.126 ...
    ..- attr(*, "modelFit")=List of 5
    .. ..$ method       : chr "normalizeTumorBoost"
    .. ..$ flavor       : chr "v4"
    .. ..$ delta        : atomic  -0.173 -0.125 -0.113 -0.116 0.103 ...
    .. .. ..- attr(*, "modelFit")=List of 1
    .. .. .. ..$ :List of 7
    .. .. .. .. ..$ flavor             : chr "density"
    .. .. .. .. ..$ cn                 : int 2
    .. .. .. .. ..$ nbrOfGenotypeGroups: int 3
    .. .. .. .. ..$ tau                : num  0.316 0.679
    .. .. .. .. ..$ n                  : int 73181
    .. .. .. .. ..$ fit                :Classes 'PeaksAndValleys' and 'data.frame':	5..
    .. .. .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 1 2 1 2 1
    .. .. .. .. .. ..$ x      : num  0.096 0.316 0.496 0.679 0.894
    .. .. .. .. .. ..$ density: num  1.709 0.437 1.12 0.466 1.673
    .. .. .. .. ..$ fitValleys         :Classes 'PeaksAndValleys' and 'data.frame':	2..
    .. .. .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 2 2
    .. .. .. .. .. ..$ x      : num  0.316 0.679
    .. .. .. .. .. ..$ density: num  0.437 0.466
    .. .. .. ..- attr(*, "class")= chr  "NaiveGenotypeModelFit" "list"
    .. ..$ preserveScale: logi FALSE
    .. ..$ scaleFactor  : num NA
   $ betaN     : num  0.827 0.875 0.887 0.884 0.103 ...
   $ muN       : atomic  1 1 1 1 0 0.5 0.5 0 0.5 0 ...
    ..- attr(*, "modelFit")=List of 1
    .. ..$ :List of 7
    .. .. ..$ flavor             : chr "density"
    .. .. ..$ cn                 : int 2
    .. .. ..$ nbrOfGenotypeGroups: int 3
    .. .. ..$ tau                : num  0.316 0.679
    .. .. ..$ n                  : int 73181
    .. .. ..$ fit                :Classes 'PeaksAndValleys' and 'data.frame':	5 obs. ..
    .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 1 2 1 2 1
    .. .. .. ..$ x      : num  0.096 0.316 0.496 0.679 0.894
    .. .. .. ..$ density: num  1.709 0.437 1.12 0.466 1.673
    .. .. ..$ fitValleys         :Classes 'PeaksAndValleys' and 'data.frame':	2 obs. ..
    .. .. .. ..$ type   : Factor w/ 2 levels "peak","valley": 2 2
    .. .. .. ..$ x      : num  0.316 0.679
    .. .. .. ..$ density: num  0.437 0.466
    .. ..- attr(*, "class")= chr  "NaiveGenotypeModelFit" "list"
 Setup up data...done
 Dropping loci for which TCNs are missing...
  Number of loci dropped: 49
 Dropping loci for which TCNs are missing...done
 Ordering data along genome...
  'data.frame':	73297 obs. of  7 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  554484 554636 557616 711153 730720 ...
   $ CT        : num  1.878 0.166 2.119 1.397 1.799 ...
   $ betaT     : num  0.0646 0.6462 0.8257 0.2598 0.1672 ...
   $ betaTN    : num  -0.0515 0.9543 0.9831 0.0832 -0.1172 ...
   $ betaN     : num  0.116 0.692 0.843 0.177 0.284 ...
   $ muN       : num  0 1 1 0 0 1 0.5 0 1 1 ...
 Ordering data along genome...done
 Keeping only current chromosome for 'knownSegments'...
  Chromosome: 1
  Known segments for this chromosome:
    chromosome    start      end   length
  1          1     -Inf 1.21e+08      Inf
  2          1 1.21e+08 1.42e+08 20517398
  3          1 1.42e+08      Inf      Inf
 Keeping only current chromosome for 'knownSegments'...done
 alphaTCN: 0.009
 alphaDH: 0.001
 Number of loci: 73297
 Calculating DHs...
  Number of SNPs: 73297
  Number of heterozygous SNPs: 20472 (27.93%)
  Normalized DHs:
   num [1:73297] NA NA NA NA NA ...
 Calculating DHs...done
 Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG")
 Produced 2 seeds from this stream for future usage
 Identification of change points by total copy numbers...
  Segmenting by CBS...
   Chromosome: 1
   Segmenting multiple segments on current chromosome...
    Number of segments: 3
    Random seed temporarily set (seed=c(407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG")
    Produced 3 seeds from this stream for future usage
     Segmenting by CBS...
      Chromosome: 1
       Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
     Segmenting by CBS...done
     Segmenting by CBS...
      Chromosome: 1
       Random seed temporarily set (seed=c(407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG")
     Segmenting by CBS...done
   Segmenting multiple segments on current chromosome...done
  Segmenting by CBS...done
  List of 4
   $ data   :'data.frame':	73297 obs. of  4 variables:
    ..$ chromosome: int [1:73297] 1 1 1 1 1 1 1 1 1 1 ...
    ..$ x         : num [1:73297] 554484 554636 557616 711153 730720 ...
    ..$ y         : num [1:73297] 1.878 0.166 2.119 1.397 1.799 ...
    ..$ index     : int [1:73297] 1 2 3 4 5 6 7 8 9 10 ...
   $ output :'data.frame':	7 obs. of  6 variables:
    ..$ sampleName: chr [1:7] NA NA NA NA ...
    ..$ chromosome: int [1:7] 1 1 1 1 1 1 1
    ..$ start     : num [1:7] 5.54e+05 1.21e+08 1.42e+08 1.86e+08 1.99e+08 ...
    ..$ end       : num [1:7] 1.21e+08 1.42e+08 1.86e+08 1.99e+08 2.07e+08 ...
    ..$ nbrOfLoci : int [1:7] 37495 0 13434 4018 2755 14 15581
    ..$ mean      : num [1:7] 1.38 NA 2.07 2.71 2.59 ...
   $ segRows:'data.frame':	7 obs. of  2 variables:
    ..$ startRow: int [1:7] 1 NA 37496 50930 54948 57703 57717
    ..$ endRow  : int [1:7] 37495 NA 50929 54947 57702 57716 73297
   $ params :List of 5
    ..$ alpha        : num 0.009
    ..$ undo         : num 0
    ..$ joinSegments : logi TRUE
    ..$ knownSegments:'data.frame':	4 obs. of  3 variables:
    .. ..$ chromosome: int [1:4] 1 1 2 1
    .. ..$ start     : num [1:4] -Inf -Inf -Inf 1.42e+08
    .. ..$ end       : num [1:4] 1.21e+08 Inf Inf Inf
    ..$ seed         : int [1:7] 407 1066287653 -51199871 161854402 -1995183193 15034..
   - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
   - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 16 0 16 NA NA
    .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
   - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
   - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
 Identification of change points by total copy numbers...done
 Restructure TCN segmentation results...
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean
  1          1 5.54e+05 1.21e+08        37495    1.38
  2          1 1.21e+08 1.42e+08            0      NA
  3          1 1.42e+08 1.86e+08        13434    2.07
  4          1 1.86e+08 1.99e+08         4018    2.71
  5          1 1.99e+08 2.07e+08         2755    2.59
  6          1 2.07e+08 2.07e+08           14    3.87
  7          1 2.07e+08 2.47e+08        15581    2.64
  Number of TCN segments: 7
 Restructure TCN segmentation results...done
 Total CN segment #1 ([    554484,1.20993e+08]) of 7...
  Number of TCN loci in segment: 37495
  Locus data for TCN segment:
  'data.frame':	37495 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  554484 554636 557616 711153 730720 ...
   $ CT        : num  1.878 0.166 2.119 1.397 1.799 ...
   $ betaT     : num  0.0646 0.6462 0.8257 0.2598 0.1672 ...
   $ betaTN    : num  -0.0515 0.9543 0.9831 0.0832 -0.1172 ...
   $ betaN     : num  0.116 0.692 0.843 0.177 0.284 ...
   $ muN       : num  0 1 1 0 0 1 0.5 0 1 1 ...
   $ index     : int  1 2 3 4 5 6 7 8 9 10 ...
   $ rho       : num  NA NA NA NA NA ...
  Number of loci: 37495
  Number of SNPs: 10146 (27.06%)
  Number of heterozygous SNPs: 10146 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	37495 obs. of  4 variables:
     ..$ chromosome: int [1:37495] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:37495] 554484 554636 557616 711153 730720 ...
     ..$ y         : num [1:37495] NA NA NA NA NA ...
     ..$ index     : int [1:37495] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	5 obs. of  6 variables:
     ..$ sampleName: chr [1:5] NA NA NA NA ...
     ..$ chromosome: int [1:5] 1 1 1 1 1
     ..$ start     : num [1:5] 5.54e+05 4.28e+06 4.27e+07 1.20e+08 1.20e+08
     ..$ end       : num [1:5] 4.28e+06 4.27e+07 1.20e+08 1.20e+08 1.21e+08
     ..$ nbrOfLoci : int [1:5] 169 3260 6657 8 52
     ..$ mean      : num [1:5] 0.4145 0.4944 0.5205 0.0767 0.5123
    $ segRows:'data.frame':	5 obs. of  2 variables:
     ..$ startRow: int [1:5] 7 693 12094 37253 37332
     ..$ endRow  : int [1:5] 684 12093 37250 37320 37449
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 554484
     .. ..$ end       : num 1.21e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 2.92 0 2.94 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1        7    684
   2      693  12093
   3    12094  37250
   4    37253  37320
   5    37332  37449
    int [1:37495] 1 2 3 4 5 6 7 8 9 10 ...
   DH segmentation rows:
     startRow endRow
   1        7    684
   2      693  12093
   3    12094  37250
   4    37253  37320
   5    37332  37449
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 5.54e+05 4.28e+06         169 0.4145
  2 4.28e+06 4.27e+07        3260 0.4944
  3 4.27e+07 1.20e+08        6657 0.5205
  4 1.20e+08 1.20e+08           8 0.0767
  5 1.20e+08 1.21e+08          52 0.5123
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  Rows:
  [1] 1 1 1 1 1
  TCN segmentation rows:
      startRow endRow
  1          1  37495
  1.1        1  37495
  1.2        1  37495
  1.3        1  37495
  1.4        1  37495
  TCN and DH segmentation rows:
      startRow endRow
  1          1  37495
  1.1        1  37495
  1.2        1  37495
  1.3        1  37495
  1.4        1  37495
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  NULL
  TCN segmentation (expanded) rows:
      startRow endRow
  1          1  37495
  1.1        1  37495
  1.2        1  37495
  1.3        1  37495
  1.4        1  37495
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  Total CN segmentation table (expanded):
      chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  1            1   554484 1.21e+08        37495    1.38        10146        10146
  1.1          1   554484 1.21e+08        37495    1.38        10146        10146
  1.2          1   554484 1.21e+08        37495    1.38        10146        10146
  1.3          1   554484 1.21e+08        37495    1.38        10146        10146
  1.4          1   554484 1.21e+08        37495    1.38        10146        10146
  (TCN,DH) segmentation for one total CN segment:
      tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  1       1    1          1   554484 1.21e+08        37495    1.38        10146
  1.1     1    2          1   554484 1.21e+08        37495    1.38        10146
  1.2     1    3          1   554484 1.21e+08        37495    1.38        10146
  1.3     1    4          1   554484 1.21e+08        37495    1.38        10146
  1.4     1    5          1   554484 1.21e+08        37495    1.38        10146
      tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  1          10146 5.54e+05 4.28e+06         169 0.4145
  1.1        10146 4.28e+06 4.27e+07        3260 0.4944
  1.2        10146 4.27e+07 1.20e+08        6657 0.5205
  1.3        10146 1.20e+08 1.20e+08           8 0.0767
  1.4        10146 1.20e+08 1.21e+08          52 0.5123
 Total CN segment #1 ([    554484,1.20993e+08]) of 7...done
 Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 7...
  Number of TCN loci in segment: 0
  Locus data for TCN segment:
  'data.frame':	0 obs. of  9 variables:
   $ chromosome: int 
   $ x         : num 
   $ CT        : num 
   $ betaT     : num 
   $ betaTN    : num 
   $ betaN     : num 
   $ muN       : num 
   $ index     : int 
   $ rho       : num 
  Number of loci: 0
  Number of SNPs: 0 (NaN%)
  Number of heterozygous SNPs: 0 (NaN%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: NA
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	0 obs. of  4 variables:
     ..$ chromosome: int(0) 
     ..$ x         : num(0) 
     ..$ y         : num(0) 
     ..$ index     : int(0) 
    $ output :'data.frame':	0 obs. of  6 variables:
     ..$ sampleName: chr(0) 
     ..$ chromosome: num(0) 
     ..$ start     : num(0) 
     ..$ end       : num(0) 
     ..$ nbrOfLoci : int(0) 
     ..$ mean      : num(0) 
    $ segRows:'data.frame':	0 obs. of  2 variables:
     ..$ startRow: int(0) 
     ..$ endRow  : int(0) 
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	0 obs. of  3 variables:
     .. ..$ chromosome: int(0) 
     .. ..$ start     : num(0) 
     .. ..$ end       : num(0) 
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0 0 0 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
   [1] startRow endRow  
   <0 rows> (or 0-length row.names)
    int(0) 
   DH segmentation rows:
   [1] startRow endRow  
   <0 rows> (or 0-length row.names)
  Segmenting DH signals...done
  DH segmentation table:
     dhStart dhEnd dhNbrOfLoci dhMean
  NA      NA    NA          NA     NA
     startRow endRow
  NA       NA     NA
  Rows:
  [1] 2
  TCN segmentation rows:
    startRow endRow
  2       NA     NA
  TCN and DH segmentation rows:
    startRow endRow
  2       NA     NA
     startRow endRow
  NA       NA     NA
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  21       NA     NA
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  6       NA     NA
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  2          1 1.21e+08 1.42e+08            0      NA            0            0
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  2     2    1          1 1.21e+08 1.42e+08            0      NA            0
    tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean
  2            0      NA    NA          NA     NA
 Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 7...done
 Total CN segment #3 ([1.4151e+08,1.85528e+08]) of 7...
  Number of TCN loci in segment: 13434
  Locus data for TCN segment:
  'data.frame':	13434 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  1.42e+08 1.42e+08 1.42e+08 1.42e+08 1.42e+08 ...
   $ CT        : num  1.74 1.98 3.48 2.11 2.48 ...
   $ betaT     : num  0.0282 0.9272 0.9103 0.0544 0.5531 ...
   $ betaTN    : num  -0.02304 0.96666 0.97572 0.00855 0.48389 ...
   $ betaN     : num  0.0512 0.9605 0.9346 0.0459 0.5715 ...
   $ muN       : num  0 1 1 0 0.5 0.5 0 0.5 0.5 1 ...
   $ index     : int  37496 37497 37498 37499 37500 37501 37502 37503 37504 37505 ...
   $ rho       : num  NA NA NA NA 0.0322 ...
  Number of loci: 13434
  Number of SNPs: 3770 (28.06%)
  Number of heterozygous SNPs: 3770 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	13434 obs. of  4 variables:
     ..$ chromosome: int [1:13434] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:13434] 1.42e+08 1.42e+08 1.42e+08 1.42e+08 1.42e+08 ...
     ..$ y         : num [1:13434] NA NA NA NA 0.0322 ...
     ..$ index     : int [1:13434] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	1 obs. of  6 variables:
     ..$ sampleName: chr NA
     ..$ chromosome: int 1
     ..$ start     : num 1.42e+08
     ..$ end       : num 1.86e+08
     ..$ nbrOfLoci : int 3770
     ..$ mean      : num 0.0943
    $ segRows:'data.frame':	1 obs. of  2 variables:
     ..$ startRow: int 5
     ..$ endRow  : int 13434
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 1.42e+08
     .. ..$ end       : num 1.86e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0.15 0 0.17 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1        5  13434
    int [1:13434] 37496 37497 37498 37499 37500 37501 37502 37503 37504 37505 ...
   DH segmentation rows:
     startRow endRow
   1    37500  50929
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 1.42e+08 1.86e+08        3770 0.0943
    startRow endRow
  1    37500  50929
  Rows:
  [1] 3
  TCN segmentation rows:
    startRow endRow
  3    37496  50929
  TCN and DH segmentation rows:
    startRow endRow
  3    37496  50929
    startRow endRow
  1    37500  50929
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  31    37496  50929
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  6       NA     NA
  7    37500  50929
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  3          1 1.42e+08 1.86e+08        13434    2.07         3770         3770
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  3     3    1          1 1.42e+08 1.86e+08        13434    2.07         3770
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  3         3770 1.42e+08 1.86e+08        3770 0.0943
 Total CN segment #3 ([1.4151e+08,1.85528e+08]) of 7...done
 Total CN segment #4 ([1.85528e+08,1.99122e+08]) of 7...
  Number of TCN loci in segment: 4018
  Locus data for TCN segment:
  'data.frame':	4018 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  1.86e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ...
   $ CT        : num  2.73 2.46 2.17 3.41 2.43 ...
   $ betaT     : num  0.499 0.751 0.147 0.954 0.197 ...
   $ betaTN    : num  0.5496 0.9681 -0.0136 1.042 0.2571 ...
   $ betaN     : num  0.444 0.783 0.16 0.912 0.383 ...
   $ muN       : num  0.5 1 0 1 0.5 1 1 1 0 1 ...
   $ index     : int  50930 50931 50932 50933 50934 50935 50936 50937 50938 50939 ...
   $ rho       : num  0.0992 NA NA NA 0.4857 ...
  Number of loci: 4018
  Number of SNPs: 1271 (31.63%)
  Number of heterozygous SNPs: 1271 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	4018 obs. of  4 variables:
     ..$ chromosome: int [1:4018] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:4018] 1.86e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ...
     ..$ y         : num [1:4018] 0.0992 NA NA NA 0.4857 ...
     ..$ index     : int [1:4018] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	1 obs. of  6 variables:
     ..$ sampleName: chr NA
     ..$ chromosome: int 1
     ..$ start     : num 1.86e+08
     ..$ end       : num 1.99e+08
     ..$ nbrOfLoci : int 1271
     ..$ mean      : num 0.256
    $ segRows:'data.frame':	1 obs. of  2 variables:
     ..$ startRow: int 1
     ..$ endRow  : int 4011
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 1.86e+08
     .. ..$ end       : num 1.99e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0.05 0 0.05 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1        1   4011
    int [1:4018] 50930 50931 50932 50933 50934 50935 50936 50937 50938 50939 ...
   DH segmentation rows:
     startRow endRow
   1    50930  54940
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 1.86e+08 1.99e+08        1271  0.256
    startRow endRow
  1    50930  54940
  Rows:
  [1] 4
  TCN segmentation rows:
    startRow endRow
  4    50930  54947
  TCN and DH segmentation rows:
    startRow endRow
  4    50930  54947
    startRow endRow
  1    50930  54940
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  41    50930  54947
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  6       NA     NA
  7    37500  50929
  8    50930  54940
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  8    50930  54947
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  4          1 1.86e+08 1.99e+08         4018    2.71         1271         1271
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  4     4    1          1 1.86e+08 1.99e+08         4018    2.71         1271
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  4         1271 1.86e+08 1.99e+08        1271  0.256
 Total CN segment #4 ([1.85528e+08,1.99122e+08]) of 7...done
 Total CN segment #5 ([1.99122e+08,2.06513e+08]) of 7...
  Number of TCN loci in segment: 2755
  Locus data for TCN segment:
  'data.frame':	2755 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  1.99e+08 1.99e+08 1.99e+08 1.99e+08 1.99e+08 ...
   $ CT        : num  2.15 2.75 2.18 2.27 2.52 ...
   $ betaT     : num  0.908 0.185 0.806 0.377 0.357 ...
   $ betaTN    : num  0.934 -0.033 0.956 0.401 0.354 ...
   $ betaN     : num  0.974 0.218 0.85 0.47 0.504 ...
   $ muN       : num  1 0 1 0.5 0.5 0.5 0.5 0.5 0 1 ...
   $ index     : int  54948 54949 54950 54951 54952 54953 54954 54955 54956 54957 ...
   $ rho       : num  NA NA NA 0.198 0.293 ...
  Number of loci: 2755
  Number of SNPs: 784 (28.46%)
  Number of heterozygous SNPs: 784 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	2755 obs. of  4 variables:
     ..$ chromosome: int [1:2755] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:2755] 1.99e+08 1.99e+08 1.99e+08 1.99e+08 1.99e+08 ...
     ..$ y         : num [1:2755] NA NA NA 0.198 0.293 ...
     ..$ index     : int [1:2755] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	1 obs. of  6 variables:
     ..$ sampleName: chr NA
     ..$ chromosome: int 1
     ..$ start     : num 1.99e+08
     ..$ end       : num 2.07e+08
     ..$ nbrOfLoci : int 784
     ..$ mean      : num 0.22
    $ segRows:'data.frame':	1 obs. of  2 variables:
     ..$ startRow: int 4
     ..$ endRow  : int 2754
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 1.99e+08
     .. ..$ end       : num 2.07e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0.03 0 0.03 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1        4   2754
    int [1:2755] 54948 54949 54950 54951 54952 54953 54954 54955 54956 54957 ...
   DH segmentation rows:
     startRow endRow
   1    54951  57701
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 1.99e+08 2.07e+08         784   0.22
    startRow endRow
  1    54951  57701
  Rows:
  [1] 5
  TCN segmentation rows:
    startRow endRow
  5    54948  57702
  TCN and DH segmentation rows:
    startRow endRow
  5    54948  57702
    startRow endRow
  1    54951  57701
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  8    50930  54947
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  51    54948  57702
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
    startRow endRow
  1        7    684
  2      693  12093
  3    12094  37250
  4    37253  37320
  5    37332  37449
  6       NA     NA
  7    37500  50929
  8    50930  54940
  9    54951  57701
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  8    50930  54947
  9    54948  57702
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  5          1 1.99e+08 2.07e+08         2755    2.59          784          784
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  5     5    1          1 1.99e+08 2.07e+08         2755    2.59          784
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  5          784 1.99e+08 2.07e+08         784   0.22
 Total CN segment #5 ([1.99122e+08,2.06513e+08]) of 7...done
 Total CN segment #6 ([2.06513e+08,2.06521e+08]) of 7...
  Number of TCN loci in segment: 14
  Locus data for TCN segment:
  'data.frame':	14 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  2.07e+08 2.07e+08 2.07e+08 2.07e+08 2.07e+08 ...
   $ CT        : num  3.55 4.92 3.73 3.45 3.18 ...
   $ betaT     : num  0.976 0.188 0.751 0.968 0.091 ...
   $ betaTN    : num  1.0103 0.2792 0.6263 1.015 0.0218 ...
   $ betaN     : num  0.9655 0.3359 0.6671 0.953 0.0692 ...
   $ muN       : num  1 0.5 0.5 1 0 0.5 0.5 0.5 0.5 0.5 ...
   $ index     : int  57703 57704 57705 57706 57707 57708 57709 57710 57711 57712 ...
   $ rho       : num  NA 0.442 0.253 NA NA ...
  Number of loci: 14
  Number of SNPs: 9 (64.29%)
  Number of heterozygous SNPs: 9 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	14 obs. of  4 variables:
     ..$ chromosome: int [1:14] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:14] 2.07e+08 2.07e+08 2.07e+08 2.07e+08 2.07e+08 ...
     ..$ y         : num [1:14] NA 0.442 0.253 NA NA ...
     ..$ index     : int [1:14] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	1 obs. of  6 variables:
     ..$ sampleName: chr NA
     ..$ chromosome: int 1
     ..$ start     : num 2.07e+08
     ..$ end       : num 2.07e+08
     ..$ nbrOfLoci : int 9
     ..$ mean      : num 0.277
    $ segRows:'data.frame':	1 obs. of  2 variables:
     ..$ startRow: int 2
     ..$ endRow  : int 14
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 2.07e+08
     .. ..$ end       : num 2.07e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0 0 0.02 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1        2     14
    int [1:14] 57703 57704 57705 57706 57707 57708 57709 57710 57711 57712 ...
   DH segmentation rows:
     startRow endRow
   1    57704  57716
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 2.07e+08 2.07e+08           9  0.277
    startRow endRow
  1    57704  57716
  Rows:
  [1] 6
  TCN segmentation rows:
    startRow endRow
  6    57703  57716
  TCN and DH segmentation rows:
    startRow endRow
  6    57703  57716
    startRow endRow
  1    57704  57716
    startRow endRow
  1        1  37495
  2        1  37495
  3        1  37495
  4        1  37495
  5        1  37495
  6       NA     NA
  7    37496  50929
  8    50930  54947
  9    54948  57702
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  9     54948  57702
  61    57703  57716
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
     startRow endRow
  1         7    684
  2       693  12093
  3     12094  37250
  4     37253  37320
  5     37332  37449
  6        NA     NA
  7     37500  50929
  8     50930  54940
  9     54951  57701
  10    57704  57716
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  9     54948  57702
  10    57703  57716
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  6          1 2.07e+08 2.07e+08           14    3.87            9            9
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  6     6    1          1 2.07e+08 2.07e+08           14    3.87            9
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  6            9 2.07e+08 2.07e+08           9  0.277
 Total CN segment #6 ([2.06513e+08,2.06521e+08]) of 7...done
 Total CN segment #7 ([2.06521e+08,2.47165e+08]) of 7...
  Number of TCN loci in segment: 15581
  Locus data for TCN segment:
  'data.frame':	15581 obs. of  9 variables:
   $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
   $ x         : num  2.07e+08 2.07e+08 2.07e+08 2.07e+08 2.07e+08 ...
   $ CT        : num  3 3.06 2.61 2.76 2.21 ...
   $ betaT     : num  0.133 0.903 0.25 0.912 0.94 ...
   $ betaTN    : num  0.0458 1.0629 0.0301 1.1428 1.0005 ...
   $ betaN     : num  0.0875 0.8402 0.2201 0.7696 0.9395 ...
   $ muN       : num  0 1 0 1 1 0 1 1 1 0 ...
   $ index     : int  57717 57718 57719 57720 57721 57722 57723 57724 57725 57726 ...
   $ rho       : num  NA NA NA NA NA NA NA NA NA NA ...
  Number of loci: 15581
  Number of SNPs: 4492 (28.83%)
  Number of heterozygous SNPs: 4492 (100.00%)
  Chromosome: 1
  Segmenting DH signals...
   Segmenting by CBS...
    Chromosome: 1
     Random seed temporarily set (seed=c(407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG")
   Segmenting by CBS...done
   List of 4
    $ data   :'data.frame':	15581 obs. of  4 variables:
     ..$ chromosome: int [1:15581] 1 1 1 1 1 1 1 1 1 1 ...
     ..$ x         : num [1:15581] 2.07e+08 2.07e+08 2.07e+08 2.07e+08 2.07e+08 ...
     ..$ y         : num [1:15581] NA NA NA NA NA NA NA NA NA NA ...
     ..$ index     : int [1:15581] 1 2 3 4 5 6 7 8 9 10 ...
    $ output :'data.frame':	1 obs. of  6 variables:
     ..$ sampleName: chr NA
     ..$ chromosome: int 1
     ..$ start     : num 2.07e+08
     ..$ end       : num 2.47e+08
     ..$ nbrOfLoci : int 4492
     ..$ mean      : num 0.229
    $ segRows:'data.frame':	1 obs. of  2 variables:
     ..$ startRow: int 30
     ..$ endRow  : int 15556
    $ params :List of 5
     ..$ alpha        : num 0.001
     ..$ undo         : num 0
     ..$ joinSegments : logi TRUE
     ..$ knownSegments:'data.frame':	1 obs. of  3 variables:
     .. ..$ chromosome: int 1
     .. ..$ start     : num 2.07e+08
     .. ..$ end       : num 2.47e+08
     ..$ seed         : int [1:7] 407 1797822437 388243314 91406689 -519578635 -138192..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")=Class 'proc_time'  Named num [1:5] 0.11 0 0.1 NA NA
     .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ..
    - attr(*, "pkgDetails")= chr "DNAcopy v1.52.0"
    - attr(*, "randomSeed")= int [1:7] 407 1797822437 388243314 91406689 -519578635 -1..
   DH segmentation (locally-indexed) rows:
     startRow endRow
   1       30  15556
    int [1:15581] 57717 57718 57719 57720 57721 57722 57723 57724 57725 57726 ...
   DH segmentation rows:
     startRow endRow
   1    57746  73272
  Segmenting DH signals...done
  DH segmentation table:
     dhStart    dhEnd dhNbrOfLoci dhMean
  1 2.07e+08 2.47e+08        4492  0.229
    startRow endRow
  1    57746  73272
  Rows:
  [1] 7
  TCN segmentation rows:
    startRow endRow
  7    57717  73297
  TCN and DH segmentation rows:
    startRow endRow
  7    57717  73297
    startRow endRow
  1    57746  73272
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  9     54948  57702
  10    57703  57716
  TCN segmentation (expanded) rows:
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  9     54948  57702
  10    57703  57716
  71    57717  73297
  TCN and DH segmentation rows:
    startRow endRow
  1        1  37495
  2       NA     NA
  3    37496  50929
  4    50930  54947
  5    54948  57702
  6    57703  57716
  7    57717  73297
     startRow endRow
  1         7    684
  2       693  12093
  3     12094  37250
  4     37253  37320
  5     37332  37449
  6        NA     NA
  7     37500  50929
  8     50930  54940
  9     54951  57701
  10    57704  57716
  11    57746  73272
     startRow endRow
  1         1  37495
  2         1  37495
  3         1  37495
  4         1  37495
  5         1  37495
  6        NA     NA
  7     37496  50929
  8     50930  54947
  9     54948  57702
  10    57703  57716
  11    57717  73297
  Total CN segmentation table (expanded):
    chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
  7          1 2.07e+08 2.47e+08        15581    2.64         4492         4492
  (TCN,DH) segmentation for one total CN segment:
    tcnId dhId chromosome tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
  7     7    1          1 2.07e+08 2.47e+08        15581    2.64         4492
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
  7         4492 2.07e+08 2.47e+08        4492  0.229
 Total CN segment #7 ([2.06521e+08,2.47165e+08]) of 7...done
    chromosome tcnId dhId tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
 1           1     1    1 5.54e+05 1.21e+08        37495    1.38        10146
 2           1     1    2 5.54e+05 1.21e+08        37495    1.38        10146
 3           1     1    3 5.54e+05 1.21e+08        37495    1.38        10146
 4           1     1    4 5.54e+05 1.21e+08        37495    1.38        10146
 5           1     1    5 5.54e+05 1.21e+08        37495    1.38        10146
 6           1     2    1 1.21e+08 1.42e+08            0      NA            0
 7           1     3    1 1.42e+08 1.86e+08        13434    2.07         3770
 8           1     4    1 1.86e+08 1.99e+08         4018    2.71         1271
 9           1     5    1 1.99e+08 2.07e+08         2755    2.59          784
 10          1     6    1 2.07e+08 2.07e+08           14    3.87            9
 11          1     7    1 2.07e+08 2.47e+08        15581    2.64         4492
    tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean
 1         10146 5.54e+05 4.28e+06         169 0.4145
 2         10146 4.28e+06 4.27e+07        3260 0.4944
 3         10146 4.27e+07 1.20e+08        6657 0.5205
 4         10146 1.20e+08 1.20e+08           8 0.0767
 5         10146 1.20e+08 1.21e+08          52 0.5123
 6             0       NA       NA          NA     NA
 7          3770 1.42e+08 1.86e+08        3770 0.0943
 8          1271 1.86e+08 1.99e+08        1271 0.2563
 9           784 1.99e+08 2.07e+08         784 0.2197
 10            9 2.07e+08 2.07e+08           9 0.2769
 11         4492 2.07e+08 2.47e+08        4492 0.2290
 Calculating (C1,C2) per segment...
 Calculating (C1,C2) per segment...done
 Number of segments: 11
Segmenting paired tumor-normal signals using Paired PSCBS...done
Post-segmenting TCNs...
 Number of segments: 11
 Number of chromosomes: 1
 [1] 1
 Chromosome 1 ('chr01') of 1...
  Rows:
   [1]  1  2  3  4  5  6  7  8  9 10 11
  Number of segments: 11
  TCN segment #1 ('1') of 7...
   Rows:
   [1] 1 2 3 4 5
   TCN & DH segRows before:
     tcn.startRow tcn.endRow dh.startRow dh.endRow
   1            1      37495           7       684
   2            1      37495         693     12093
   3            1      37495       12094     37250
   4            1      37495       37253     37320
   5            1      37495       37332     37449
   Range [1,37495]
   DH segment #1 of 5...
    [xStart,xEnd] = [554484,4278527]
    [idxStart,idxEnd] = [1,687]
    Number of TCN loci: 687
    [idxStart,idxEnd] = [1,687]
    Number of non-missing TCN loci: 687
   DH segment #1 of 5...done
   DH segment #2 of 5...
    [xStart,xEnd] = [4278527,42651414]
    [idxStart,idxEnd] = [688,12093]
    Number of TCN loci: 11406
    [idxStart,idxEnd] = [688,12093]
    Number of non-missing TCN loci: 11406
   DH segment #2 of 5...done
   DH segment #3 of 5...
    [xStart,xEnd] = [42651414,119796081]
    [idxStart,idxEnd] = [12094,37252]
    Number of TCN loci: 25159
    [idxStart,idxEnd] = [12094,37252]
    Number of non-missing TCN loci: 25159
   DH segment #3 of 5...done
   DH segment #4 of 5...
    [xStart,xEnd] = [119796081,119932126]
    [idxStart,idxEnd] = [37253,37324]
    Number of TCN loci: 72
    [idxStart,idxEnd] = [37253,37324]
    Number of non-missing TCN loci: 72
   DH segment #4 of 5...done
   DH segment #5 of 5...
    [xStart,xEnd] = [119932126,120992603]
    [idxStart,idxEnd] = [37325,37495]
    Number of TCN loci: 171
    [idxStart,idxEnd] = [37325,37495]
    Number of non-missing TCN loci: 171
   DH segment #5 of 5...done
   TCN & DH segRows afterward:
     tcn.startRow tcn.endRow dh.startRow dh.endRow
   1            1        687           7       684
   2          688      12093         693     12093
   3        12094      37252       12094     37250
   4        37253      37324       37253     37320
   5        37325      37495       37332     37449
   Number of TCNs before: 37495
   Number of TCNs after: 37495
  TCN segment #1 ('1') of 7...done
  TCN segment #2 ('2') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #2 ('2') of 7...done
  TCN segment #3 ('3') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #3 ('3') of 7...done
  TCN segment #4 ('4') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #4 ('4') of 7...done
  TCN segment #5 ('5') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #5 ('5') of 7...done
  TCN segment #6 ('6') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #6 ('6') of 7...done
  TCN segment #7 ('7') of 7...
   Nothing todo. Only one DH segmentation. Skipping.
  TCN segment #7 ('7') of 7...done
 Chromosome 1 ('chr01') of 1...done
 Update (C1,C2) per segment...
 Update (C1,C2) per segment...done
Post-segmenting TCNs...done
  chromosome tcnId dhId tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
1          1     1    1 5.54e+05 4.28e+06          687    1.40          169
2          1     1    2 4.28e+06 4.27e+07        11406    1.38         3260
3          1     1    3 4.27e+07 1.20e+08        25159    1.38         6657
4          1     1    4 1.20e+08 1.20e+08           72    1.47            8
5          1     1    5 1.20e+08 1.21e+08          171    1.44           52
6          1     2    1 1.21e+08 1.42e+08            0      NA            0
  tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
1          169 5.54e+05 4.28e+06         169 0.4145  0.411  0.992
2         3260 4.28e+06 4.27e+07        3260 0.4944  0.348  1.030
3         6657 4.27e+07 1.20e+08        6657 0.5205  0.332  1.052
4            8 1.20e+08 1.20e+08           8 0.0767  0.679  0.792
5           52 1.20e+08 1.21e+08          52 0.5123  0.351  1.089
6            0       NA       NA          NA     NA     NA     NA
   chromosome tcnId dhId tcnStart   tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
6           1     2    1 1.21e+08 1.42e+08            0      NA            0
7           1     3    1 1.42e+08 1.86e+08        13434    2.07         3770
8           1     4    1 1.86e+08 1.99e+08         4018    2.71         1271
9           1     5    1 1.99e+08 2.07e+08         2755    2.59          784
10          1     6    1 2.07e+08 2.07e+08           14    3.87            9
11          1     7    1 2.07e+08 2.47e+08        15581    2.64         4492
   tcnNbrOfHets  dhStart    dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
6             0       NA       NA          NA     NA     NA     NA
7          3770 1.42e+08 1.86e+08        3770 0.0943  0.935   1.13
8          1271 1.86e+08 1.99e+08        1271 0.2563  1.007   1.70
9           784 1.99e+08 2.07e+08         784 0.2197  1.009   1.58
10            9 2.07e+08 2.07e+08           9 0.2769  1.400   2.47
11         4492 2.07e+08 2.47e+08        4492 0.2290  1.017   1.62
Calling ROH...
 Segment #1 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 687
  Calling ROH for a single segment...done
 Segment #1 of 11...done
 Segment #2 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 11406
  Calling ROH for a single segment...done
 Segment #2 of 11...done
 Segment #3 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 25159
  Calling ROH for a single segment...done
 Segment #3 of 11...done
 Segment #4 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 72
  Calling ROH for a single segment...done
 Segment #4 of 11...done
 Segment #5 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 171
  Calling ROH for a single segment...done
 Segment #5 of 11...done
 Segment #6 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 0
  Calling ROH for a single segment...done
 Segment #6 of 11...done
 Segment #7 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 13434
  Calling ROH for a single segment...done
 Segment #7 of 11...done
 Segment #8 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 4018
  Calling ROH for a single segment...done
 Segment #8 of 11...done
 Segment #9 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 2755
  Calling ROH for a single segment...done
 Segment #9 of 11...done
 Segment #10 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 14
  Calling ROH for a single segment...done
 Segment #10 of 11...done
 Segment #11 of 11...
  Calling ROH for a single segment...
   Number of SNPs: 15581
  Calling ROH for a single segment...done
 Segment #11 of 11...done
 ROH calls:
  logi [1:11] FALSE FALSE FALSE TRUE FALSE NA ...
    Mode   FALSE    TRUE    NA's 
 logical       9       1       1 
Calling ROH...done
Error: processing vignette 'PairedPSCBS.tex.rsp' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted