[1] "ofn"        "-oTKIRP-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/KIRP-TP/19775272/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/20139337/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=290, in cluster file=291, common to both=290
[1]  10 290
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
113  76  46  52 
  1   2   3   4 
113  76  46  52 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 82  71 121 
  1   2   3 
 82  71 121 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
75 82 57 
 1  2  3 
75 82 57 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
39 67 64 44 
 1  2  3  4 
39 67 64 44 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
34 97 67 91 
 1  2  3  4 
34 97 67 91 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
118 125  46 
  1   2   3 
118 125  46 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
 91 110  89 
  1   2   3 
 91 110  89 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
121  81  88 
  1   2   3 
121  81  88 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
70 83 70 
 1  2  3 
70 83 70 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
105  75  14  29 
  1   2   3   4 
105  75  14  29 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 290 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=44,	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=237,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "203"   "1"    
freq.contrast "1"     "203"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 290 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
193  33  60   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  193    33    62 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
193  33  60   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  193    33    62 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
49 24  5 
[1] "table(vv)"
vv
N0 N1 N2 
49 24  5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
49 24  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
49 24  5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=37, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=34, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 96 16
  subtype2 66  8
  subtype3 40  5
  subtype4 36 15
subtype1 subtype2 subtype3 subtype4 
     112       74       45       51 
subtype1 subtype2 subtype3 subtype4 
      16        8        5       15 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        7.04        59.01        91.73        75.42        39.88        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JT TCGA-4A-A93X TCGA-4A-A93Y 
       33.07        24.33        31.20        22.49        12.82        11.57 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       67.17       106.55        15.48        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       27.09        67.43        19.63         0.10        21.37        35.18 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8312 TCGA-A4-8516 
        7.82         0.23        16.64        30.48        23.28         0.76 
TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 
       12.46        70.19        62.66        19.56        16.87        16.77 
TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.32        12.46        17.23         0.16        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5883 
       86.76        19.27        63.72        22.92        43.20        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-7044 TCGA-BQ-7048 
       26.04        26.04        25.35        10.82       123.62        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
        7.63         7.17       129.86        24.46        13.78        14.63 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A97G TCGA-G7-6792 
       80.88        61.02        74.60        19.00         0.43        90.90 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DC 
       71.44        25.15        12.92        27.65         1.05        12.89 
TCGA-GL-A9DE TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W 
       16.31        19.99        85.78        88.24        96.69        67.17 
TCGA-IZ-8195 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       22.26        30.38        27.65        17.62        12.13        31.13 
TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       29.26        99.78        42.94         6.61        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       50.60        78.90        19.73        27.06        11.93        41.33 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      125.29        37.35        98.96        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.05        15.62         3.68        13.28 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JM 
       75.55        58.22         4.57        34.85        56.81        30.71 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-5P-A9JZ 
       29.36        25.58         5.29        16.18         0.13        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 
       22.26        71.80        62.93        61.05        19.13         0.89 
TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3472 
       25.64        23.31        19.63        12.46        76.64        66.71 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4104 TCGA-B9-4113 
       21.67        24.56        20.25        33.83        34.49        50.50 
TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5891 TCGA-BQ-7051 
       26.40         1.15        19.23        17.49         0.95        50.40 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7842 TCGA-EV-5901 
       48.85        13.61        37.55         3.75         3.02        34.19 
TCGA-EV-5903 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LE TCGA-GL-A59R TCGA-HE-A5NH 
       24.89        39.25         6.38        80.65        12.43        26.01 
TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-MH-A55W 
       56.75        21.34        16.34        12.36        12.76        34.29 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-SX-A71R 
       27.78        20.25        15.48        87.09        16.01        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UZ-A9PJ 
       49.45        44.61        19.00        26.47        43.76        26.20 
TCGA-UZ-A9PL TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 
      103.63        62.83        86.37        30.67        65.13       110.73 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$subtype3
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-A4-7286 TCGA-A4-8311 
      100.27        56.91        49.58        78.64        18.21        23.97 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A657 
       19.73        14.33        16.96        49.32         2.20        21.07 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       30.58        10.16        28.18        15.12        43.99        22.06 
TCGA-BQ-5881 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 
       47.80        48.26        96.92         7.04         3.81        35.93 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-GL-6846 
       40.77        51.19         2.40        51.78        17.98       194.79 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GE TCGA-KV-A74V 
       17.95        11.21        11.84        25.22        29.10        11.41 
TCGA-PJ-A5Z9 TCGA-SX-A7SP TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PV 
       17.75        16.31        53.10       117.40        71.24        47.47 
TCGA-UZ-A9PZ TCGA-UZ-A9Q1 TCGA-Y8-A895 
       21.60        51.35        15.91 

$subtype4
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9JU TCGA-5P-A9K9 TCGA-A4-8098 TCGA-A4-A57E 
       54.64        51.52        12.26        19.36        29.46         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-7173 
       16.31        15.75         8.28        12.99         9.63        67.73 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A44B 
       49.25        37.51        10.09        20.61         0.46         2.10 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 
        8.88        21.63        30.28        13.25         7.66        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
        7.92         2.76        79.86        10.68        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        11.05        20.52        25.84        23.08        16.90 
TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-J7-8537 
        3.68        84.89        73.25        16.80         2.04        10.55 
TCGA-KV-A6GD TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UN-AAZ9 
       18.41        99.12        14.07        28.80        41.62        18.02 
TCGA-UZ-A9PQ TCGA-V9-A7HT TCGA-Y8-A896 
       86.27        31.73        18.64 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     2.20     0.46 
subtype1 subtype2 subtype3 subtype4 
  129.86   110.73   194.79    99.12 
subtype1 subtype2 subtype3 subtype4 
   25.68    26.30    25.22    16.80 
[1] "0.1 - 129.9 (25.7)" "0.1 - 110.7 (26.3)" "2.2 - 194.8 (25.2)"
[4] "0.5 - 99.1 (16.8)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      68       10        23        3
  subtype2      53        6         7        1
  subtype3      34        3         2        2
  subtype4      16        3        20        9
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         68       53       34       16
  STAGE II        10        6        3        3
  STAGE III       23        7        2       20
  STAGE IV         3        1        2        9
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 77 10    24
  subtype2 59 10     7
  subtype3 36  6     4
  subtype4 18  7    27
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          77       59       36       18
  T2          10       10        6        7
  T3+T4       24        7        4       27
[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"
          vv
clus       N0 N1 N2
  subtype1 20 10  1
  subtype2 11  1  0
  subtype3  7  1  0
  subtype4 10 12  4
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       20       11        7       10
  N1       10        1        1       12
  N2        1        0        0        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"
D1V6, binary
          cls
clus        0  1
  subtype1 42  2
  subtype2 22  1
  subtype3 14  0
  subtype4 15  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    2
  subtype2   22    1
  subtype3   14    0
  subtype4   15    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       42       22       14       15
  1        2        1        0        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 35 78
  subtype2 10 66
  subtype3  8 38
  subtype4 23 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   78
  subtype2   10   66
  subtype3    8   38
  subtype4   23   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       10        8       23
  MALE         78       66       38       29
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        26
  subtype2                                1     1                        17
  subtype3                                1     0                         6
  subtype4                                0     3                        12
          vv
clus       WHITE
  subtype1    82
  subtype2    53
  subtype3    37
  subtype4    32
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        1        0        3
  BLACK OR AFRICAN AMERICAN              26       17        6       12
  WHITE                                  82       53       37       32
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus        0  1
  subtype1  7 88
  subtype2  2 69
  subtype3  2 39
  subtype4  1 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   88
  subtype2    2   69
  subtype3    2   39
  subtype4    1   43
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7        2        2        1
  NOT HISPANIC OR LATINO       88       69       39       43
[1] 2 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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1  69  11
  subtype2  50  20
  subtype3 110   9
subtype1 subtype2 subtype3 
      80       70      119 
subtype1 subtype2 subtype3 
      11       20        9 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J9 TCGA-2Z-A9JI TCGA-2Z-A9JJ 
        7.04        75.55       100.27        75.42        51.52        39.88 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JT TCGA-4A-A93Y TCGA-5P-A9JV 
       38.99        30.71        24.33        22.49        11.57        67.17 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
      106.55        90.21        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-8312 
       67.43        18.21        19.63        35.18         7.82        23.28 
TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 
       19.73        12.46        67.73        19.56        16.87        16.77 
TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5881 TCGA-BQ-5883 
       20.32        12.46        17.23        14.86        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7045 TCGA-BQ-7049 
       26.04        30.28        13.25        10.82        48.26        44.84 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7841 
       26.27         7.63         7.04         3.81        24.46        14.63 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A97G 
       40.77        80.88        61.02        24.89        13.08         0.43 
TCGA-G7-6792 TCGA-G7-6796 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NK 
       90.90        71.44         1.05        11.21        84.89        73.25 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD 
       85.78        88.24        96.69        16.34        10.55        18.41 
TCGA-MH-A560 TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SP 
       30.38        12.13        29.26        92.58        19.73        16.31 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
      125.29        37.35        62.83        31.73        26.01        39.06 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$subtype2
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JO TCGA-4A-A93X TCGA-5P-A9JU 
       59.01        91.73        54.64        31.20        12.82        12.26 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A57E 
       22.26        15.48        19.36         0.23        29.46         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YI 
        8.28        12.99        49.25         2.10         0.16        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       21.63        26.04        25.35         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DZ-6131 
       50.40        49.84        20.12        11.28         7.17        79.86 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LD 
       10.68         1.18         4.01        11.05        20.52        16.90 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A9DE TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
      194.79         3.68        16.31        19.99         2.04        22.26 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM 
       99.78        42.94         6.61        99.12        52.27        50.60 
TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 
       78.90        12.49        14.07        11.93        41.33        18.02 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9Q1 TCGA-Y8-A8RZ 
       86.27        71.24        51.35         3.68 

$subtype3
TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL 
       58.22        56.91         4.57        34.85        56.81        33.07 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-5P-A9JY 
       29.36        25.58         5.29        16.18         0.13        49.58 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KF TCGA-A4-7288 TCGA-A4-7583 
       78.64        71.80        62.93        27.78        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       21.37        19.13         0.89        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.97        23.31         0.76        19.63        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
       16.31        15.75        12.46         2.20        37.51        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-5156 
       24.56        20.25        21.07        10.16        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       22.06        19.23        17.49        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6133 
       35.93        37.55        13.78         3.75         3.02        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 
       74.60        34.19        19.00         2.40        51.78        39.25 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        25.84         6.38        17.98        23.08        80.65 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-HE-A5NH 
       12.92        27.65        12.43        17.95        12.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83W TCGA-IZ-8196 
       11.84        56.75        25.22        16.80        67.17        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        12.76        29.10        11.41        34.29        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 
       27.65        20.25        17.62        31.13        15.48        87.09 
TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       16.01        17.75        47.90        49.45        44.61        28.80 
TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       35.38        27.06        19.00        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        26.20       117.40       103.63        98.96        86.37 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-Y8-A894 
       30.67        47.47        65.13        21.60       110.73        18.64 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.02 

subtype1 subtype2 subtype3 
    0.43     0.16     0.10 
subtype1 subtype2 subtype3 
  125.29   194.79   129.86 
subtype1 subtype2 subtype3 
  26.025   20.055   25.150 
[1] "0.4 - 125.3 (26.0)" "0.2 - 194.8 (20.1)" "0.1 - 129.9 (25.1)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      50        9        11        2
  subtype2      23        4        31       10
  subtype3      95        6         9        2
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         50       23       95
  STAGE II         9        4        6
  STAGE III       11       31        9
  STAGE IV         2       10        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2 T3+T4
  subtype1  58   7    15
  subtype2  26   8    37
  subtype3 102  11     8
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          58       26      102
  T2           7        8       11
  T3+T4       15       37        8
[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"
          vv
clus       N0 N1 N2
  subtype1 14  3  1
  subtype2 16 20  4
  subtype3 17  0  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       14       16       17
  N1        3       20        0
  N2        1        4        0
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 31  1
  subtype2 24  6
  subtype3 29  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    1
  subtype2   24    6
  subtype3   29    1
   clus
vv  subtype1 subtype2 subtype3
  0       31       24       29
  1        1        6        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 22 60
  subtype2 29 42
  subtype3 22 99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   60
  subtype2   29   42
  subtype3   22   99
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       29       22
  MALE         60       42       99
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        19
  subtype2                                0     1                        17
  subtype3                                1     1                        18
          vv
clus       WHITE
  subtype1    55
  subtype2    50
  subtype3    93
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   3        1        1
  BLACK OR AFRICAN AMERICAN              19       17       18
  WHITE                                  55       50       93
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
          cls
clus         0   1
  subtype1   1  70
  subtype2   5  51
  subtype3   6 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   70
  subtype2    5   51
  subtype3    6  105
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        6
  NOT HISPANIC OR LATINO       70       51      105
[1] 2 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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 62 13
  subtype2 69 12
  subtype3 48  7
subtype1 subtype2 subtype3 
      75       81       55 
subtype1 subtype2 subtype3 
      13       12        7 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-A4-7583 
        7.04        75.55       100.27        56.91        51.52         0.10 
TCGA-A4-7584 TCGA-A4-8517 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37        19.63        62.66        67.73        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-5156 TCGA-B9-A44B 
       16.87        21.07        12.46        10.16        43.99         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       19.23        17.23        17.49         8.88        22.92        21.63 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7049 TCGA-DW-7837 TCGA-DW-7838 
       25.35        13.25        10.82        44.84        37.55        24.46 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
        3.75        14.63        40.77        79.86        80.88        61.02 
TCGA-DZ-6135 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
       74.60        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       39.25        71.44        12.92        12.43        12.89        11.21 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40Y TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-P4-A5E6 
        2.04        96.69        67.17        22.26        10.55        99.78 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A7SN 
        6.61        92.58        19.73        17.75        44.61        19.00 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-UZ-A9PL TCGA-UZ-A9PZ TCGA-V9-A7HT TCGA-WN-A9G9 
       16.31        26.47       103.63        21.60        31.73        26.01 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       15.91        18.64        18.05 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JE TCGA-2Z-A9JJ 
       58.22         4.57        91.73        75.42        56.81        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-5P-A9JU TCGA-5P-A9JY TCGA-5P-A9KF 
       33.07        25.58         0.13        12.26        49.58        27.78 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 
        0.89         0.23        16.64        30.48        23.97         0.76 
TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       14.33         8.48        66.71        37.51        24.56        20.25 
TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7050 
       15.12        22.06         0.16        30.28         0.95        61.28 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 
       50.40         3.81        48.85        13.61       129.86        13.78 
TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY 
        3.02        51.19        34.19        19.00         2.40         1.18 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       90.90        25.15        20.52        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-IZ-8196 
       23.08        16.90        80.65       194.79        27.65        21.34 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 
       12.76        18.41        29.10        11.41        27.78        20.25 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A7SQ TCGA-SX-A7SS 
       87.09        42.94        16.01        47.90        41.62        53.10 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       18.02        26.20       117.40        98.96        86.27        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       71.24        30.67        47.47        65.13       110.73        18.64 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       25.28         3.68         6.02 

$subtype3
TCGA-2Z-A9JD TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-4A-A93X TCGA-4A-A93Y 
       34.85        31.20        29.36        22.49        12.82        11.57 
TCGA-5P-A9KE TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-8098 TCGA-B1-5398 TCGA-B9-A69E 
       27.09        61.05        35.18        29.46        19.56        14.86 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       12.30        86.76        63.72        43.20        47.80        40.83 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
        7.66        11.97         7.92         2.76       123.62        96.92 
TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-G7-6790 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM 
        7.04         7.17        51.78        11.05         3.68         1.05 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-MH-A855 
       16.31        84.89        19.99        16.34        30.38        12.13 
TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-Q2-A5QZ 
       99.12        52.27        50.60        78.90        12.49        14.07 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9Q1 
       11.93        41.33       125.29        37.35        62.83        51.35 
TCGA-Y8-A8S1 
       13.28 

subtype1 subtype2 subtype3 
    0.10     0.13     1.05 
subtype1 subtype2 subtype3 
  103.63   194.79   125.29 
subtype1 subtype2 subtype3 
   21.60    25.58    27.09 
[1] "0.1 - 103.6 (21.6)" "0.1 - 194.8 (25.6)" "1.1 - 125.3 (27.1)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      42        8        18        4
  subtype2      57        6        11        5
  subtype3      30        3        17        5
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         42       57       30
  STAGE II         8        6        3
  STAGE III       18       11       17
  STAGE IV         4        5        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 46  8    21
  subtype2 58 14    10
  subtype3 32  3    22
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          46       58       32
  T2           8       14        3
  T3+T4       21       10       22
[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"
          vv
clus       N0 N1 N2
  subtype1 18  7  2
  subtype2 19  6  0
  subtype3  9  8  2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18       19        9
  N1        7        6        8
  N2        2        0        2
[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"
D3V6, binary
          cls
clus        0  1
  subtype1 24  2
  subtype2 25  3
  subtype3 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    2
  subtype2   25    3
  subtype3   23    3
   clus
vv  subtype1 subtype2 subtype3
  0       24       25       23
  1        2        3        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 18 57
  subtype2 21 61
  subtype3 17 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   57
  subtype2   21   61
  subtype3   17   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       21       17
  MALE         57       61       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
D3V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        17
  subtype2                                0     2                        16
  subtype3                                1     0                        12
          vv
clus       WHITE
  subtype1    47
  subtype2    63
  subtype3    40
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        2        0
  BLACK OR AFRICAN AMERICAN              17       16       12
  WHITE                                  47       63       40
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
          cls
clus        0  1
  subtype1  1 58
  subtype2  2 75
  subtype3  4 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    2   75
  subtype3    4   43
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        4
  NOT HISPANIC OR LATINO       58       75       43
[1] 2 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(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 37  1
  subtype2 57  9
  subtype3 44 19
  subtype4 41  3
subtype1 subtype2 subtype3 subtype4 
      38       66       63       44 
subtype1 subtype2 subtype3 subtype4 
       1        9       19        3 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-A4-7583 
        7.04        75.55       100.27        56.91        51.52         0.10 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5156 TCGA-B9-A5W7 
       21.67        16.87        21.07        10.16        43.99        19.23 
TCGA-B9-A8YH TCGA-BQ-5888 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7838 
       17.49        13.25         7.63         3.81        37.55        24.46 
TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 TCGA-G7-7502 TCGA-GL-7773 
       14.63        80.88        61.02        24.89        25.84        12.92 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NL TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E7 
       12.89        26.01        25.22         2.04        18.41        87.09 
TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A7SP TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PZ 
       17.75        44.61        16.31       117.40        71.24        21.60 
TCGA-V9-A7HT TCGA-WN-A9G9 
       31.73        26.01 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       58.22         4.57        91.73        56.81        33.07        25.58 
TCGA-4A-A93W TCGA-5P-A9JU TCGA-5P-A9JY TCGA-5P-A9KF TCGA-A4-7734 TCGA-A4-7996 
        0.13        12.26        49.58        27.78         0.89        16.64 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 
       30.48        23.97         0.76        14.33         8.48        66.71 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 
       37.51        24.56        20.25        15.12        22.06         0.16 
TCGA-BQ-5878 TCGA-BQ-5891 TCGA-BQ-7051 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       63.72         0.95        50.40        48.85        13.61       129.86 
TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF 
       13.78         3.02        51.19        34.19        19.00         2.40 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       90.90        25.15        20.52         6.38        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-HE-A5NI TCGA-IZ-8196 TCGA-KV-A6GE 
       80.65       194.79        27.65        11.84        21.34        29.10 
TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A7SQ 
       11.41        27.78        20.25        16.01        47.90        41.62 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
       18.02        26.20        98.96        86.37        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       65.13       110.73        18.64        25.28         3.68         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JT TCGA-A4-7915 TCGA-AL-3473 TCGA-AL-7173 
       75.42        39.88        22.49         0.23        62.66        67.73 
TCGA-AL-A5DJ TCGA-B3-8121 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5877 TCGA-BQ-5879 
       49.25        12.46         2.10        17.23         8.88        22.92 
TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 
       21.63        30.28        25.35        10.82        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 
        2.76        96.92        44.84        61.28        49.84        20.12 
TCGA-DW-7840 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
        3.75        79.86        74.60        10.68        13.08         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A8LD 
        0.43         4.01        11.05        39.25        71.44        16.90 
TCGA-GL-7966 TCGA-GL-A59R TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
        3.68        12.43        56.75        73.25        16.80        19.99 
TCGA-IA-A83V TCGA-IA-A83W TCGA-J7-6720 TCGA-J7-8537 TCGA-P4-A5E6 TCGA-P4-A5E8 
       96.69        67.17        12.76        10.55        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM 
        6.61        99.12        92.58        19.73        14.07        11.93 
TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       19.00        26.47        53.10       103.63        37.35        86.27 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       15.91        18.64        18.05 

$subtype4
TCGA-2Z-A9JD TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9KE 
       34.85        31.20        29.36        12.82        11.57        27.09 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8517 TCGA-B1-5398 
       61.05        21.37        35.18        29.46        19.63        19.56 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       14.86        12.30        86.76        43.20        47.80        40.83 
TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 
        7.66       123.62        93.34        26.27        11.28         7.04 
TCGA-BQ-7061 TCGA-DW-7963 TCGA-G7-6790 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-GL-A9DE 
        7.17        40.77        51.78         1.05        11.21        16.31 
TCGA-HE-A5NF TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-AAVK 
       84.89        22.26        16.34        30.38        12.13        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PM TCGA-UZ-A9PO 
       50.60        78.90        12.49        41.33       125.29        62.83 
TCGA-UZ-A9Q1 TCGA-Y8-A8S1 
       51.35        13.28 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.23     1.05 
subtype1 subtype2 subtype3 subtype4 
  117.40   194.79   103.63   125.29 
subtype1 subtype2 subtype3 subtype4 
  23.065   24.855   20.120   29.410 
[1] "0.1 - 117.4 (23.1)" "0.1 - 194.8 (24.9)" "0.2 - 103.6 (20.1)"
[4] "1.1 - 125.3 (29.4)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      30        4         4        0
  subtype2      48        4         8        4
  subtype3      24        5        24        9
  subtype4      27        4        10        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         30       48       24       27
  STAGE II         4        4        5        4
  STAGE III        4        8       24       10
  STAGE IV         0        4        9        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 31  4     4
  subtype2 49 10     8
  subtype3 27  7    30
  subtype4 29  4    11
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          31       49       27       29
  T2           4       10        7        4
  T3+T4        4        8       30       11
[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"
          vv
clus       N0 N1 N2
  subtype1  7  1  0
  subtype2 14  3  0
  subtype3 17 14  3
  subtype4  8  3  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        7       14       17        8
  N1        1        3       14        3
  N2        0        0        3        1
[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"
D4V6, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 19  2
  subtype3 27  6
  subtype4 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   19    2
  subtype3   27    6
  subtype4   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       10       19       27       16
  1        0        2        6        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  8 31
  subtype2 16 51
  subtype3 23 41
  subtype4  9 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   31
  subtype2   16   51
  subtype3   23   41
  subtype4    9   35
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       16       23        9
  MALE         31       51       41       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
D4V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                        10
  subtype2                                0     0                        11
  subtype3                                0     5                        14
  subtype4                                1     0                        10
          vv
clus       WHITE
  subtype1    25
  subtype2    54
  subtype3    39
  subtype4    32
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   0        0        5        0
  BLACK OR AFRICAN AMERICAN              10       11       14       10
  WHITE                                  25       54       39       32
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus        0  1
  subtype1  0 33
  subtype2  1 59
  subtype3  4 48
  subtype4  2 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    1   59
  subtype3    4   48
  subtype4    2   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        4        2
  NOT HISPANIC OR LATINO       33       59       48       36
[1] 2 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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 26  6
  subtype2 85 10
  subtype3 62  5
  subtype4 67 23
subtype1 subtype2 subtype3 subtype4 
      32       95       67       90 
subtype1 subtype2 subtype3 subtype4 
       6       10        5       23 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-5P-A9KA TCGA-A4-7997 TCGA-AL-7173 
        7.04        33.07        30.71        12.99        30.48        67.73 
TCGA-B1-A657 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-5156 TCGA-BQ-5889 TCGA-BQ-7045 
       21.07        12.46        28.18        43.99        10.82        48.26 
TCGA-BQ-7049 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
       44.84         7.63         3.81       129.86        37.55        24.46 
TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       14.63        80.88        61.02        74.60        34.19        24.89 
TCGA-G7-6792 TCGA-GL-A9DD TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-J7-6720 
       90.90        11.21        88.24        96.69        67.17        12.76 
TCGA-KV-A6GD TCGA-Y8-A898 
       18.41        15.62 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       75.55        58.22         4.57        56.81        25.58         5.29 
TCGA-2Z-A9JS TCGA-4A-A93W TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-A4-7583 
       16.18         0.13        90.21        78.64        71.80         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A4ZT 
       19.13         0.89        23.97        23.31        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU 
       16.31        12.46        76.64        49.32        66.71         2.20 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-A6W5 TCGA-B9-4113 
       21.67        24.56        20.25        33.83        10.16        50.50 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 
       26.40         0.46         1.15        15.12        22.06        19.23 
TCGA-B9-A8YH TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7840 
       17.49        48.85        13.61        35.93        13.78         3.75 
TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 
        3.02        51.19        19.00         2.40        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R 
       25.84         6.38        17.98        80.65        27.65        12.43 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M9 
       12.89        26.01        11.84        56.75        21.34        12.36 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       34.29        27.78        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       15.48        87.09        16.01        17.75        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR 
       44.61        35.38        27.06        19.00        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP 
       53.10        43.76        26.20       117.40       103.63        98.96 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       86.37        30.67        47.47        65.13        21.60       110.73 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        15.91        18.05        25.28         6.02 

$subtype3
TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JG 
       59.01       100.27        56.91        91.73        34.85        54.64 
TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9K0 
       29.36        22.49        12.26       106.55        49.58        22.26 
TCGA-5P-A9K6 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7288 
       62.93        12.39        27.09        27.78        18.21        61.05 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
       21.37        35.18        16.64        25.64         0.76        19.63 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 
       19.73        12.46        15.75        62.66        19.56        37.51 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B9-A5W8 TCGA-B9-A8YI TCGA-BQ-5880 
       16.77        20.32        30.58        17.23        12.30        43.20 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 
       47.80        26.04         7.66        96.92        50.40         7.04 
TCGA-DW-7963 TCGA-G7-6790 TCGA-G7-6796 TCGA-GL-A59T TCGA-GL-A9DE TCGA-HE-A5NF 
       40.77        51.78        71.44        17.95        16.31        84.89 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IZ-A6M8 TCGA-KV-A6GE 
       25.22        16.80        19.99        85.78        16.34        29.10 
TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-SX-A71V 
       11.41        99.78        99.12        52.27        50.60        28.80 
TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       16.31       125.29        62.83        51.35        31.73        26.01 
TCGA-Y8-A8RZ 
        3.68 

$subtype4
TCGA-2Z-A9J9 TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       75.42        51.52        39.88        38.99        24.33        31.20 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JV TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 
       12.82        11.57        67.17        15.48        43.04        19.36 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
       67.43        19.63         7.82         0.23        29.46        23.28 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-A5DJ 
        8.48         8.28        12.99         9.63        70.19        49.25 
TCGA-B1-A47O TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 
       16.87        10.09        34.49        20.61         2.10         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
        0.95        11.97         7.92         2.76       123.62        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 
       61.28        49.84        26.27        20.12        11.28         7.17 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       79.86        10.68        13.08         1.18         0.43         4.01 
TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
       11.05        20.52        23.08        16.90       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 
        3.68         1.05        73.25         2.04        22.26        10.55 
TCGA-MH-A560 TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       30.38        12.13        29.26        42.94         6.61        92.58 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 
       78.90        19.73        14.07        11.93        41.33        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8S1 
       37.35        86.27        71.24        39.06        18.64        13.28 

subtype1 subtype2 subtype3 subtype4 
    3.81     0.10     0.76     0.16 
subtype1 subtype2 subtype3 subtype4 
  129.86   117.40   125.29   194.79 
subtype1 subtype2 subtype3 subtype4 
  30.595   24.560   28.800   19.925 
[1] "3.8 - 129.9 (30.6)" "0.1 - 117.4 (24.6)" "0.8 - 125.3 (28.8)"
[4] "0.2 - 194.8 (19.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      27        2         0        2
  subtype2      74        5         8        2
  subtype3      38        9        11        0
  subtype4      33        6        33       11
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         27       74       38       33
  STAGE II         2        5        9        6
  STAGE III        0        8       11       33
  STAGE IV         2        2        0       11
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 29  2     2
  subtype2 79 11     7
  subtype3 46  9    11
  subtype4 38 11    42
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          29       79       46       38
  T2           2       11        9       11
  T3+T4        2        7       11       42
[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"
          vv
clus       N0 N1 N2
  subtype1  4  1  1
  subtype2 13  1  0
  subtype3 15  3  0
  subtype4 17 19  4
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        4       13       15       17
  N1        1        1        3       19
  N2        1        0        0        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"
D5V6, binary
          cls
clus        0  1
  subtype1 13  1
  subtype2 27  1
  subtype3 19  0
  subtype4 35  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   27    1
  subtype3   19    0
  subtype4   35    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       13       27       19       35
  1        1        1        0        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  4 30
  subtype2 19 78
  subtype3 10 57
  subtype4 43 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   30
  subtype2   19   78
  subtype3   10   57
  subtype4   43   48
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       19       10       43
  MALE         30       78       57       48
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
D5V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         8
  subtype2                                1     0                        19
  subtype3                                1     0                        11
  subtype4                                0     4                        23
          vv
clus       WHITE
  subtype1    22
  subtype2    71
  subtype3    53
  subtype4    60
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        0        0        4
  BLACK OR AFRICAN AMERICAN               8       19       11       23
  WHITE                                  22       71       53       60
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
          cls
clus        0  1
  subtype1  1 26
  subtype2  5 85
  subtype3  2 59
  subtype4  4 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   26
  subtype2    5   85
  subtype3    2   59
  subtype4    4   71
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        5        2        4
  NOT HISPANIC OR LATINO       26       85       59       71
[1] 2 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  98  19
  subtype2 111  12
  subtype3  31  13
subtype1 subtype2 subtype3 
     117      123       44 
subtype1 subtype2 subtype3 
      19       12       13 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JG 
        7.04        59.01       100.27        91.73        34.85        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-4A-A93X 
       51.52        38.99        31.20        29.36        22.49        12.82 
TCGA-4A-A93Y TCGA-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9K0 TCGA-5P-A9K3 
       11.57        12.26        67.17       106.55        22.26        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7288 
       62.93        19.36        12.39        27.09        18.21        61.05 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-8518 
       21.37        35.18        29.46        25.64        19.63        19.73 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 
       12.46         8.48         8.28        12.99         9.63        62.66 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 
       49.25        19.56        16.87        16.77        20.32        30.58 
TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
        0.46         2.10        17.23         0.16        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       86.76        19.27        63.72        43.20        47.80        21.63 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        26.04        25.35         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
       11.97       123.62        96.92        93.34        61.28        49.84 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-F9-A97G TCGA-G7-6796 
       24.46        40.77        79.86        61.02         0.43        71.44 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DD 
       20.52        16.90       194.79         1.05        17.95        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       16.31        84.89        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 
       96.69        22.26        16.34        10.55        18.41        30.38 
TCGA-MH-A855 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       12.13        99.78        99.12        52.27        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SP TCGA-UZ-A9PM 
       14.07        28.80        11.93        41.33        16.31       125.29 
TCGA-UZ-A9PO TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       62.83        86.27        71.24        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       39.06         3.68        13.28 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JL 
       75.55        58.22        56.91         4.57        56.81        33.07 
TCGA-2Z-A9JM TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-5P-A9JY 
       30.71        25.58         5.29        16.18         0.13        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9KA TCGA-5P-A9KF TCGA-A4-7583 
       90.21        78.64        71.80        12.99        27.78         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 
       19.13         0.89        16.64        30.48        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
        0.76        14.33        16.96        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-7332 
       70.19        76.64        49.32        66.71         2.20        37.51 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-A6W5 
       21.67        24.56        20.25        21.07        33.83        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       50.50        28.18        26.40         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-7045 TCGA-BQ-7051 TCGA-DW-5560 
       22.06        19.23        17.49        48.26        50.40        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       14.63         3.02        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       24.89         2.40        51.78        90.90        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R 
       25.84         6.38        17.98        80.65        27.65        12.43 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       12.89        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V 
       67.17        21.34        12.36        12.76        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z 
       34.29        27.78        27.65        20.25        17.62        15.48 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL 
       17.75        47.90        49.45        44.61        35.38        27.06 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       19.00        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       103.63        98.96        86.37        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       65.13        21.60       110.73        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.62        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JN TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7287 
       75.42        39.88        24.33        43.04        67.43        19.63 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-AL-7173 TCGA-B3-3926 TCGA-B3-4104 
        7.82         0.23        23.28        67.73        10.09        34.49 
TCGA-B3-8121 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5888 
       12.46        20.61         8.88        22.92        40.83        13.25 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-DZ-6132 
       10.82         7.92         2.76        44.84        26.27        80.88 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LC 
       10.68        13.08         1.18         4.01        11.05        23.08 
TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-A5NK TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E7 
       12.92         3.68        73.25        31.13        29.26        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-UN-AAZ9 
       42.94         6.61        92.58        16.01        19.73        18.02 
TCGA-UZ-A9PN TCGA-Y8-A896 
       37.35        18.64 

subtype1 subtype2 subtype3 
    0.16     0.10     0.23 
subtype1 subtype2 subtype3 
  194.79   129.86    92.58 
subtype1 subtype2 subtype3 
   24.46    25.84    20.17 
[1] "0.2 - 194.8 (24.5)" "0.1 - 129.9 (25.8)" "0.2 - 92.6 (20.2)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      56       12        34        5
  subtype2      94        8         8        2
  subtype3      22        2        10        8
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         56       94       22
  STAGE II        12        8        2
  STAGE III       34        8       10
  STAGE IV         5        2        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2 T3+T4
  subtype1  65  14    37
  subtype2 103  15     7
  subtype3  24   4    18
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          65      103       24
  T2          14       15        4
  T3+T4       37        7       18
[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"
          vv
clus       N0 N1 N2
  subtype1 25 14  2
  subtype2 20  0  0
  subtype3  4 10  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       25       20        4
  N1       14        0       10
  N2        2        0        3
[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"
D6V6, binary
          cls
clus        0  1
  subtype1 41  3
  subtype2 36  1
  subtype3 17  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    3
  subtype2   36    1
  subtype3   17    5
   clus
vv  subtype1 subtype2 subtype3
  0       41       36       17
  1        3        1        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  29  89
  subtype2  22 103
  subtype3  25  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   89
  subtype2   22  103
  subtype3   25   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       22       25
  MALE         89      103       21
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        24
  subtype2                                1     1                        25
  subtype3                                0     2                        12
          vv
clus       WHITE
  subtype1    88
  subtype2    90
  subtype3    28
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   2        1        2
  BLACK OR AFRICAN AMERICAN              24       25       12
  WHITE                                  88       90       28
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
          cls
clus         0   1
  subtype1   4 100
  subtype2   4 109
  subtype3   4  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  100
  subtype2    4  109
  subtype3    4   32
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        4
  NOT HISPANIC OR LATINO      100      109       32
[1] 2 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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 79 11
  subtype2 95 11
  subtype3 67 22
subtype1 subtype2 subtype3 
      90      106       89 
subtype1 subtype2 subtype3 
      11       11       22 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JD 
        7.04        59.01       100.27        56.91        91.73        34.85 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-4A-A93X TCGA-5P-A9JU TCGA-5P-A9JW TCGA-5P-A9JY 
       38.99        33.07        12.82        12.26       106.55        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE 
       22.26        15.48        71.80        43.04        12.39        27.09 
TCGA-5P-A9KF TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
       27.78        35.18        30.48        29.46        25.64         0.76 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 
       19.73        12.46         8.48        15.75         8.28        62.66 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3925 TCGA-B9-4114 TCGA-B9-4115 
       19.56        37.51        16.77        33.83        28.18        26.40 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-B9-A8YI 
        0.46        43.99         2.10        17.23        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 
       86.76        63.72        43.20        47.80        21.63        26.04 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7050 TCGA-BQ-7051 
       26.04         7.66         0.95        11.97        61.28        50.40 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 
       11.28         7.63         3.81        37.55         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 
       40.77        74.60         0.43        51.78        90.90        20.52 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-A6M8 
       11.21        16.31        25.22        85.78        67.17        16.34 
TCGA-KV-A74V TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVM 
       11.41        30.38        12.13        99.78        99.12        50.60 
TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-SX-A7SP TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PO 
       12.49        41.33        16.31       103.63       125.29        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       86.37       110.73        31.73        26.01        18.05         3.68 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       75.55        58.22         4.57        56.81        54.64        51.52 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
       90.21        78.64        67.43        18.21        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
       21.37        19.13        16.64        23.97        23.31        19.63 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       14.33        16.96        16.31        12.46        70.19        76.64 
TCGA-AL-3471 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47O TCGA-B3-3926 TCGA-B3-A6W5 
       49.32        49.25         2.20        16.87        10.09        10.16 
TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 
       50.50        20.61         1.15        15.12        22.06        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5893 TCGA-BQ-7044 
        0.16        14.86        30.28        13.25         7.92       123.62 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 
       96.92        26.27        13.78         3.02        51.19        19.00 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
       13.08         2.40         1.18        39.25        25.15        25.84 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       17.98        23.08        12.92        27.65        12.43        17.95 
TCGA-GL-A9DC TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-IA-A40U 
       12.89        84.89        26.01        11.84        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       19.99         2.04        12.36        29.10        34.29        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5ED TCGA-P4-AAVO 
       27.65        20.25        17.62        31.13        92.58        78.90 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
       17.75        47.90        44.61        28.80        27.06        19.00 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PS 
       41.62        26.47        53.10        18.02        26.20        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PZ TCGA-UZ-A9Q1 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        47.47        21.60        51.35        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        15.62        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-4A-A93W TCGA-4A-A93Y 
       75.42        39.88        30.71        24.33         0.13        11.57 
TCGA-5P-A9JV TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-A4-7287 TCGA-A4-7734 
       67.17        62.93        19.36        12.99        19.63         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3472 
        7.82         0.23        23.28        12.99         9.63        66.71 
TCGA-AL-7173 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 
       67.73        21.67        24.56        20.25        20.32        21.07 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
       30.58        34.49        12.46        19.27         8.88        22.92 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 
       40.83        25.35        10.82         2.76        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 
       44.84        49.84        20.12         7.04         7.17        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6131 TCGA-DZ-6132 
       13.61       129.86        35.93        24.46        79.86        80.88 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 
       61.02        34.19        24.89        10.68         4.01        11.05 
TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
       71.44         6.38        16.90        80.65       194.79         3.68 
TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        1.05        56.75        88.24        96.69        22.26        21.34 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 
       12.76        10.55        18.41        29.26        15.48        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       42.94         6.61        52.27        16.01        19.73        14.07 
TCGA-SX-A71S TCGA-SX-A71W TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PN 
       49.45        35.38        11.93        43.76       117.40        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PX TCGA-Y8-A895 TCGA-Y8-A8S1 
       98.96        86.27        65.13        15.91        13.28 

subtype1 subtype2 subtype3 
    0.43     0.10     0.13 
subtype1 subtype2 subtype3 
  125.29   123.62   194.79 
subtype1 subtype2 subtype3 
  26.745   22.785   23.280 
[1] "0.4 - 125.3 (26.7)" "0.1 - 123.6 (22.8)" "0.1 - 194.8 (23.3)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      46       12        19        2
  subtype2      77        5        14        4
  subtype3      50        5        19        9
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         46       77       50
  STAGE II        12        5        5
  STAGE III       19       14       19
  STAGE IV         2        4        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 54 16    20
  subtype2 84 10    16
  subtype3 55  7    26
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          54       84       55
  T2          16       10        7
  T3+T4       20       16       26
[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"
          vv
clus       N0 N1 N2
  subtype1 21  5  1
  subtype2 14  4  0
  subtype3 14 15  4
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       21       14       14
  N1        5        4       15
  N2        1        0        4
[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"
D7V6, binary
          cls
clus        0  1
  subtype1 30  1
  subtype2 28  3
  subtype3 36  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    1
  subtype2   28    3
  subtype3   36    5
   clus
vv  subtype1 subtype2 subtype3
  0       30       28       36
  1        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 18 73
  subtype2 29 81
  subtype3 30 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   73
  subtype2   29   81
  subtype3   30   59
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       29       30
  MALE         73       81       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        24
  subtype2                                1     2                        16
  subtype3                                1     2                        21
          vv
clus       WHITE
  subtype1    63
  subtype2    83
  subtype3    61
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              24       16       21
  WHITE                                  63       83       61
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
          cls
clus        0  1
  subtype1  3 79
  subtype2  4 92
  subtype3  5 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   79
  subtype2    4   92
  subtype3    5   71
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        4        5
  NOT HISPANIC OR LATINO       79       92       71
[1] 2 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(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 102  17
  subtype2  70   9
  subtype3  69  18
subtype1 subtype2 subtype3 
     119       79       87 
subtype1 subtype2 subtype3 
      17        9       18 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 
        7.04        75.55        59.01       100.27        56.91        91.73 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JP 
       34.85        56.81        54.64        38.99        33.07        29.36 
TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9JU TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 
        5.29        12.82        12.26       106.55        90.21        22.26 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 
       27.09        18.21        21.37        35.18        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 
       25.64         0.76        14.33        12.46         8.48         8.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 
       12.99         9.63        70.19        62.66        49.25        19.56 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3925 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       37.51        16.77        33.83        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        0.46        43.99         2.10        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5885 
       19.27        63.72        43.20        47.80        21.63        30.28 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
       26.04         7.66         0.95        11.97       123.62        96.92 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3.81        13.61        37.55        13.78         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       40.77        74.60        19.00         0.43        51.78        90.90 
TCGA-G7-7501 TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IA-A40X 
       20.52        12.89        11.21        16.31        25.22        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-KV-A6GE TCGA-KV-A74V 
       85.78        88.24        67.17        16.34        29.10        11.41 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A855 TCGA-P4-A5EB TCGA-P4-AAVK 
       27.78        30.38        20.25        12.13        99.12        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       50.60        78.90        12.49        27.06        11.93        41.33 
TCGA-SX-A7SP TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9PR 
       16.31        26.20       103.63       125.29        62.83        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       71.24        65.13        51.35        26.01         3.68 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JI TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JY 
       58.22         4.57        51.52        16.18        22.49        49.58 
TCGA-5P-A9K2 TCGA-5P-A9KF TCGA-5P-A9KH TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
       78.64        27.78        67.43        61.05         0.10        19.13 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A4ZT TCGA-A4-A5DU 
       16.64        23.97        23.31        19.63        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47N 
       15.75        12.46        76.64        49.32         2.20        24.56 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 
       16.87        21.07        10.09        30.58        10.16        50.50 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5888 
        1.15        15.12        22.06        19.23        17.23        13.25 
TCGA-BQ-7055 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6796 TCGA-G7-6797 
       26.27        51.19        13.08         2.40        71.44        25.15 
TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       25.84        17.98        23.08        27.65        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-IA-A40U TCGA-IZ-A6M9 
       84.89        26.01        11.84        73.25        16.80        12.36 
TCGA-MH-A55W TCGA-MH-A854 TCGA-P4-A5E6 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U 
       34.29        17.62        99.78        17.75        47.90        44.61 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       28.80        19.00        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-V9-A7HT 
       18.02        30.67        47.47        21.60       110.73        31.73 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8S0 
        6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ 
       75.42        39.88        30.71        24.33        31.20        25.58 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JV TCGA-5P-A9K6 TCGA-A4-7287 TCGA-A4-7734 
        0.13        11.57        67.17        62.93        19.63         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-A4-8518 TCGA-AL-3472 TCGA-AL-7173 
        7.82         0.23        23.28        19.73        66.71        67.73 
TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A5W9 
       21.67        20.25        20.32        34.49        12.46         0.16 
TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       14.86         8.88        22.92        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
       10.82         7.92         2.76        48.26        93.34        44.84 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       49.84        20.12        48.85       129.86        35.93        24.46 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
        3.02        79.86        80.88        61.02        34.19        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-A4TM 
       10.68         1.18         4.01        11.05        39.25         6.38 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92         3.68         1.05 
TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-6720 
       56.75         2.04        96.69        22.26        21.34        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       10.55        18.41        27.65        31.13        29.26        15.48 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z8 
       87.09        42.94         6.61        92.58        16.01        19.73 
TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71W TCGA-UZ-A9PK TCGA-UZ-A9PN TCGA-UZ-A9PP 
       14.07        49.45        35.38       117.40        37.35        98.96 
TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A8S1 
       86.27        39.06        13.28 

subtype1 subtype2 subtype3 
    0.43     0.10     0.13 
subtype1 subtype2 subtype3 
  125.29   110.73   194.79 
subtype1 subtype2 subtype3 
   26.40    22.06    24.46 
[1] "0.4 - 125.3 (26.4)" "0.1 - 110.7 (22.1)" "0.1 - 194.8 (24.5)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      67       11        23        4
  subtype2      55        7         9        2
  subtype3      51        4        20        9
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         67       55       51
  STAGE II        11        7        4
  STAGE III       23        9       20
  STAGE IV         4        2        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 77 14    28
  subtype2 62 12     7
  subtype3 54  7    27
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          77       62       54
  T2          14       12        7
  T3+T4       28        7       27
[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"
          vv
clus       N0 N1 N2
  subtype1 23  8  2
  subtype2 12  2  0
  subtype3 14 14  3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       23       12       14
  N1        8        2       14
  N2        2        0        3
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 38  3
  subtype2 24  1
  subtype3 32  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    3
  subtype2   24    1
  subtype3   32    5
   clus
vv  subtype1 subtype2 subtype3
  0       38       24       32
  1        3        1        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 27 94
  subtype2 16 65
  subtype3 34 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   94
  subtype2   16   65
  subtype3   34   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       16       34
  MALE         94       65       54
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        28
  subtype2                                1     1                        12
  subtype3                                0     3                        21
          vv
clus       WHITE
  subtype1    86
  subtype2    61
  subtype3    60
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        1        3
  BLACK OR AFRICAN AMERICAN              28       12       21
  WHITE                                  86       61       60
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus         0   1
  subtype1   4 103
  subtype2   2  71
  subtype3   6  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  103
  subtype2    2   71
  subtype3    6   68
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        6
  NOT HISPANIC OR LATINO      103       71       68
[1] 2 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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 62  7
  subtype2 77  5
  subtype3 44 25
subtype1 subtype2 subtype3 
      69       82       69 
subtype1 subtype2 subtype3 
       7        5       25 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JD 
        7.04        75.55        59.01       100.27        56.91        34.85 
TCGA-2Z-A9JI TCGA-2Z-A9JO TCGA-2Z-A9JT TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K0 
       51.52        31.20        22.49        12.82       106.55        22.26 
TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7585 
       43.04        12.39        27.09        18.21        61.05        35.18 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A57E 
       16.64        30.48        29.46        19.63        19.73         8.48 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47O TCGA-B9-4117 
       15.75         8.28        62.66        19.56        16.87         0.46 
TCGA-B9-5156 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       43.99        14.86        12.30        43.20        47.80        21.63 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 
       26.04        26.04         7.66         0.95        11.97        96.92 
TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       61.28        26.27        11.28         7.63         7.04         3.81 
TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-A9DD 
       79.86         0.43        51.78        71.44        20.52        11.21 
TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IA-A40X TCGA-MH-A855 TCGA-P4-AAVK TCGA-P4-AAVM 
       16.31        25.22        19.99        12.13        52.27        50.60 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-UZ-A9PO TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       41.33        16.31        62.83        31.73        26.01        39.06 
TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.05         3.68        13.28 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JL TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       58.22        75.42        54.64        33.07        29.36        25.58 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9KF TCGA-A4-8310 
        5.29         0.13        49.58        90.21        27.78        25.64 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-AL-3472 TCGA-AT-A5NU 
       23.28        23.31         0.76        14.33        66.71         2.20 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-5155 
       24.56        20.25        21.07        33.83        26.40        15.12 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5878 TCGA-BQ-7044 TCGA-BQ-7051 TCGA-DW-5560 
        0.16        17.49        63.72       123.62        50.40        48.85 
TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
       13.61        35.93        37.55        13.78         3.75         3.02 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6792 TCGA-G7-6795 
       51.19        74.60        19.00        13.08        90.90        39.25 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59T 
        6.38        17.98        23.08        12.92        27.65        17.95 
TCGA-GL-A9DC TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M9 
       12.89        56.75        16.80         2.04        21.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       12.76        29.10        11.41        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W 
       99.78        17.75        47.90        49.45        44.61        35.38 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       27.06        19.00        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       103.63        98.96        86.37        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-Y8-A8RY TCGA-Y8-A8S0 
       65.13        21.60        25.28         6.02 

$subtype3
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-4A-A93Y TCGA-5P-A9JV 
       39.88        38.99        30.71        24.33        11.57        67.17 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7828 
       62.93        19.36        12.99        19.63         0.89         7.82 
TCGA-A4-7915 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-4104 
        0.23        12.99         9.63        67.73        20.32        34.49 
TCGA-B3-8121 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 
       12.46         2.10        19.27         8.88        22.92        40.83 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       25.35        13.25        10.82         7.92         2.76        48.26 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DW-7834 
       93.34        44.84        49.84        20.12         7.17       129.86 
TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       24.46        80.88        61.02        34.19        24.89        10.68 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-G7-A8LE 
        1.18         4.01        11.05        25.84        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
      194.79         3.68         1.05        85.78        88.24        96.69 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-A5E7 
       67.17        22.26        10.55        18.41        29.26        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM 
       42.94         6.61        16.01        19.73        14.07        11.93 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A898 
       37.35        86.27        15.62 

subtype1 subtype2 subtype3 
    0.43     0.13     0.23 
subtype1 subtype2 subtype3 
  106.55   123.62   194.79 
subtype1 subtype2 subtype3 
   22.49    26.30    20.32 
[1] "0.4 - 106.5 (22.5)" "0.1 - 123.6 (26.3)" "0.2 - 194.8 (20.3)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      39        6        14        2
  subtype2      63        4        10        1
  subtype3      30        6        19       11
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         39       63       30
  STAGE II         6        4        6
  STAGE III       14       10       19
  STAGE IV         2        1       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 45  8    17
  subtype2 67  7     9
  subtype3 34  6    28
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          45       67       34
  T2           8        7        6
  T3+T4       17        9       28
[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"
          vv
clus       N0 N1 N2
  subtype1 17  4  1
  subtype2 13  3  0
  subtype3 10 16  4
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       13       10
  N1        4        3       16
  N2        1        0        4
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 24  1
  subtype2 25  0
  subtype3 26  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2   25    0
  subtype3   26    7
   clus
vv  subtype1 subtype2 subtype3
  0       24       25       26
  1        1        0        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 19 51
  subtype2 14 69
  subtype3 29 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   51
  subtype2   14   69
  subtype3   29   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       19       14       29
  MALE         51       69       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        11
  subtype2                                1     2                        14
  subtype3                                0     2                        15
          vv
clus       WHITE
  subtype1    54
  subtype2    62
  subtype3    50
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              11       14       15
  WHITE                                  54       62       50
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus        0  1
  subtype1  3 58
  subtype2  4 71
  subtype3  3 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   58
  subtype2    4   71
  subtype3    3   54
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        4        3
  NOT HISPANIC OR LATINO       58       71       54
[1] 2 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 94  9
  subtype2 53 22
  subtype3  7  6
  subtype4 29  0
subtype1 subtype2 subtype3 subtype4 
     103       75       13       29 
subtype1 subtype2 subtype3 subtype4 
       9       22        6        0 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JD 
        7.04        75.55        58.22       100.27        56.91        34.85 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        51.52        33.07        30.71        29.36         5.29 
TCGA-2Z-A9JT TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       22.49        12.82       106.55        49.58        90.21        22.26 
TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 
       12.99        27.09        27.78        61.05        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       29.46        25.64        23.31         0.76        19.63        14.33 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-3925 
       15.75         8.28        19.56        16.87        21.07        33.83 
TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A8YH 
       12.46        26.40         0.46        15.12        43.99        17.49 
TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7044 
       12.30        63.72        26.04        13.25         7.66       123.62 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7837 
       96.92        50.40         7.63         7.04         3.81        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7Q0 
       13.78         3.75        51.19        74.60        19.00        13.08 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LC 
       90.90        39.25        71.44        25.84        17.98        23.08 
TCGA-GL-8500 TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL 
       27.65        17.95        12.89        11.21        16.31        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A855 TCGA-P4-A5E6 TCGA-P4-AAVM 
       12.36        29.10        11.41        12.13        99.78        50.60 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.90        44.61        35.38        27.06        19.00        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PO 
       26.47        53.10        26.20       117.40       103.63        62.83 
TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-V9-A7HT TCGA-Y8-A897 TCGA-Y8-A898 
       98.96        30.67        47.47        31.73        18.05        15.62 
TCGA-Y8-A8RZ 
        3.68 

$subtype2
TCGA-2Z-A9J2 TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y 
       59.01        39.88        38.99        24.33        31.20        11.57 
TCGA-5P-A9JV TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7286 
       67.17        62.93        43.04        19.36        12.39        18.21 
TCGA-A4-7585 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 
       35.18        23.28        19.73         8.48        12.99         9.63 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-A656 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5876 
       62.66        67.73        20.32         2.10        14.86        19.27 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7045 TCGA-BQ-7048 
       25.35        10.82         0.95        11.97        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
        7.17       129.86        24.46        79.86        80.88        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 
       34.19        24.89         0.43         4.01        51.78        11.05 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM TCGA-IA-A83V TCGA-IZ-8195 
       20.52        16.90       194.79         1.05        96.69        22.26 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-AAVK TCGA-P4-AAVL 
       12.76        10.55        18.41        29.26        52.27        16.01 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       19.73        14.07        11.93        41.33        37.35        86.27 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A8S1 
       26.01        39.06        13.28 

$subtype3
TCGA-2Z-A9J9 TCGA-A4-7287 TCGA-A4-7828 TCGA-A4-7915 TCGA-B3-4104 TCGA-BQ-5879 
       75.42        19.63         7.82         0.23        34.49        22.92 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-GL-7966 TCGA-P4-A5E8 
        7.92         2.76        10.68         1.18         3.68        42.94 
TCGA-P4-A5EA 
        6.61 

$subtype4
TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-A4-7734 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N 
       25.58         0.13         0.89        66.71         2.20        24.56 
TCGA-B1-A654 TCGA-B9-A5W9 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7842 
       20.25         0.16        48.85        13.61        35.93         3.02 
TCGA-G7-A4TM TCGA-G7-A8LE TCGA-GL-7773 TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-MH-A854 
        6.38        80.65        12.92        56.75        21.34        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71S TCGA-SX-A7SU 
       31.13        15.48        87.09        17.75        49.45        43.76 
TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-Y8-A8RY TCGA-Y8-A8S0 
       86.37        65.13        21.60        25.28         6.02 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.43     0.23     0.13 
subtype1 subtype2 subtype3 subtype4 
  123.62   194.79    75.42    87.09 
subtype1 subtype2 subtype3 subtype4 
   26.20    24.46     7.92    21.60 
[1] "0.5 - 123.6 (26.2)" "0.4 - 194.8 (24.5)" "0.2 - 75.4 (7.9)"  
[4] "0.1 - 87.1 (21.6)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      69       11        13        2
  subtype2      34        3        23        9
  subtype3       3        2         6        3
  subtype4      26        0         1        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         69       34        3       26
  STAGE II        11        3        2        0
  STAGE III       13       23        6        1
  STAGE IV         2        9        3        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 78 12    13
  subtype2 38  5    32
  subtype3  3  3     8
  subtype4 27  1     1
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          78       38        3       27
  T2          12        5        3        1
  T3+T4       13       32        8        1
[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"
          vv
clus       N0 N1 N2
  subtype1 18  4  0
  subtype2 18 12  5
  subtype3  1  7  0
  subtype4  3  0  0
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       18       18        1        3
  N1        4       12        7        0
  N2        0        5        0        0
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 28  0
  subtype2 33  5
  subtype3  5  3
  subtype4  9  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   33    5
  subtype3    5    3
  subtype4    9    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       28       33        5        9
  1        0        5        3        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 20 85
  subtype2 25 50
  subtype3  9  5
  subtype4  8 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   85
  subtype2   25   50
  subtype3    9    5
  subtype4    8   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       25        9        8
  MALE         85       50        5       21
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      32       22        1       10 
 [1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype4" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype4"
[19] "subtype4" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
[25] "subtype1" "subtype4" "subtype2" "subtype1" "subtype2" "subtype1"
[31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype4" "subtype1" "subtype1" "subtype2"
[43] "subtype4" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[49] "subtype2" "subtype1" "subtype4" "subtype1" "subtype1" "subtype1"
[55] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[61] "subtype4" "subtype1" "subtype4" "subtype1"
D10V9, continuous
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        16
  subtype2                                0     3                        15
  subtype3                                0     1                         4
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1    82
  subtype2    55
  subtype3     7
  subtype4    22
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0
  ASIAN                                   1        3        1        0
  BLACK OR AFRICAN AMERICAN              16       15        4        5
  WHITE                                  82       55        7       22
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus        0  1
  subtype1  2 91
  subtype2  4 57
  subtype3  1 10
  subtype4  3 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   91
  subtype2    4   57
  subtype3    1   10
  subtype4    3   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        1        3
  NOT HISPANIC OR LATINO       91       57       10       25
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
