
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.85.4149/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KICH-TP/3537611/KICH-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/KICH-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=25, in cluster file=66, common to both=25
[1]  8 25
[1] "CN_CNMF"
[1] 3
 1  2  3 
 1 19  5 
 2  3 
19  5 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
 4 16  5 
 1  2  3 
 4 16  5 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
 3 11  7  4 
 1  2  3  4 
 3 11  7  4 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 
5 5 9 3 3 
1 2 3 4 5 
5 5 9 3 3 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 
9 8 8 
1 2 3 
9 8 8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2 
 4 21 
 1  2 
 4 21 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
10  7  8 
 1  2  3 
10  7  8 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
2 6 2 4 7 4 
2 4 5 6 
6 4 7 4 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[11] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[13] "YEAROFTOBACCOSMOKINGONSET"        "DISTANT.METASTASIS"              
[15] "LYMPH.NODE.METASTASIS"            "TUMOR.STAGECODE"                 
[17] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 18 rows and 25 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
        3126           NA         4335          247         1552         3473 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
         714         2674          775          788         1983         2211 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 
         107           17           NA         2063           NA          712 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
          76          341         1124         2727          636         2303 
TCGA-KO-8409 
        2445 
Variable 1:'AGE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T1B  T2 T2B T3A  T4 
  3   5   8   4   4   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=24, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype2 16  2
  subtype3  5  0
subtype2 subtype3 
      18        5 
subtype2 subtype3 
       2        0 
$subtype2
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8418 
      102.77        28.08       142.52         8.12        51.02       114.18 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
       23.47        87.91        25.48        25.91        65.19         3.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8437 TCGA-KO-8409 
        0.56        52.27        67.82        23.41        75.72        80.38 

$subtype3
TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 
       72.69         2.50        11.21        89.65        20.91 

subtype2 subtype3 
    0.56     2.50 
subtype2 subtype3 
  142.52    89.65 
subtype2 subtype3 
  51.645   20.910 
[1] "0.6 - 142.5 (51.6)" "2.5 - 89.7 (20.9)" 
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[1] "hr="     "2.4e+08"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype2  8 11
  subtype3  2  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    8   11
  subtype3    2    3
        clus
vv       subtype2 subtype3
  FEMALE        8        2
  MALE         11        3
          vv
clus       M0 M1 MX
  subtype2  2  2  3
  subtype3  0  0  0
D1V4, multiclass
          vv
clus       N0 N1 NX
  subtype2 12  2  5
  subtype3  1  0  4
D1V5, multiclass
D1V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype2       7        8         1        3
  subtype3       1        3         1        0
D1V7, multiclass

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  4  0
  subtype2 13  2
  subtype3  5  0
subtype1 subtype2 subtype3 
       4       15        5 
subtype1 subtype2 subtype3 
       0        2        0 
$subtype1
TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8434 TCGA-KO-8409 
       23.47        72.69        36.95        80.38 

$subtype2
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      102.77        28.08       142.52       114.18        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19         3.52        52.27        67.82        23.41 
TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
        2.50        89.65        20.91 

$subtype3
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 
        8.12        51.02         0.56        11.21        75.72 

subtype1 subtype2 subtype3 
   23.47     2.50     0.56 
subtype1 subtype2 subtype3 
   80.38   142.52    75.72 
subtype1 subtype2 subtype3 
   54.82    52.27    11.21 
[1] "23.5 - 80.4 (54.8)" "2.5 - 142.5 (52.3)" "0.6 - 75.7 (11.2)" 
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 1 3
  subtype2 8 8
  subtype3 2 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2    8    8
  subtype3    2    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        8        2
  MALE          3        8        3
          vv
clus       M0 M1 MX
  subtype1  1  0  0
  subtype2  1  2  1
  subtype3  0  0  2
D2V4, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        4        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       N0 N1 NX
  subtype1  3  0  1
  subtype2 10  1  5
  subtype3  0  1  4
D2V5, multiclass
D2V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        3         0        0
  subtype2       4        9         1        2
  subtype3       3        0         1        1
D2V7, multiclass

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  3  0
  subtype2 10  0
  subtype3  5  2
  subtype4  4  0
subtype1 subtype2 subtype3 subtype4 
       3       10        7        4 
subtype1 subtype2 subtype3 subtype4 
       0        0        2        0 
$subtype1
TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 
       65.19        36.95        89.65 

$subtype2
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      142.52        23.47        25.48        25.91        72.69         3.52 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KO-8409 
       23.41         2.50        11.21        80.38 

$subtype3
TCGA-KL-8328 TCGA-KL-8339 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8428 TCGA-KN-8429 
      102.77        28.08       114.18        87.91        52.27        67.82 
TCGA-KN-8436 
       20.91 

$subtype4
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8427 TCGA-KN-8437 
        8.12        51.02         0.56        75.72 

subtype1 subtype2 subtype3 subtype4 
   36.95     2.50    20.91     0.56 
subtype1 subtype2 subtype3 subtype4 
   89.65   142.52   114.18    75.72 
subtype1 subtype2 subtype3 subtype4 
  65.190   24.475   67.820   29.570 
[1] "37.0 - 89.7 (65.2)"  "2.5 - 142.5 (24.5)"  "20.9 - 114.2 (67.8)"
[4] "0.6 - 75.7 (29.6)"  
 [1] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype4" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype4" "subtype2"
 [1] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype4" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype4" "subtype2"
 [1] "subtype3" "subtype3" "subtype2" "subtype4" "subtype4" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[13] "subtype2" "subtype4" "subtype3" "subtype3" "subtype2" "subtype2"
[19] "subtype2" "subtype1" "subtype1" "subtype3" "subtype4" "subtype2"
D3V2, continuous
D3V3, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 5 6
  subtype3 3 4
  subtype4 1 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    5    6
  subtype3    3    4
  subtype4    1    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        2        5        3        1
  MALE          1        6        4        3
          vv
clus       M0 M1 MX
  subtype1  0  0  0
  subtype2  1  1  1
  subtype3  1  1  0
  subtype4  0  0  2
D3V4, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype2 subtype3 subtype4 
       3        2        2 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       N0 N1 NX
  subtype1  1  0  2
  subtype2  7  0  4
  subtype3  5  1  1
  subtype4  0  1  3
D3V5, multiclass
D3V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        2         0        0
  subtype2       4        5         1        1
  subtype3       0        5         1        1
  subtype4       3        0         0        1
D3V7, multiclass

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 3 2
  subtype2 5 0
  subtype3 8 0
  subtype4 3 0
  subtype5 3 0
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        5        8        3        3 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        0        0        0        0 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KN-8418 TCGA-KN-8428 TCGA-KN-8429 
      102.77        28.08       114.18        52.27        67.82 

$subtype2
TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8427 TCGA-KN-8437 
        8.12        51.02        23.47         0.56        75.72 

$subtype3
TCGA-KM-8438 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8431 
      142.52        25.48        25.91        72.69         3.52        23.41 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

$subtype4
TCGA-KN-8421 TCGA-KN-8432 TCGA-KN-8436 
       87.91         2.50        20.91 

$subtype5
TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 
       65.19        36.95        89.65 

subtype1 subtype2 subtype3 subtype4 subtype5 
   28.08     0.56     3.52     2.50    36.95 
subtype1 subtype2 subtype3 subtype4 subtype5 
  114.18    75.72   142.52    87.91    89.65 
subtype1 subtype2 subtype3 subtype4 subtype5 
  67.820   23.470   25.695   20.910   65.190 
[1] "28.1 - 114.2 (67.8)" "0.6 - 75.7 (23.5)"   "3.5 - 142.5 (25.7)" 
[4] "2.5 - 87.9 (20.9)"   "37.0 - 89.7 (65.2)" 
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype4" "subtype3" "subtype3" "subtype5" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype5" "subtype4" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype4" "subtype3" "subtype3" "subtype5" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype5" "subtype4" "subtype2" "subtype3"
 [1] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype4" "subtype3" "subtype3" "subtype5" "subtype3"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[19] "subtype3" "subtype5" "subtype5" "subtype4" "subtype2" "subtype3"
D4V2, continuous
D4V3, binary
          cls
clus       0 1
  subtype1 2 3
  subtype2 1 4
  subtype3 4 5
  subtype4 2 1
  subtype5 2 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2    1    4
  subtype3    4    5
  subtype4    2    1
  subtype5    2    1
          vv
clus       M0 M1 MX
  subtype1  1  1  0
  subtype2  0  0  2
  subtype3  1  1  1
  subtype4  0  0  0
  subtype5  0  0  0
D4V4, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        2        3 
[1] "subtype3" "subtype3" "subtype3"
          vv
clus       N0 N1 NX
  subtype1  4  1  0
  subtype2  1  1  3
  subtype3  6  0  3
  subtype4  1  0  2
  subtype5  1  0  2
D4V5, multiclass
D4V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        3         1        1
  subtype2       3        1         0        1
  subtype3       4        3         1        1
  subtype4       0        3         0        0
  subtype5       1        2         0        0
D4V7, multiclass

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 6 2
  subtype2 8 0
  subtype3 8 0
subtype1 subtype2 subtype3 
       8        8        8 
subtype1 subtype2 subtype3 
       2        0        0 
$subtype1
TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8427 TCGA-KN-8428 
       28.08       142.52         8.12        51.02         0.56        52.27 
TCGA-KN-8432 TCGA-KN-8437 
        2.50        75.72 

$subtype2
TCGA-KL-8328 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8434 
      102.77        23.47        87.91        65.19         3.52        36.95 
TCGA-KN-8435 TCGA-KN-8436 
       89.65        20.91 

$subtype3
TCGA-KN-8418 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 
      114.18        25.48        25.91        72.69        67.82        23.41 
TCGA-KN-8433 TCGA-KO-8409 
       11.21        80.38 

subtype1 subtype2 subtype3 
    0.56     3.52    11.21 
subtype1 subtype2 subtype3 
  142.52   102.77   114.18 
subtype1 subtype2 subtype3 
  39.550   51.070   46.865 
[1] "0.6 - 142.5 (39.5)"  "3.5 - 102.8 (51.1)"  "11.2 - 114.2 (46.9)"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
D5V2, continuous
D5V3, binary
          cls
clus       0 1
  subtype1 3 6
  subtype2 3 5
  subtype3 5 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    3    5
  subtype3    5    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        3        5
  MALE          6        5        3
          vv
clus       M0 M1 MX
  subtype1  0  1  3
  subtype2  1  1  0
  subtype3  1  0  0
D5V4, multiclass
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        2        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       N0 N1 NX
  subtype1  3  2  4
  subtype2  4  0  4
  subtype3  6  0  2
D5V5, multiclass
D5V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       4        3         0        2
  subtype2       1        6         0        1
  subtype3       3        3         2        0
D5V7, multiclass

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1  3  1
  subtype2 19  1
subtype1 subtype2 
       4       20 
subtype1 subtype2 
       1        1 
$subtype1
TCGA-KM-8439 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8437 
        8.12         0.56        52.27        75.72 

$subtype2
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 
      102.77        28.08       142.52        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-8409 
       20.91        80.38 

subtype1 subtype2 
    0.56     2.50 
subtype1 subtype2 
   75.72   142.52 
subtype1 subtype2 
  30.195   43.985 
[1] "0.6 - 75.7 (30.2)"  "2.5 - 142.5 (44.0)"
 [1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[1] "hr=" "5.2"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1  1  3
  subtype2 10 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    3
  subtype2   10   11
        clus
vv       subtype1 subtype2
  FEMALE        1       10
  MALE          3       11
          vv
clus       M0 M1 MX
  subtype1  0  0  1
  subtype2  2  2  2
D6V4, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 
       1        6 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       N0 N1 NX
  subtype1  1  1  2
  subtype2 12  1  8
D6V5, multiclass
D6V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2        1         0        1
  subtype2       6       11         2        2
D6V7, multiclass

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 10  0
  subtype2  7  0
  subtype3  5  2
subtype1 subtype2 subtype3 
      10        7        7 
subtype1 subtype2 subtype3 
       0        0        2 
$subtype1
TCGA-KL-8328 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      102.77        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
        3.52         2.50        89.65        20.91 

$subtype2
TCGA-KN-8418 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
      114.18        72.69        67.82        23.41        11.21        36.95 
TCGA-KO-8409 
       80.38 

$subtype3
TCGA-KL-8339 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8477 TCGA-KN-8427 TCGA-KN-8428 
       28.08       142.52         8.12        51.02         0.56        52.27 
TCGA-KN-8437 
       75.72 

subtype1 subtype2 subtype3 
    2.50    11.21     0.56 
subtype1 subtype2 subtype3 
  102.77   114.18   142.52 
subtype1 subtype2 subtype3 
  25.695   67.820   51.020 
[1] "2.5 - 102.8 (25.7)"  "11.2 - 114.2 (67.8)" "0.6 - 142.5 (51.0)" 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
D7V2, continuous
D7V3, binary
          cls
clus       0 1
  subtype1 4 6
  subtype2 5 2
  subtype3 2 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    5    2
  subtype3    2    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        5        2
  MALE          6        2        6
          vv
clus       M0 M1 MX
  subtype1  1  1  0
  subtype2  1  0  0
  subtype3  0  1  3
D7V4, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        1        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       N0 N1 NX
  subtype1  6  0  4
  subtype2  4  0  3
  subtype3  3  2  3
D7V5, multiclass
D7V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3        6         0        1
  subtype2       1        4         2        0
  subtype3       4        2         0        2
D7V7, multiclass

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype2 5 1
  subtype4 3 1
  subtype5 7 0
  subtype6 4 0
subtype2 subtype4 subtype5 subtype6 
       6        4        7        4 
subtype2 subtype4 subtype5 subtype6 
       1        1        0        0 
$subtype2
TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8429 TCGA-KN-8431 TCGA-KO-8409 
       28.08       142.52       114.18        67.82        23.41        80.38 

$subtype4
TCGA-KM-8439 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8437 
        8.12         0.56        52.27        75.72 

$subtype5
TCGA-KL-8328 TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8435 
      102.77        87.91        25.91         3.52         2.50        89.65 
TCGA-KN-8436 
       20.91 

$subtype6
TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8425 
       51.02        23.47        25.48        72.69 

subtype2 subtype4 subtype5 subtype6 
   23.41     0.56     2.50    23.47 
subtype2 subtype4 subtype5 subtype6 
  142.52    75.72   102.77    72.69 
subtype2 subtype4 subtype5 subtype6 
  74.100   30.195   25.910   38.250 
[1] "23.4 - 142.5 (74.1)" "0.6 - 75.7 (30.2)"   "2.5 - 102.8 (25.9)" 
[4] "23.5 - 72.7 (38.2)" 
 [1] "subtype5" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [7] "subtype6" "subtype5" "subtype6" "subtype5" "subtype6" "subtype5"
[13] "subtype4" "subtype4" "subtype2" "subtype2" "subtype5" "subtype5"
[19] "subtype5" "subtype4" "subtype2"
 [1] "subtype5" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [7] "subtype6" "subtype5" "subtype6" "subtype5" "subtype6" "subtype5"
[13] "subtype4" "subtype4" "subtype2" "subtype2" "subtype5" "subtype5"
[19] "subtype5" "subtype4" "subtype2"
 [1] "subtype5" "subtype2" "subtype2" "subtype4" "subtype6" "subtype2"
 [7] "subtype6" "subtype5" "subtype6" "subtype5" "subtype6" "subtype5"
[13] "subtype4" "subtype4" "subtype2" "subtype2" "subtype5" "subtype5"
[19] "subtype5" "subtype4" "subtype2"
D8V2, continuous
D8V3, binary
          cls
clus       0 1
  subtype2 4 2
  subtype4 1 3
  subtype5 2 5
  subtype6 1 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    4    2
  subtype4    1    3
  subtype5    2    5
  subtype6    1    3
        clus
vv       subtype2 subtype4 subtype5 subtype6
  FEMALE        4        1        2        1
  MALE          2        3        5        3
          vv
clus       M0 M1 MX
  subtype2  1  1  1
  subtype4  0  0  1
  subtype5  1  1  0
  subtype6  0  0  1
D8V4, multiclass
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
[4] "subtype6"              
clus
subtype2 subtype4 subtype5 subtype6 
       3        1        2        1 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       N0 N1 NX
  subtype2  4  1  1
  subtype4  1  1  2
  subtype5  3  0  4
  subtype6  3  0  1
D8V5, multiclass
D8V6, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype2       0        4         1        1
  subtype4       2        1         0        1
  subtype5       1        5         0        1
  subtype6       3        1         0        0
D8V7, multiclass
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
