
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/6159637/KICH-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KICH-TP/6154424/KICH-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=KICH-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KICH-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KICH-TP/6154424/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/6159637/KICH-TP.mergedcluster.txt"

nPatients in clinical file=70, in cluster file=66, common to both=66
[1]  8 66
[1] "CN_CNMF"
[1] 3
 1  2  3 
 5 47 14 
 1  2  3 
 5 47 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
18 35 13 
 1  2  3 
18 35 13 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
19 22 15 10 
 1  2  3  4 
19 22 15 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
10 10 17  6 23 
 1  2  3  4  5 
10 10 17  6 23 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
20 24 22 
 1  2  3 
20 24 22 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2 
 9 57 
 1  2 
 9 57 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5 
10 16 16 10 14 
 1  2  3  4  5 
10 16 16 10 14 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
12  8 25 21 
 1  2  3  4 
12  8 25 21 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[15] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[17] "YEAROFTOBACCOSMOKINGONSET"        "GLEASON_SCORE"                   
[19] "PSA_VALUE"                        "DAYS_TO_PSA"                     
[21] "BATCHNUMBER"                     

Input Data has 21 rows and 66 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
          NA         4311           NA         3321         4169         3126 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
        2752         3304         3009         2582         2990         2949 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
        2815           NA         1364         2632           NA         2024 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
          NA         2248         1815          876         1664         1896 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
        4621          247          994          400         1082         1128 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
        3745         1552          953         3473          714         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
         775          788         1983         2211          107           17 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
          NA         2063           NA          712           76          341 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
        1124         2727          636         2303         2339           NA 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
        2279         2404         2820           NA         2445         2670 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        3141         2618         2368         1739         1873         1944 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
[9] "YEAROFTOBACCOSMOKINGONSET"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 66 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
21 25 18  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   21    25    20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
21 25 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   21    25    20 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
40  3  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   40     5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   40     5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=8, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  4  1
  subtype2 39  7
  subtype3 14  0
subtype1 subtype2 subtype3 
       5       46       14 
subtype1 subtype2 subtype3 
       1        7        0 
$subtype1
TCGA-KL-8323 TCGA-KL-8329 TCGA-KM-8440 TCGA-KN-8434 TCGA-KO-8407 
       38.07        90.48        32.68        36.95        92.71 

$subtype2
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 
      141.73        23.84       109.18       102.77       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 
       84.89        98.30        96.95        92.55        30.21        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.08        66.54        24.79        73.91        59.67        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 
       54.71        62.33       151.92         8.12        13.15        35.57 
TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
       37.08        51.02        31.33       114.18        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91        65.19         3.52         0.56        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       67.82        23.41        75.72        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       79.04        16.67        80.38        87.78 

$subtype3
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8433 
      137.06        44.84       123.12        72.69         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       89.65        20.91       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

subtype1 subtype2 subtype3 
   32.68     0.56     2.50 
subtype1 subtype2 subtype3 
   92.71   151.92   137.06 
subtype1 subtype2 subtype3 
   38.07    63.76    68.30 
[1] "32.7 - 92.7 (38.1)" "0.6 - 151.9 (63.8)" "2.5 - 137.1 (68.3)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[49] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[55] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        2         2        0
  subtype2      13       18        10        6
  subtype3       7        5         2        0
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  2     2
  subtype2 13 18    16
  subtype3  7  5     2
D1V4, multiclass
          vv
clus       N0 N1+N2
  subtype1  2     0
  subtype2 30     5
  subtype3  8     0
D1V5, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       35        8 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3"
       clus
vv      subtype2 subtype3
  N0          30        8
  N1+N2        5        0
          vv
clus       M0 M1 MX
  subtype1  3  0  1
  subtype2 23  2  7
  subtype3  8  0  1
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 18 29
  subtype3  6  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   18   29
  subtype3    6    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3       18        6
  MALE          2       29        8
D1V8, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        7        3 
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3"
D1V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype2 subtype3 
       9        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[8] "subtype2" "subtype2"
D1V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype2 subtype3 
       7        1 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16  2
  subtype2 29  5
  subtype3 12  1
subtype1 subtype2 subtype3 
      18       34       13 
subtype1 subtype2 subtype3 
       2        5        1 
$subtype1
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8443 
       38.07        23.84       137.06        73.91        54.71        37.08 
TCGA-KM-8476 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8434 TCGA-KO-8403 TCGA-KO-8406 
      123.12        23.47        72.69        36.95        76.90        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       92.71        80.38       103.27        57.17        61.58        63.91 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
      141.73       109.18       102.77        90.48       108.62        98.93 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.21        44.84        86.53 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 
       28.08        66.54        24.79        28.80        62.33       151.92 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       32.68        35.57       114.18        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19         3.52        52.27        67.82        23.41         2.50 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8408 TCGA-KO-8414 
       89.65        20.91        16.67        77.85 

$subtype3
TCGA-KL-8333 TCGA-KL-8343 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
       98.30        59.67         8.12        13.15        51.02        31.33 
TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8410 
        0.56        11.21        75.72        10.68        74.93        87.78 
TCGA-KO-8413 
       86.07 

subtype1 subtype2 subtype3 
   23.47     2.50     0.56 
subtype1 subtype2 subtype3 
  137.06   151.92    98.30 
subtype1 subtype2 subtype3 
  68.300   65.865   51.020 
[1] "23.5 - 137.1 (68.3)" "2.5 - 151.9 (65.9)"  "0.6 - 98.3 (51.0)"  
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[25] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
[43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype2" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[55] "subtype1" "subtype1" "subtype2" "subtype1" "subtype3" "subtype1"
[61] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       8        7         3        0
  subtype2       6       17         8        4
  subtype3       7        1         3        2
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  8  7     3
  subtype2  6 17    12
  subtype3  7  1     5
D2V4, multiclass
          vv
clus       N0 N1+N2
  subtype1 12     0
  subtype2 23     4
  subtype3  5     1
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          12       23        5
  N1+N2        0        4        1
          vv
clus       M0 M1 MX
  subtype1 12  0  2
  subtype2 17  2  3
  subtype3  5  0  4
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 15 20
  subtype3  4  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   15   20
  subtype3    4    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       15        4
  MALE         10       20        9
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        6        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[8] "subtype1" "subtype1"
D2V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        4        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 17  2
  subtype2 20  1
  subtype3 11  4
  subtype4  9  1
subtype1 subtype2 subtype3 subtype4 
      19       21       15       10 
subtype1 subtype2 subtype3 subtype4 
       2        1        4        1 
$subtype1
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8338 TCGA-KL-8341 
       38.07       137.06        98.93        96.95        86.53        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8434 
       73.91        54.71        37.08       123.12        65.19        36.95 
TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8416 
       89.65        76.90        79.04        92.71       103.27        61.58 
TCGA-KO-8417 
       63.91 

$subtype2
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8346 TCGA-KM-8438 
      141.73        23.84       108.62        84.89        62.33       151.92 
TCGA-KM-8442 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       35.57        23.47        25.48        25.91        72.69         3.52 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       23.41         2.50        11.21        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       86.07        77.85        57.17 

$subtype3
TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
      109.18       102.77        90.48        92.55        30.21        44.84 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KM-8440 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8428 
       28.08        66.54        32.68       114.18        87.91        52.27 
TCGA-KN-8429 TCGA-KN-8436 TCGA-KO-8408 
       67.82        20.91        16.67 

$subtype4
TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 
       98.30        59.67        28.80         8.12        13.15        51.02 
TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 
       31.33         0.56        75.72        10.68 

subtype1 subtype2 subtype3 subtype4 
   24.79     2.50    16.67     0.56 
subtype1 subtype2 subtype3 subtype4 
  137.06   151.92   114.18    98.30 
subtype1 subtype2 subtype3 subtype4 
  76.900   62.330   66.540   30.065 
[1] "24.8 - 137.1 (76.9)" "2.5 - 151.9 (62.3)"  "16.7 - 114.2 (66.5)"
[4] "0.6 - 98.3 (30.1)"  
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype2"
[25] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype1"
[31] "subtype1" "subtype4" "subtype4" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype4"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype2"
[25] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype1"
[31] "subtype1" "subtype4" "subtype4" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype4"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype1" "subtype1" "subtype4" "subtype4" "subtype1" "subtype2"
[25] "subtype2" "subtype4" "subtype3" "subtype4" "subtype2" "subtype1"
[31] "subtype1" "subtype4" "subtype4" "subtype3" "subtype2" "subtype3"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype4"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
[49] "subtype1" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       7        6         5        1
  subtype2       8       11         2        1
  subtype3       1        7         5        2
  subtype4       5        1         2        2
D3V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  7  6     6
  subtype2  8 11     3
  subtype3  1  7     7
  subtype4  5  1     4
D3V4, multiclass
          vv
clus       N0 N1+N2
  subtype1 12     1
  subtype2 15     0
  subtype3 10     3
  subtype4  3     1
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          12       15       10        3
  N1+N2        1        0        3        1
          vv
clus       M0 M1 MX
  subtype1 13  0  2
  subtype2 11  1  2
  subtype3  7  1  1
  subtype4  3  0  4
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1  9 10
  subtype2 11 11
  subtype3  5 10
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   10
  subtype2   11   11
  subtype3    5   10
  subtype4    2    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       11        5        2
  MALE         10       11       10        8
D3V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        3        1        4 
 [1] "subtype2" "subtype4" "subtype4" "subtype2" "subtype1" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2"
D3V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        4        3        1 
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype1"
D3V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        3        2        1 
[1] "subtype2" "subtype2" "subtype2"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  6  4
  subtype2  9  1
  subtype3 16  0
  subtype4  6  0
  subtype5 20  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       10       16        6       23 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        1        0        0        3 
$subtype1
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8339 TCGA-KM-8440 
      102.77        90.48        92.55        30.21        28.08        32.68 
TCGA-KN-8418 TCGA-KN-8428 TCGA-KN-8429 TCGA-KO-8408 
      114.18        52.27        67.82        16.67 

$subtype2
TCGA-KL-8333 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
       98.30        28.80         8.12        13.15        51.02        31.33 
TCGA-KN-8419 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 
       23.47         0.56        75.72        10.68 

$subtype3
TCGA-KL-8324 TCGA-KL-8330 TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8422 TCGA-KN-8423 
      141.73       108.62       151.92        35.57        25.48        25.91 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 
       72.69         3.52        23.41        11.21        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       87.78        86.07        77.85        57.17 

$subtype4
TCGA-KL-8326 TCGA-KL-8337 TCGA-KL-8343 TCGA-KN-8421 TCGA-KN-8432 TCGA-KN-8436 
      109.18        44.84        59.67        87.91         2.50        20.91 

$subtype5
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 
       38.07        23.84       137.06        98.93        84.89        96.95 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 
       86.53        66.54        24.79        73.91        54.71        62.33 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 
       37.08       123.12        65.19        36.95        89.65        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71       103.27        61.58        63.91 

subtype1 subtype2 subtype3 subtype4 subtype5 
   16.67     0.56     3.52     2.50    23.84 
subtype1 subtype2 subtype3 subtype4 subtype5 
  114.18    98.30   151.92   109.18   137.06 
subtype1 subtype2 subtype3 subtype4 subtype5 
  60.045   26.135   73.810   52.255   73.910 
[1] "16.7 - 114.2 (60.0)" "0.6 - 98.3 (26.1)"   "3.5 - 151.9 (73.8)" 
[4] "2.5 - 109.2 (52.3)"  "23.8 - 137.1 (73.9)"
 [1] "subtype5" "subtype3" "subtype5" "subtype4" "subtype5" "subtype1"
 [7] "subtype1" "subtype3" "subtype5" "subtype5" "subtype2" "subtype5"
[13] "subtype1" "subtype1" "subtype4" "subtype5" "subtype1" "subtype5"
[19] "subtype5" "subtype5" "subtype4" "subtype2" "subtype5" "subtype5"
[25] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype5"
[31] "subtype5" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[37] "subtype3" "subtype3" "subtype5" "subtype3" "subtype3" "subtype2"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
[49] "subtype5" "subtype4" "subtype2" "subtype5" "subtype2" "subtype3"
[55] "subtype5" "subtype5" "subtype1" "subtype3" "subtype3" "subtype5"
[61] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [1] "subtype5" "subtype3" "subtype5" "subtype4" "subtype5" "subtype1"
 [7] "subtype1" "subtype3" "subtype5" "subtype5" "subtype2" "subtype5"
[13] "subtype1" "subtype1" "subtype4" "subtype5" "subtype1" "subtype5"
[19] "subtype5" "subtype5" "subtype4" "subtype2" "subtype5" "subtype5"
[25] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype5"
[31] "subtype5" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[37] "subtype3" "subtype3" "subtype5" "subtype3" "subtype3" "subtype2"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
[49] "subtype5" "subtype4" "subtype2" "subtype5" "subtype2" "subtype3"
[55] "subtype5" "subtype5" "subtype1" "subtype3" "subtype3" "subtype5"
[61] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
 [1] "subtype5" "subtype3" "subtype5" "subtype4" "subtype5" "subtype1"
 [7] "subtype1" "subtype3" "subtype5" "subtype5" "subtype2" "subtype5"
[13] "subtype1" "subtype1" "subtype4" "subtype5" "subtype1" "subtype5"
[19] "subtype5" "subtype5" "subtype4" "subtype2" "subtype5" "subtype5"
[25] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype5"
[31] "subtype5" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[37] "subtype3" "subtype3" "subtype5" "subtype3" "subtype3" "subtype2"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype5"
[49] "subtype5" "subtype4" "subtype2" "subtype5" "subtype2" "subtype3"
[55] "subtype5" "subtype5" "subtype1" "subtype3" "subtype3" "subtype5"
[61] "subtype3" "subtype3" "subtype3" "subtype5" "subtype5"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        3         4        2
  subtype2       5        2         1        2
  subtype3       7        7         2        1
  subtype4       0        4         2        0
  subtype5       8        9         5        1
D4V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  3     6
  subtype2  5  2     3
  subtype3  7  7     3
  subtype4  0  4     2
  subtype5  8  9     6
D4V4, multiclass
          vv
clus       N0 N1+N2
  subtype1  6     3
  subtype2  3     1
  subtype3 12     0
  subtype4  4     0
  subtype5 15     1
D4V5, multiclass
          vv
clus       M0 M1 MX
  subtype1  4  1  1
  subtype2  2  0  4
  subtype3  8  1  2
  subtype4  3  0  0
  subtype5 17  0  2
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1  4  6
  subtype2  2  8
  subtype3  9  8
  subtype4  2  4
  subtype5 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    2    8
  subtype3    9    8
  subtype4    2    4
  subtype5   10   13
D4V8, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype5 
       1        4        3        3 
 [1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype5" "subtype5"
 [7] "subtype2" "subtype2" "subtype5" "subtype3"
D4V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 subtype5 
       3        1        4        3 
 [1] "subtype3" "subtype3" "subtype1" "subtype5" "subtype5" "subtype1"
 [7] "subtype3" "subtype1" "subtype3" "subtype5"
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype5"              
clus
subtype1 subtype2 subtype3 subtype5 
       2        1        3        2 
[1] "subtype3" "subtype3" "subtype3"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 15  4
  subtype2 22  2
  subtype3 20  2
subtype1 subtype2 subtype3 
      19       24       22 
subtype1 subtype2 subtype3 
       4        2        2 
$subtype1
TCGA-KL-8323 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8338 TCGA-KL-8339 
       38.07        98.30        96.95        92.55        86.53        28.08 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 
       59.67        28.80       151.92         8.12        13.15        51.02 
TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8432 TCGA-KN-8437 TCGA-KO-8404 
       31.33         0.56        52.27         2.50        75.72        10.68 
TCGA-KO-8405 
       74.93 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 
      141.73       109.18       137.06       102.77        90.48        98.93 
TCGA-KL-8336 TCGA-KL-8341 TCGA-KL-8345 TCGA-KM-8476 TCGA-KN-8419 TCGA-KN-8421 
       30.21        24.79        54.71       123.12        23.47        87.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       65.19         3.52        36.95        89.65        20.91        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
       79.04        92.71        87.78       103.27        57.17        61.58 

$subtype3
TCGA-KL-8325 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8337 TCGA-KL-8340 TCGA-KL-8342 
       23.84       108.62        84.89        44.84        66.54        73.91 
TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KN-8418 TCGA-KN-8422 
       62.33        32.68        35.57        37.08       114.18        25.48 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KO-8408 
       25.91        72.69        67.82        23.41        11.21        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8417 
       80.38        86.07        77.85        63.91 

subtype1 subtype2 subtype3 
    0.56     3.52    11.21 
subtype1 subtype2 subtype3 
  151.92   141.73   114.18 
subtype1 subtype2 subtype3 
   51.02    83.41    63.12 
[1] "0.6 - 151.9 (51.0)"  "3.5 - 141.7 (83.4)"  "11.2 - 114.2 (63.1)"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[25] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype2"
[61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       6        4         7        3
  subtype2       9        9         3        3
  subtype3       6       12         4        0
D5V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  6  4    10
  subtype2  9  9     6
  subtype3  6 12     4
D5V4, multiclass
          vv
clus       N0 N1+N2
  subtype1 10     2
  subtype2 14     2
  subtype3 16     1
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          10       14       16
  N1+N2        2        2        1
          vv
clus       M0 M1 MX
  subtype1  8  1  5
  subtype2 15  1  1
  subtype3 11  0  3
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1  6 14
  subtype2 11 13
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   14
  subtype2   11   13
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       11       10
  MALE         14       13       12
D5V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       5        2        4 
[1] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[8] "subtype1" "subtype3"
D5V9, continuous
D5V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  7  2
  subtype2 50  6
subtype1 subtype2 
       9       56 
subtype1 subtype2 
       2        6 
$subtype1
TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8427 
       59.67        28.80         8.12        13.15        31.33         0.56 
TCGA-KN-8428 TCGA-KN-8437 TCGA-KO-8404 
       52.27        75.72        10.68 

$subtype2
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.18       137.06       102.77 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.93        84.89        98.30        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.21        44.84        86.53        28.08        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       24.79        73.91        54.71        62.33       151.92        32.68 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
       35.57        37.08       123.12        51.02       114.18        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19        72.69         3.52 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       67.82        23.41         2.50        11.21        36.95        89.65 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       20.91        76.90        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.07        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.91 

subtype1 subtype2 
    0.56     2.50 
subtype1 subtype2 
   75.72   151.92 
subtype1 subtype2 
  28.800   70.255 
[1] "0.6 - 75.7 (28.8)"  "2.5 - 151.9 (70.3)"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[61] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[1] "hr=" "3.4"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       4        1         2        2
  subtype2      17       24        12        4
D6V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  4  1     4
  subtype2 17 24    16
D6V4, multiclass
          vv
clus       N0 N1+N2
  subtype1  3     1
  subtype2 37     4
D6V5, multiclass
       clus
vv      subtype1 subtype2
  N0           3       37
  N1+N2        1        4
          vv
clus       M0 M1 MX
  subtype1  2  0  3
  subtype2 32  2  6
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype1  2  7
  subtype2 25 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2   25   32
        clus
vv       subtype1 subtype2
  FEMALE        2       25
  MALE          7       32
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 
       2        9 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[8] "subtype2" "subtype2"
D6V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 
       1        7 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  8  2
  subtype2 16  0
  subtype3 13  3
  subtype4 10  0
  subtype5 10  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       16       16       10       13 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        0        3        0        3 
$subtype1
TCGA-KL-8323 TCGA-KL-8329 TCGA-KL-8334 TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8426 
       38.07        90.48        96.95        30.21        65.19         3.52 
TCGA-KO-8403 TCGA-KO-8410 TCGA-KO-8415 TCGA-KO-8416 
       76.90        87.78        57.17        61.58 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8330 TCGA-KL-8343 TCGA-KM-8439 TCGA-KM-8476 
      141.73       109.18       108.62        59.67         8.12       123.12 
TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
       51.02        23.47        87.91        25.48        25.91        72.69 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8414 
       23.41         2.50        20.91        77.85 

$subtype3
TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8337 TCGA-KL-8339 
       23.84       137.06       102.77        98.93        44.84        28.08 
TCGA-KL-8341 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8418 TCGA-KN-8435 
       24.79        54.71        62.33        37.08       114.18        89.65 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8417 
       79.04        92.71       103.27        63.91 

$subtype4
TCGA-KL-8332 TCGA-KL-8340 TCGA-KL-8342 TCGA-KM-8440 TCGA-KM-8442 TCGA-KN-8429 
       84.89        66.54        73.91        32.68        35.57        67.82 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KO-8409 TCGA-KO-8413 
       11.21        36.95        80.38        86.07 

$subtype5
TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8338 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8441 
       98.30        92.55        86.53        28.80       151.92        13.15 
TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 
       31.33         0.56        52.27        75.72        10.68        74.93 
TCGA-KO-8408 
       16.67 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.52     2.50    23.84    11.21     0.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
   96.95   141.73   137.06    86.07   151.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  63.385   55.345   71.475   67.180   52.270 
[1] "3.5 - 97.0 (63.4)"   "2.5 - 141.7 (55.3)"  "23.8 - 137.1 (71.5)"
[4] "11.2 - 86.1 (67.2)"  "0.6 - 151.9 (52.3)" 
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype2" "subtype3" "subtype4" "subtype5" "subtype1"
[13] "subtype5" "subtype1" "subtype3" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype4" "subtype2" "subtype5" "subtype3" "subtype3"
[25] "subtype5" "subtype2" "subtype4" "subtype5" "subtype4" "subtype3"
[31] "subtype2" "subtype2" "subtype5" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype5"
[43] "subtype5" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
[49] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype5"
[55] "subtype3" "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
[61] "subtype4" "subtype2" "subtype1" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype2" "subtype3" "subtype4" "subtype5" "subtype1"
[13] "subtype5" "subtype1" "subtype3" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype4" "subtype2" "subtype5" "subtype3" "subtype3"
[25] "subtype5" "subtype2" "subtype4" "subtype5" "subtype4" "subtype3"
[31] "subtype2" "subtype2" "subtype5" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype5"
[43] "subtype5" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
[49] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype5"
[55] "subtype3" "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
[61] "subtype4" "subtype2" "subtype1" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype2" "subtype3" "subtype4" "subtype5" "subtype1"
[13] "subtype5" "subtype1" "subtype3" "subtype5" "subtype3" "subtype4"
[19] "subtype3" "subtype4" "subtype2" "subtype5" "subtype3" "subtype3"
[25] "subtype5" "subtype2" "subtype4" "subtype5" "subtype4" "subtype3"
[31] "subtype2" "subtype2" "subtype5" "subtype3" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype5"
[43] "subtype5" "subtype4" "subtype2" "subtype2" "subtype4" "subtype4"
[49] "subtype3" "subtype2" "subtype5" "subtype1" "subtype5" "subtype5"
[55] "subtype3" "subtype3" "subtype5" "subtype4" "subtype1" "subtype3"
[61] "subtype4" "subtype2" "subtype1" "subtype1" "subtype3"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       5        0         3        2
  subtype2       6        8         2        0
  subtype3       4        9         1        2
  subtype4       2        5         3        0
  subtype5       4        3         5        2
D7V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  5  0     5
  subtype2  6  8     2
  subtype3  4  9     3
  subtype4  2  5     3
  subtype5  4  3     7
D7V4, multiclass
          vv
clus       N0 N1+N2
  subtype1  6     1
  subtype2  9     0
  subtype3 11     2
  subtype4  6     0
  subtype5  8     2
D7V5, multiclass
          vv
clus       M0 M1 MX
  subtype1  7  1  0
  subtype2  5  0  3
  subtype3 12  1  1
  subtype4  5  0  2
  subtype5  5  0  3
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1  7  3
  subtype2  7  9
  subtype3  6 10
  subtype4  4  6
  subtype5  3 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    3
  subtype2    7    9
  subtype3    6   10
  subtype4    4    6
  subtype5    3   11
D7V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype2 subtype3 subtype4 subtype5 
       3        2        3        3 
[1] "subtype5" "subtype2" "subtype4" "subtype5" "subtype4" "subtype2" "subtype2"
[8] "subtype5" "subtype4"
D7V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        2        2        2        4 
[1] "subtype5" "subtype5" "subtype5" "subtype5"
D7V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype2 subtype3 subtype4 subtype5 
       1        2        2        3 
[1] "subtype5" "subtype5" "subtype5"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 10  2
  subtype2  8  0
  subtype3 21  3
  subtype4 18  3
subtype1 subtype2 subtype3 subtype4 
      12        8       24       21 
subtype1 subtype2 subtype3 subtype4 
       2        0        3        3 
$subtype1
TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
       98.30        92.55        59.67        28.80         8.12        13.15 
TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 
       31.33         0.56        52.27        75.72        10.68        74.93 

$subtype2
TCGA-KL-8324 TCGA-KL-8328 TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8432 
      141.73       102.77        87.91        25.91         3.52         2.50 
TCGA-KN-8436 TCGA-KO-8410 
       20.91        87.78 

$subtype3
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8337 TCGA-KL-8339 
       23.84       109.18       108.62        84.89        44.84        28.08 
TCGA-KL-8340 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8477 
       66.54        62.33       151.92        32.68        35.57        51.02 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 
      114.18        23.47        25.48        72.69        67.82        23.41 
TCGA-KN-8433 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8417 
       11.21        16.67        80.38        86.07        77.85        63.91 

$subtype4
TCGA-KL-8323 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8336 
       38.07       137.06        90.48        98.93        96.95        30.21 
TCGA-KL-8338 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8443 TCGA-KM-8476 
       86.53        24.79        73.91        54.71        37.08       123.12 
TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       65.19        36.95        89.65        76.90        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
      103.27        57.17        61.58 

subtype1 subtype2 subtype3 subtype4 
    0.56     2.50    11.21    24.79 
subtype1 subtype2 subtype3 subtype4 
   98.30   141.73   151.92   137.06 
subtype1 subtype2 subtype3 subtype4 
  41.800   56.845   63.120   76.900 
[1] "0.6 - 98.3 (41.8)"   "2.5 - 141.7 (56.8)"  "11.2 - 151.9 (63.1)"
[4] "24.8 - 137.1 (76.9)"
 [1] "subtype4" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
 [7] "subtype4" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
[13] "subtype1" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[31] "subtype4" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype4"
[49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
[55] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [1] "subtype4" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
 [7] "subtype4" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
[13] "subtype1" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[31] "subtype4" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype4"
[49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
[55] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
 [1] "subtype4" "subtype2" "subtype3" "subtype3" "subtype4" "subtype2"
 [7] "subtype4" "subtype3" "subtype4" "subtype3" "subtype1" "subtype4"
[13] "subtype1" "subtype4" "subtype3" "subtype4" "subtype3" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
[25] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype4"
[31] "subtype4" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[37] "subtype3" "subtype2" "subtype4" "subtype3" "subtype2" "subtype1"
[43] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype4"
[49] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype1"
[55] "subtype4" "subtype4" "subtype3" "subtype3" "subtype2" "subtype4"
[61] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       4        2         4        2
  subtype2       2        5         0        1
  subtype3       7       12         5        1
  subtype4       8        6         5        2
D8V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  4  2     6
  subtype2  2  5     1
  subtype3  7 12     6
  subtype4  8  6     7
D8V4, multiclass
          vv
clus       N0 N1+N2
  subtype1  6     1
  subtype2  4     0
  subtype3 17     2
  subtype4 13     2
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0           6        4       17       13
  N1+N2        1        0        2        2
          vv
clus       M0 M1 MX
  subtype1  5  0  3
  subtype2  3  1  0
  subtype3 11  1  4
  subtype4 15  0  2
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype1  2 10
  subtype2  4  4
  subtype3 10 15
  subtype4 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   10
  subtype2    4    4
  subtype3   10   15
  subtype4   11   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        4       10       11
  MALE         10        4       15       10
D8V8, continuous
D8V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        1        4        3 
 [1] "subtype3" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
 [7] "subtype3" "subtype3" "subtype3" "subtype4"
D8V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        4        2 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
> q(save="no")
