Errors in running code in vignettes:
when running code in 'PairedPSCBS.tex.rsp'

> t0 <- Sys.time()

> R.utils::use("R.utils")

> R.rsp <- R.oo::Package("R.rsp")

> withCapture <- R.utils::withCapture

> options(`withCapture/newline` = FALSE)

> options(str = strOptions(strict.width = "cut"))

> options(width = 85)

> options(digits = 3)

> use("R.devices")

> options(`devEval/args/field` = "fullname")

> devOptions("png", width = 840)

> use("PSCBS")

> PSCBS <- R.oo::Package("PSCBS")

> fixLocations <- function(fit, ...) {
+     for (key in grep("(end|start)$", colnames(fit$output))) {
+         fit$output[[key]] <- as.integer(fit$o .... [TRUNCATED] 

> R.rsp$version
[1] "0.44.0"

> R.rsp$author
[1] "Henrik Bengtsson"

> format(as.Date(PSCBS$date), format = "%B %d, %Y")
[1] "May 05, 2019"

> fullname <- "PairedPSCBS,exData,chr01"

> withCapture({
+     data <- PSCBS::exampleData("paired.chr01")
+     str(data)
+ })
> data <- PSCBS::exampleData("paired.chr01")
> str(data)
'data.frame':	73346 obs. of  6 variables:
 $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
 $ x         : int  1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127..
 $ CT        : num  1.625 1.071 1.406 1.18 0.856 ...
 $ betaT     : num  0.757 0.771 0.834 0.778 0.229 ...
 $ CN        : num  2.36 2.13 2.59 1.93 1.71 ...
 $ betaN     : num  0.827 0.875 0.887 0.884 0.103 ...
> withCapture({
+     data <- dropSegmentationOutliers(data)
+ })
> data <- dropSegmentationOutliers(data)
> withCapture({
+     gaps <- findLargeGaps(data, minLength = 1e+06)
+     gaps
+ })
> gaps <- findLargeGaps(data, minLength = 1e+06)
> gaps
  chromosome     start       end   length
1          1 120992604 141510002 20517398
> withCapture({
+     knownSegments <- gapsToSegments(gaps)
+     knownSegments
+ })
> knownSegments <- gapsToSegments(gaps)
> knownSegments
  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
> withCapture({
+     fit <- segmentByPairedPSCBS(data, knownSegments = knownSegments, 
+         seed = 48879, verbose = -10)
+ })
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:
   num [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   : chr [1:5] "peak" "valley" "peak" "valley" ...
    .. .. ..$ 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   : chr [1:2] "valley" "valley"
    .. .. ..$ 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:
   num [1:73346] 0.93 0.896 0.947 0.894 0.126 ...
   - attr(*, "modelFit")=List of 5
    ..$ method       : chr "normalizeTumorBoost"
    ..$ flavor       : chr "v4"
    ..$ delta        : num [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   : chr [1:5] "peak" "valley" "peak" "valley" ...
    .. .. .. .. ..$ 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   : chr [1:2] "valley" "valley"
    .. .. .. .. ..$ 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    : num  0.93 0.896 0.947 0.894 0.126 ...
    ..- attr(*, "modelFit")=List of 5
    .. ..$ method       : chr "normalizeTumorBoost"
    .. ..$ flavor       : chr "v4"
    .. ..$ delta        : num [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..
    .. .. .. .. .. ..$ type   : chr [1:5] "peak" "valley" "peak" "valley" ...
    .. .. .. .. .. ..$ 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..
    .. .. .. .. .. ..$ type   : chr [1:2] "valley" "valley"
    .. .. .. .. .. ..$ 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
   $ betaN     : num  0.827 0.875 0.887 0.884 0.103 ...
   $ muN       : num  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. ..
    .. .. .. ..$ type   : chr [1:5] "peak" "valley" "peak" "valley" ...
    .. .. .. ..$ 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. ..
    .. .. .. ..$ type   : chr [1:2] "valley" "valley"
    .. .. .. ..$ x      : num [1:2] 0.316 0.679
    .. .. .. ..$ density: num [1:2] 0.437 0.466
    .. ..- attr(*, "class")= chr [1:2] "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(10407, 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(10407, 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(10407, -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] 10407 1066287653 -51199871 161854402 -1995183193 150..
   - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
   - attr(*, "processingTime")= 'proc_time' Named num [1:5] 13.67 0.04 13.7 NA NA
    ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
   - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
   - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
 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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= 'proc_time' Named num [1:5] 3.67 0 3.72 NA NA
     ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
    - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 NA NA
     ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
    - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.19 0 0.19 NA NA
     ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
    - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.06 0 0.06 NA NA
     ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
    - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= '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 v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= '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 v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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(10407, 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] 10407 1797822437 388243314 91406689 -519578635 -1381..
    - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS"
    - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.14 0 0.16 NA NA
     ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
    - attr(*, "pkgDetails")= chr "DNAcopy v1.66.0"
    - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 ..
   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
> fit <- segmentByPairedPSCBS(data, knownSegments = knownSegments, 
+     seed = 48879, verbose = -10)
> nbrOfSegments(fit)
[1] 11

> fit <- fixLocations(fit)

> withCapture({
+     getSegments(fit, simplify = TRUE)
+ })
> getSegments(fit, simplify = TRUE)
   chromosome tcnId dhId    start      end 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
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 dhNbrOfLoci dhMean c1Mean c2Mean
1           169         169 0.4145  0.411  0.992
2          3260        3260 0.4944  0.348  1.030
3          6657        6657 0.5205  0.332  1.052
4             8           8 0.0767  0.679  0.792
5            52          52 0.5123  0.351  1.089
6             0          NA     NA     NA     NA
7          3770        3770 0.0943  0.935  1.130
8          1271        1271 0.2563  1.007  1.701
9           784         784 0.2197  1.009  1.577
10            9           9 0.2769  1.400  2.472
11         4492        4492 0.2290  1.017  1.621
> segs <- getSegments(fit, simplify = TRUE)

> which(segs$tcnNbrOfLoci == 0)
[1] 6

> which(segs$dhNbrOfLoci == 0)
integer(0)

> toPNG(fullname, tags = c(class(fit)[1], "tracks"), 
+     aspectRatio = 0.6, {
+         plotTracks(fit)
+     })
[1] "PairedPSCBS,exData,chr01,PairedPSCBS,tracks"

> withCapture({
+     fit <- callROH(fit, verbose = -10)
+ })
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
> fit <- callROH(fit, verbose = -10)
> withCapture({
+     fit <- callAB(fit, verbose = -10)
+ })

  When sourcing 'PairedPSCBS.R':
Error: there is no package called 'Hmisc'
Execution halted

  'CBS.tex.rsp'... OK
  'PairedPSCBS.tex.rsp'... failed