[1] "ofn"       "-oTUCS-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/15096025/UCS-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/15115115/UCS-TP.mergedcluster.txt"

nPatients in clinical file=57, in cluster file=57, common to both=57
[1] 10 57
[1] "CN_CNMF"
[1] 3
 1  2  3 
18 21 17 
 1  2  3 
18 21 17 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
12  9 10 13 13 
 1  2  3  4  5 
12  9 10 13 13 
[1] "RPPA_CNMF"
[1] 3
 1  2 
27 21 
 1  2 
27 21 
[1] "RPPA_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 
9 8 7 7 7 5 5 
1 2 3 4 5 6 7 
9 8 7 7 7 5 5 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
15 20 12 10 
 1  2  3  4 
15 20 12 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
11  4  8  6  8  6 14 
 1  2  3  4  5  6  7 
11  4  8  6  8  6 14 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
11 22  4 19 
 1  2  3  4 
11 22  4 19 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
24  8 18  6 
 1  2  3  4 
24  8 18  6 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
13 23 20 
 1  2  3 
13 23 20 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
25  7 17  7 
 1  2  3  4 
25  7 17  7 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 57 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "43"                  
freq.contrast "43"               "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 57 columns, 1 survival variables, and 2 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "RACE"          
YEARS_TO_BIRTH, nv=30, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  8 10
  subtype2  9 12
  subtype3  4 12
subtype1 subtype2 subtype3 
      18       21       16 
subtype1 subtype2 subtype3 
      10       12       12 
$subtype1
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT 
       52.31        18.08        34.62        22.52        29.95        81.70 
TCGA-N5-A59E TCGA-N6-A4VE TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       14.70         9.57        26.70        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-NF-A4WX 
       35.80       140.35        80.78         6.67        23.47        14.86 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
        4.67        59.38        67.13        11.87        17.42        19.63 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
        3.68        17.16        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q7 TCGA-NA-A4R0 TCGA-ND-A4WC 
       27.25        20.09        12.20        19.86        17.79        25.18 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NG-A4VW 
        9.80         2.66        31.20 

$subtype3
TCGA-N5-A4RM TCGA-N5-A4RU TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PO 
        4.87        50.17        39.75        25.35         0.26        25.68 
TCGA-N8-A4PQ TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 
       18.81        15.81        27.55         3.75        88.11        10.42 
TCGA-ND-A4WF TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        5.49         5.49        14.53        19.30 

subtype1 subtype2 subtype3 
    6.67     2.66     0.26 
subtype1 subtype2 subtype3 
  140.35    67.13    88.11 
subtype1 subtype2 subtype3 
  28.325   17.420   17.310 
[1] "6.7 - 140.3 (28.3)" "2.7 - 67.1 (17.4)"  "0.3 - 88.1 (17.3)" 
D1V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         5    11
  subtype2     1                         2    18
  subtype3     1                         2    14
D1V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        1
  BLACK OR AFRICAN AMERICAN        5        2        2
  WHITE                           11       18       14
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 4 8
  subtype2 3 6
  subtype3 3 7
  subtype4 6 6
  subtype5 5 8
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        9       10       12       13 
subtype1 subtype2 subtype3 subtype4 subtype5 
       8        6        7        6        8 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PN 
      102.41        52.31        18.08         0.26        12.43        26.70 
TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NG-A4VU 
       18.81        67.17        35.80        80.78        27.55        14.53 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
        4.67         4.87        22.52        81.70        50.17        67.13 
TCGA-N5-A59E TCGA-N6-A4V9 TCGA-ND-A4WF 
       14.70        17.42         5.49 

$subtype3
TCGA-N5-A4RF TCGA-N5-A59F TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PP TCGA-N9-A4Q7 
       59.38        11.87        25.35        26.63        20.09        19.86 
TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-NF-A5CP TCGA-NG-A4VW 
       17.79        25.18         5.49        31.20 

$subtype4
TCGA-N5-A4RN TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A59B TCGA-N8-A4PO 
       34.62         3.68         9.57        17.16        13.38        25.68 
TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4R1 TCGA-NF-A4X2 TCGA-QM-A5NM 
       21.93        15.81       140.35         6.67         2.66        19.30 

$subtype5
TCGA-N5-A4RS TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A56S 
       29.95        19.63        39.75        13.74        27.25        12.20 
TCGA-N9-A4Q3 TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU 
       54.97         3.75        88.11        10.42        23.47         9.80 
TCGA-NF-A4WX 
       14.86 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.26     4.67     5.49     2.66     3.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
  102.41    81.70    59.38   140.35    88.11 
subtype1 subtype2 subtype3 subtype4 subtype5 
  27.125   17.420   22.635   16.485   19.630 
[1] "0.3 - 102.4 (27.1)" "4.7 - 81.7 (17.4)"  "5.5 - 59.4 (22.6)" 
[4] "2.7 - 140.3 (16.5)" "3.8 - 88.1 (19.6)" 
D2V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    10
  subtype2     0                         1     8
  subtype3     1                         2     7
  subtype4     1                         3     9
  subtype5     1                         1    10
D2V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        1        1
  BLACK OR AFRICAN AMERICAN        2        1        2        3        1
  WHITE                           10        8        7        9       10
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 10 17
  subtype2  6 14
subtype1 subtype2 
      27       20 
subtype1 subtype2 
      17       14 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
      102.41         4.67        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD 
       29.95        81.70        67.13        11.87        19.63         3.68 
TCGA-N6-A4VE TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S 
        9.57        12.43        13.38        27.25        25.68        12.20 
TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WA 
       54.97        19.86         3.75        17.79         6.67        23.47 
TCGA-ND-A4WC TCGA-NF-A4X2 TCGA-NF-A5CP 
       25.18         2.66         5.49 

$subtype2
TCGA-N5-A4RA TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI 
       52.31        14.70        17.42        25.35         0.26        26.63 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 
       13.74        26.70        20.09        18.81        21.93        67.17 
TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4W6 TCGA-ND-A4WF 
       35.80       140.35        80.78        27.55        10.42         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW 
       14.53        31.20 

subtype1 subtype2 
    2.66     0.26 
subtype1 subtype2 
  102.41   140.35 
subtype1 subtype2 
   18.08    23.64 
[1] "2.7 - 102.4 (18.1)" "0.3 - 140.3 (23.6)"
[1] "hr=" "1.2"
D3V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         5    20
  subtype2     1                         4    16
D3V3, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            2        1
  BLACK OR AFRICAN AMERICAN        5        4
  WHITE                           20       16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 3 6
  subtype2 2 5
  subtype3 3 4
  subtype4 2 5
  subtype5 3 4
  subtype6 2 3
  subtype7 1 4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       9        7        7        7        7        5        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        5        4        5        4        3        4 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 
      102.41        52.31         0.26        26.70        18.81        67.17 
TCGA-N9-A4Q4 TCGA-NA-A4QX TCGA-NG-A4VU 
       35.80        27.55        14.53 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RT TCGA-N5-A59F TCGA-N7-A4Y8 TCGA-NA-A4QY TCGA-NA-A4R1 
        4.67        81.70        11.87        12.43         3.75         6.67 
TCGA-NF-A4X2 
        2.66 

$subtype3
TCGA-N5-A4RJ TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-NA-A4QW 
       18.08        14.70        17.42        12.20        54.97        80.78 
TCGA-NA-A4R0 
       17.79 

$subtype4
TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RV TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PP 
        4.87        34.62        67.13        26.63        13.74        20.09 
TCGA-ND-A4WF 
        5.49 

$subtype5
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N6-A4VC TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N9-A4Q7 
       22.52        29.95        19.63        27.25        25.68        19.86 
TCGA-ND-A4WA 
       23.47 

$subtype6
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N7-A59B TCGA-ND-A4WC TCGA-NF-A5CP 
        3.68         9.57        13.38        25.18         5.49 

$subtype7
TCGA-N7-A4Y0 TCGA-N9-A4PZ TCGA-NA-A4QV TCGA-ND-A4W6 TCGA-NG-A4VW 
       25.35        21.93       140.35        10.42        31.20 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.26     2.66    12.20     4.87    19.63     3.68    10.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  102.41    81.70    80.78    67.13    29.95    25.18   140.35 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   27.55     6.67    17.79    20.09    23.47     9.57    25.35 
[1] "0.3 - 102.4 (27.6)"  "2.7 - 81.7 (6.7)"    "12.2 - 80.8 (17.8)" 
[4] "4.9 - 67.1 (20.1)"   "19.6 - 29.9 (23.5)"  "3.7 - 25.2 (9.6)"   
[7] "10.4 - 140.3 (25.4)"
D4V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2     7
  subtype2     1                         2     5
  subtype3     0                         0     7
  subtype4     0                         0     7
  subtype5     1                         3     3
  subtype6     1                         0     4
  subtype7     0                         2     3
D4V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        0        0        1
  BLACK OR AFRICAN AMERICAN        2        2        0        0        3
  WHITE                            7        5        7        7        3
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        0
  BLACK OR AFRICAN AMERICAN        0        2
  WHITE                            4        3
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  4 11
  subtype2  9 10
  subtype3  4  8
  subtype4  4  6
subtype1 subtype2 subtype3 subtype4 
      15       19       12       10 
subtype1 subtype2 subtype3 subtype4 
      11       10        8        6 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PN 
      102.41        52.31         4.67         0.26        12.43        26.70 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QX 
       20.09        18.81        67.17        35.80        80.78        27.55 
TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NG-A4VU 
       10.42         5.49        14.53 

$subtype2
TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE 
       59.38        34.62        17.42        19.63         3.68         9.57 
TCGA-N6-A4VF TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N9-A4PZ 
       17.16        13.38        26.63        27.25        25.68        21.93 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-NF-A5CP TCGA-NG-A4VW 
       19.86        15.81        17.79        25.18         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

$subtype3
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PL TCGA-N8-A56S 
       18.08        29.95        11.87        39.75        13.74        12.20 
TCGA-N9-A4Q3 TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
       54.97         3.75        88.11        23.47         9.80        14.86 

$subtype4
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
        4.87        22.52        81.70        50.17        67.13        14.70 
TCGA-N7-A4Y0 TCGA-NA-A4QV TCGA-NA-A4R1 TCGA-NF-A4X2 
       25.35       140.35         6.67         2.66 

subtype1 subtype2 subtype3 subtype4 
    0.26     3.68     3.75     2.66 
subtype1 subtype2 subtype3 subtype4 
  102.41    59.38    88.11   140.35 
subtype1 subtype2 subtype3 subtype4 
  20.090   19.630   16.470   23.935 
[1] "0.3 - 102.4 (20.1)" "3.7 - 59.4 (19.6)"  "3.8 - 88.1 (16.5)" 
[4] "2.7 - 140.3 (23.9)"
D5V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    12
  subtype2     2                         2    16
  subtype3     1                         1     9
  subtype4     0                         3     7
D5V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        2        1        0
  BLACK OR AFRICAN AMERICAN        3        2        1        3
  WHITE                           12       16        9        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 4 7
  subtype2 0 4
  subtype3 4 4
  subtype4 1 5
  subtype5 4 4
  subtype6 3 3
  subtype7 5 8
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      11        4        8        6        8        6       13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       7        4        4        5        4        3        8 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RA TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 
      102.41        52.31         0.26        26.70        18.81        67.17 
TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-ND-A4W6 TCGA-NG-A4VU 
       35.80        80.78        27.55        10.42        14.53 

$subtype2
TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N7-A4Y8 TCGA-ND-A4WF 
        4.67        22.52        12.43         5.49 

$subtype3
TCGA-N5-A4RF TCGA-N5-A59F TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N9-A4Q7 
       59.38        11.87        26.63        27.25        20.09        19.86 
TCGA-NA-A4R0 TCGA-ND-A4WC 
       17.79        25.18 

$subtype4
TCGA-N5-A4RJ TCGA-N5-A59E TCGA-N8-A56S TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-NF-A4WX 
       18.08        14.70        12.20         3.75        88.11        14.86 

$subtype5
TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N7-A4Y0 
        4.87        34.62        81.70        50.17        67.13        25.35 
TCGA-NA-A4R1 TCGA-NF-A4X2 
        6.67         2.66 

$subtype6
TCGA-N5-A4RS TCGA-N6-A4VG TCGA-N8-A4PL TCGA-N9-A4Q3 TCGA-ND-A4WA TCGA-NF-A4WU 
       29.95        39.75        13.74        54.97        23.47         9.80 

$subtype7
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A59B 
       17.42        19.63         3.68         9.57        17.16        13.38 
TCGA-N8-A4PO TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NF-A5CP TCGA-NG-A4VW 
       25.68        21.93        15.81       140.35         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.26     4.67    11.87     3.75     2.66     9.80     3.68 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  102.41    22.52    59.38    88.11    81.70    54.97   140.35 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  27.550    8.960   22.635   14.780   29.985   26.710   17.420 
[1] "0.3 - 102.4 (27.6)" "4.7 - 22.5 (9.0)"   "11.9 - 59.4 (22.6)"
[4] "3.8 - 88.1 (14.8)"  "2.7 - 81.7 (30.0)"  "9.8 - 55.0 (26.7)" 
[7] "3.7 - 140.3 (17.4)"
D6V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3     8
  subtype2     0                         1     3
  subtype3     1                         2     5
  subtype4     0                         0     5
  subtype5     0                         1     7
  subtype6     1                         0     5
  subtype7     1                         2    11
D6V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        3        1        2        0        1
  WHITE                            8        3        5        5        7
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        1
  BLACK OR AFRICAN AMERICAN        0        2
  WHITE                            5       11
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  3  8
  subtype2  9 13
  subtype3  3  1
  subtype4  6 12
subtype1 subtype2 subtype3 subtype4 
      11       22        4       18 
subtype1 subtype2 subtype3 subtype4 
       8       13        1       12 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N8-A4PP TCGA-N8-A4PQ 
      102.41         4.67        59.38        18.08        20.09        18.81 
TCGA-N9-A4Q4 TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NG-A4VU 
       35.80        27.55         6.67         5.49        14.53 

$subtype2
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV 
       52.31         4.87        34.62        22.52        50.17        67.13 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL 
       11.87        17.42         0.26        12.43        26.63        13.74 
TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A5I1 
       26.70        67.17        54.97       140.35        80.78        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
       10.42        23.47         9.80        14.86 

$subtype3
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N6-A4VG TCGA-NF-A4X2 
       29.95        81.70        39.75         2.66 

$subtype4
TCGA-N5-A59E TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A59B 
       14.70        19.63         3.68         9.57        17.16        13.38 
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       27.25        25.68        12.20        21.93        19.86        15.81 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        3.75        17.79        25.18         5.49        31.20        19.30 

subtype1 subtype2 subtype3 subtype4 
    4.67     0.26     2.66     3.68 
subtype1 subtype2 subtype3 subtype4 
  102.41   140.35    81.70    31.20 
subtype1 subtype2 subtype3 subtype4 
  18.810   25.050   34.850   17.475 
[1] "4.7 - 102.4 (18.8)" "0.3 - 140.3 (25.0)" "2.7 - 81.7 (34.9)" 
[4] "3.7 - 31.2 (17.5)" 
D7V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2     9
  subtype2     1                         5    15
  subtype3     0                         0     4
  subtype4     2                         2    15
D7V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        2
  BLACK OR AFRICAN AMERICAN        2        5        0        2
  WHITE                            9       15        4       15
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  9 14
  subtype2  2  6
  subtype3  7 11
  subtype4  3  3
subtype1 subtype2 subtype3 subtype4 
      23        8       18        6 
subtype1 subtype2 subtype3 subtype4 
      14        6       11        3 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A59E 
      102.41         4.67        59.38        18.08        81.70        14.70 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N8-A4PM TCGA-N8-A4PP 
        3.68         9.57        17.16        39.75        27.25        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4R1 
       18.81        12.20        21.93        35.80        19.86         6.67 
TCGA-ND-A4WF TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49         2.66         5.49        31.20        19.30 

$subtype2
TCGA-N5-A4RA TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-NA-A4QW TCGA-NA-A4QX 
       52.31         0.26        26.70        67.17        80.78        27.55 
TCGA-ND-A4W6 TCGA-NG-A4VU 
       10.42        14.53 

$subtype3
TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV 
        4.87        34.62        22.52        29.95        50.17        67.13 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N9-A4Q3 
       11.87        17.42        12.43        26.63        13.74        54.97 
TCGA-NA-A4QV TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
      140.35         3.75        88.11        23.47         9.80        14.86 

$subtype4
TCGA-N6-A4VC TCGA-N7-A59B TCGA-N8-A4PO TCGA-N9-A4Q8 TCGA-NA-A4R0 TCGA-ND-A4WC 
       19.63        13.38        25.68        15.81        17.79        25.18 

subtype1 subtype2 subtype3 subtype4 
    2.66     0.26     3.75    13.38 
subtype1 subtype2 subtype3 subtype4 
  102.41    80.78   140.35    25.68 
subtype1 subtype2 subtype3 subtype4 
  18.810   27.125   22.995   18.710 
[1] "2.7 - 102.4 (18.8)" "0.3 - 80.8 (27.1)"  "3.8 - 140.3 (23.0)"
[4] "13.4 - 25.7 (18.7)"
D8V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    20
  subtype2     0                         2     6
  subtype3     1                         3    13
  subtype4     1                         1     4
D8V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        1
  BLACK OR AFRICAN AMERICAN        3        2        3        1
  WHITE                           20        6       13        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1  5  8
  subtype2  9 14
  subtype3  7 12
subtype1 subtype2 subtype3 
      13       23       19 
subtype1 subtype2 subtype3 
       8       14       12 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A59E 
      102.41         4.67        59.38        18.08        81.70        14.70 
TCGA-N8-A4PQ TCGA-N9-A4Q4 TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4X2 
       18.81        35.80         3.75         6.67         5.49         2.66 
TCGA-NG-A4VU 
       14.53 

$subtype2
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
       52.31         4.87        34.62        22.52        29.95        50.17 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PL 
       67.13        11.87        17.42         0.26        12.43        13.74 
TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       26.70        67.17        54.97       140.35        80.78        27.55 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
       88.11        10.42        23.47         9.80        14.86 

$subtype3
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A59B 
       19.63         3.68         9.57        17.16        39.75        13.38 
TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ 
       26.63        27.25        25.68        20.09        12.20        21.93 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-NF-A5CP TCGA-NG-A4VW 
       19.86        15.81        17.79        25.18         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

subtype1 subtype2 subtype3 
    2.66     0.26     3.68 
subtype1 subtype2 subtype3 
  102.41   140.35    39.75 
subtype1 subtype2 subtype3 
   14.70    26.70    19.63 
[1] "2.7 - 102.4 (14.7)" "0.3 - 140.3 (26.7)" "3.7 - 39.8 (19.6)" 
D9V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    11
  subtype2     1                         5    16
  subtype3     2                         2    16
D9V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        2
  BLACK OR AFRICAN AMERICAN        2        5        2
  WHITE                           11       16       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1  9 15
  subtype2  2  5
  subtype3  7 10
  subtype4  3  4
subtype1 subtype2 subtype3 subtype4 
      24        7       17        7 
subtype1 subtype2 subtype3 subtype4 
      15        5       10        4 
$subtype1
TCGA-N5-A4R8 TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A59E 
      102.41         4.67        59.38        18.08        81.70        14.70 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N8-A4PM TCGA-N8-A4PP 
        3.68         9.57        17.16        39.75        27.25        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QY 
       18.81        12.20        21.93        35.80        19.86         3.75 
TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        6.67         5.49         2.66         5.49        31.20        19.30 

$subtype2
TCGA-N5-A4RA TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-NA-A4QW TCGA-NA-A4QX 
       52.31         0.26        26.70        67.17        80.78        27.55 
TCGA-NG-A4VU 
       14.53 

$subtype3
TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV 
        4.87        34.62        22.52        29.95        50.17        67.13 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N9-A4Q3 TCGA-NA-A4QV 
       11.87        17.42        12.43        13.74        54.97       140.35 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
       88.11        10.42        23.47         9.80        14.86 

$subtype4
TCGA-N6-A4VC TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N9-A4Q8 TCGA-NA-A4R0 
       19.63        13.38        26.63        25.68        15.81        17.79 
TCGA-ND-A4WC 
       25.18 

subtype1 subtype2 subtype3 subtype4 
    2.66     0.26     4.87    13.38 
subtype1 subtype2 subtype3 subtype4 
  102.41    80.78   140.35    26.63 
subtype1 subtype2 subtype3 subtype4 
  18.445   27.550   22.520   19.630 
[1] "2.7 - 102.4 (18.4)" "0.3 - 80.8 (27.6)"  "4.9 - 140.3 (22.5)"
[4] "13.4 - 26.6 (19.6)"
D10V2, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    21
  subtype2     0                         1     6
  subtype3     1                         4    11
  subtype4     1                         1     5
D10V3, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        1
  BLACK OR AFRICAN AMERICAN        3        1        4        1
  WHITE                           21        6       11        5
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
