[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/22507257/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/22542911/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=291, in cluster file=291, common to both=291
[1]  10 291
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
106  73  49  60 
  1   2   3   4 
106  73  49  60 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6 
56 43 59 59 29 29 
 1  2  3  4  5  6 
56 43 59 59 29 29 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
75 83 57 
 1  2  3 
75 83 57 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
39 67 65 44 
 1  2  3  4 
39 67 65 44 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
32 91 71 32 64 
 1  2  3  4  5 
32 91 71 32 64 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
118 125  47 
  1   2   3 
118 125  47 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
29 39 66 43 81 33 
 1  2  3  4  5  6 
29 39 66 43 81 33 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
121  81  89 
  1   2   3 
121  81  89 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
71 76 77 
 1  2  3 
71 76 77 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
93 99 32 
 1  2  3 
93 99 32 
[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 291 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=232,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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   "209"   "1"    
freq.contrast "1"     "209"  
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 291 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 
194  33  60   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  194    33    62 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
194  33  60   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  194    33    62 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
50 24  4 
[1] "table(vv)"
vv
N0 N1 N2 
50 24  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
50 24  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
50 24  4 
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 90 15
  subtype2 61 10
  subtype3 44  5
  subtype4 46 14
subtype1 subtype2 subtype3 subtype4 
     105       71       49       60 
subtype1 subtype2 subtype3 subtype4 
      15       10        5       14 
$subtype1
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JV TCGA-BQ-5886 TCGA-BQ-5888 
       75.42        39.88        33.07        67.17        26.04        13.25 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-7838 TCGA-DZ-6134 TCGA-IA-A83W 
       44.84        26.27        20.12        24.46        61.02        67.17 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-2K-A9WE 
       12.13        29.26        19.73        41.33         6.74         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X 
       59.01        91.73        38.99        24.33        31.20        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH 
       11.57       106.55        43.04        12.99        12.39        67.43 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7997 TCGA-A4-8312 
       19.63         0.10        35.18         7.82        30.48        23.28 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-AL-3467 TCGA-AL-3473 
        0.76        19.73        12.46         8.28        70.19        62.66 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 
       67.73        41.13        16.77        20.32        34.49        12.46 
TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 
       28.18        20.61        14.86        12.30        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 
       22.92        43.20        40.83        26.04        30.28        10.82 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 
      123.62        93.34        61.28        49.84         7.63         7.17 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 
       80.88        74.60         0.43        90.90        71.44        25.15 
TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DD 
       20.52        12.92         3.68        27.65         1.05        11.21 
TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       16.31        58.19        73.25        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A856 TCGA-P4-A5E6 
       96.69        12.76        10.55        10.09        31.13        99.78 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SM 
        6.61        99.12        92.58        50.60        78.90        11.93 
TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      125.29        86.27        51.35        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S1 
       18.64        18.05        13.28 

$subtype2
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7734 TCGA-AL-3468 
       34.85        25.58        12.26        61.05         0.89        76.64 
TCGA-B1-A47M TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7840 
       21.67        48.85        13.61        35.93        37.55         3.75 
TCGA-DW-7842 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A895 TCGA-2Z-A9J1 TCGA-2Z-A9J3 
        3.02        62.83        86.37        15.91        75.55        58.22 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.91         4.57        56.81        30.71        29.36         5.29 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K4 TCGA-A4-7732 TCGA-A4-8515 TCGA-A4-A6HP 
       49.58        90.21        71.80        19.13        23.31        12.46 
TCGA-AL-3472 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4115 
       66.71        36.49        20.25        33.83        50.50        26.40 
TCGA-B9-4617 TCGA-B9-A8YH TCGA-BQ-7045 TCGA-DW-7963 TCGA-EV-5901 TCGA-EV-5903 
        1.15        17.49        48.26        40.77        34.19        24.89 
TCGA-F9-A7VF TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
        2.40        11.05        39.25        25.25        17.98        80.65 
TCGA-GL-6846 TCGA-GL-A59R TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL 
      194.79        12.43        81.93        26.01        11.84        25.22 
TCGA-IZ-8196 TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK 
       21.34        27.78        20.25        15.48        87.09        52.27 
TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SR TCGA-SX-A7SU 
       16.01        47.90        49.45        44.61        26.47        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-Y8-A8RY TCGA-Y8-A8S0 
       26.20        30.67        65.13        25.28         6.02 

$subtype3
TCGA-AL-A5DJ TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-7046 
       49.25        21.07        10.16        21.86        11.87        96.92 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-2Z-A9J5 TCGA-5P-A9K2 TCGA-A4-7286 
       17.95        84.89        17.75       100.27        78.64        18.21 
TCGA-A4-8311 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3471 
       23.97        14.33        16.96        16.31        15.75        49.32 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4117 TCGA-B9-5156 
        2.20        37.51        29.03        30.58         0.46        43.99 
TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5894 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6133 
       86.76        47.80         2.76         7.04         3.81        51.19 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-7502 TCGA-IA-A40U 
       19.00        10.68         1.18        51.78        25.84        16.80 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-SX-A71V 
       18.41        29.10        11.41        34.29        42.94        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS 
       27.06        19.00        41.62        53.10       117.40        71.24 
TCGA-V9-A7HT 
       31.73 

$subtype4
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7584 TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-B9-A5W7 
       16.18        22.49        21.37        12.99        27.68        19.23 
TCGA-BQ-5892 TCGA-BQ-7058 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7841 TCGA-IZ-A6M8 
       11.97        11.28       129.86        13.78        14.63        16.34 
TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93W TCGA-5P-A9K0 
       21.60        15.62        54.64        51.52         0.13        22.26 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7915 TCGA-A4-7996 
       15.48        62.93        19.36        27.09         0.23        16.64 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A57E TCGA-AL-3466 TCGA-B9-7268 
       29.46        25.64        19.63         8.48         9.63        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5890 
       17.23         0.16         8.88        21.63        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7051 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 
        0.95         7.92        50.40        79.86        13.08         4.01 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-A9DC TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IZ-8195 
       23.08        16.90        12.89        56.75         2.04        22.26 
TCGA-IZ-A6M9 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-Q2-A5QZ TCGA-SX-A7SP 
       12.36        30.38        27.65        17.62        14.07        16.31 
TCGA-UN-AAZ9 TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       18.02       103.63        37.35        98.96        47.47       110.73 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.89     0.46     0.13 
subtype1 subtype2 subtype3 subtype4 
  125.29   194.79   117.40   129.86 
subtype1 subtype2 subtype3 subtype4 
  26.270   29.360   25.840   18.625 
[1] "0.1 - 125.3 (26.3)" "0.9 - 194.8 (29.4)" "0.5 - 117.4 (25.8)"
[4] "0.1 - 129.9 (18.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      60        6        24        4
  subtype2      51        4         7        4
  subtype3      31        5         7        2
  subtype4      29        6        14        5
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         60       51       31       29
  STAGE II         6        4        5        6
  STAGE III       24        7        7       14
  STAGE IV         4        4        2        5
[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 69  9    26
  subtype2 55  9     9
  subtype3 33  7     9
  subtype4 34  8    18
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          69       55       33       34
  T2           9        9        7        8
  T3+T4       26        9        9       18
[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 12  1
  subtype2 10  3  1
  subtype3  4  3  0
  subtype4 15  6  2
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       20       10        4       15
  N1       12        3        3        6
  N2        1        1        0        2
[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 43  2
  subtype2 19  1
  subtype3 18  2
  subtype4 14  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    2
  subtype2   19    1
  subtype3   18    2
  subtype4   14    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       43       19       18       14
  1        2        1        2        4
[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 37 69
  subtype2 10 63
  subtype3 14 35
  subtype4 15 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   69
  subtype2   10   63
  subtype3   14   35
  subtype4   15   45
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       37       10       14       15
  MALE         69       63       35       45
[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     4                        25
  subtype2                                1     0                        16
  subtype3                                1     1                         9
  subtype4                                0     1                        11
          vv
clus       WHITE
  subtype1    72
  subtype2    51
  subtype3    35
  subtype4    46
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   4        0        1        1
  BLACK OR AFRICAN AMERICAN              25       16        9       11
  WHITE                                  72       51       35       46
[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  5 84
  subtype2  4 63
  subtype3  2 40
  subtype4  1 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   84
  subtype2    4   63
  subtype3    2   40
  subtype4    1   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        4        2        1
  NOT HISPANIC OR LATINO       84       63       40       53
[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 46  9
  subtype2 39  4
  subtype3 54  5
  subtype4 53  5
  subtype5 22  7
  subtype6 18 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      55       43       59       58       29       28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9        4        5        5        7       10 
$subtype1
TCGA-5P-A9JV TCGA-B1-A47O TCGA-BQ-5888 TCGA-BQ-7049 TCGA-DW-7838 TCGA-DZ-6134 
       67.17        27.68        13.25        44.84        24.46        61.02 
TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z8 TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J1 
       84.89        16.34        19.73        15.62         7.04        75.55 
TCGA-2Z-A9J5 TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-4A-A93Y TCGA-5P-A9K8 TCGA-5P-A9KA 
      100.27        51.52        38.99        11.57        43.04        12.99 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 
       67.43        18.21        19.73        12.46        67.73        41.13 
TCGA-B3-8121 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5880 TCGA-BQ-5884 
       12.46        43.99        17.23        14.86        43.20        26.04 
TCGA-BQ-5889 TCGA-BQ-7045 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
       10.82        48.26         7.63         3.81        40.77        80.88 
TCGA-F9-A97G TCGA-G7-6796 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-HE-A5NK TCGA-HE-A5NL 
        0.43        71.44         1.05        11.21        73.25        25.22 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-J7-8537 TCGA-KV-A6GD TCGA-P4-A5ED 
       85.78        88.24        96.69        10.55        18.41        92.58 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A896 
      125.29        37.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A8S1 
       13.28 

$subtype2
TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 TCGA-BQ-5886 TCGA-BQ-5892 
       34.85        22.49        61.05        21.37        26.04        11.97 
TCGA-BQ-7058 TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-2Z-A9J2 
       11.28        12.13        12.49        41.33        62.83        59.01 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-5P-A9JW TCGA-5P-A9K0 TCGA-5P-A9K6 TCGA-5P-A9KC 
       31.20        29.36       106.55        22.26        62.93        12.39 
TCGA-5P-A9KE TCGA-A4-7585 TCGA-A4-8517 TCGA-A4-A57E TCGA-B1-A655 TCGA-B1-A656 
       27.09        35.18        19.63         8.48        16.77        20.32 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-7044 TCGA-BQ-7048 
       12.30        19.27        47.80        21.63       123.62        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-GL-6846 
       61.28        49.84         7.04         7.17        79.86       194.79 
TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A560 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM 
       16.31        19.99        30.38        99.12        52.27        50.60 
TCGA-UZ-A9Q1 
       51.35 

$subtype3
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-A4-7734 TCGA-B9-A5W7 TCGA-DW-5560 TCGA-DW-5561 
       33.07        25.58         0.89        19.23        48.85        13.61 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        13.78         3.75        14.63         3.02 
TCGA-IA-A83W TCGA-UZ-A9PR TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9JE TCGA-2Z-A9JM 
       67.17        86.37        58.22        56.91        56.81        30.71 
TCGA-4A-A93W TCGA-5P-A9JZ TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8516 TCGA-A4-A6HP 
        0.13        90.21        19.13        30.48         0.76        12.46 
TCGA-B1-A654 TCGA-B9-A8YH TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 
       20.25        17.49        74.60        34.19        24.89        90.90 
TCGA-G7-A4TM TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC 
       25.25        80.65        12.92        27.65        12.43        12.89 
TCGA-HE-A5NH TCGA-IZ-8196 TCGA-J7-6720 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
       26.01        21.34        12.76        27.78        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-SX-A71R 
       17.62        31.13        15.48        87.09        16.01        47.90 
TCGA-SX-A71S TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       49.45        19.00        41.62        43.76        26.20       103.63 
TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-Y8-A894 TCGA-Y8-A8RY 
       98.96        30.67        65.13        18.64        25.28 

$subtype4
TCGA-2Z-A9JS TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-BQ-7046 
       16.18        21.67        21.07        10.16        21.86        96.92 
TCGA-DW-7834 TCGA-GL-A59T TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PZ TCGA-Y8-A895 
      129.86        17.95        17.75        35.38        21.60        15.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JR TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9KF TCGA-A4-7583 
        4.57         5.29        49.58        78.64        27.78         0.10 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A4ZT 
       16.64        25.64        23.97        23.31        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B9-7268 
       16.31        15.75         2.20        37.51        36.49        22.06 
TCGA-BQ-7051 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
       50.40        51.19         2.40        51.78        39.25        25.84 
TCGA-G7-A8LB TCGA-HE-7129 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IZ-A6M9 
       17.98        81.93        11.84        56.75        16.80        12.36 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E6 TCGA-SX-A71U TCGA-SX-A71V 
       29.10        11.41        34.29        99.78        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS 
       27.06        16.31        26.47        53.10       117.40        71.24 
TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-Y8-A897 TCGA-Y8-A8S0 
       47.47       110.73        18.05         6.02 

$subtype5
TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-7056 TCGA-Y8-A8RZ TCGA-2Z-A9J8 
       12.26        12.99        11.87        20.12         6.74        91.73 
TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-A4-8098 TCGA-A4-A5Y0 
       54.64        12.82        15.48        71.80        29.46         8.28 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5890 
        0.16        86.76         8.88        63.72        30.28         7.66 
TCGA-BQ-5891 TCGA-EV-5902 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-IA-A40Y 
        0.95        19.00        25.15        20.52        16.90         2.04 
TCGA-IZ-8195 TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PQ 
       22.26        78.90        14.07        11.93        86.27 

$subtype6
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-AL-A5DJ TCGA-BQ-7055 TCGA-MH-A857 TCGA-2Z-A9JN 
       75.42        39.88        49.25        26.27        29.26        24.33 
TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-BQ-5879 
       19.36        19.63         7.82         0.23        23.28        22.92 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       40.83        25.35         7.92         2.76        10.68        13.08 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 
        1.18         4.01        11.05        23.08         3.68        58.19 
TCGA-J7-A8I2 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-UN-AAZ9 
       10.09        42.94         6.61        18.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.43     7.04     0.13     0.10     0.16     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  125.29   194.79   103.63   129.86    91.73    75.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  27.680   29.360   26.200   23.640   16.900   19.495 
[1] "0.4 - 125.3 (27.7)" "7.0 - 194.8 (29.4)" "0.1 - 103.6 (26.2)"
[4] "0.1 - 129.9 (23.6)" "0.2 - 91.7 (16.9)"  "0.2 - 75.4 (19.5)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      30        6         9        2
  subtype2      25        1         9        2
  subtype3      52        2         3        0
  subtype4      40        7         6        2
  subtype5       8        1        15        3
  subtype6      13        1         9        5
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         30       25       52       40        8       13
  STAGE II         6        1        2        7        1        1
  STAGE III        9        9        3        6       15        9
  STAGE IV         2        2        0        2        3        5
[1] 4 6
[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 35  6    13
  subtype2 31  2    10
  subtype3 53  3     3
  subtype4 44 10     5
  subtype5 11  3    15
  subtype6 13  2    14
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1          35       31       53       44       11       13
  T2           6        2        3       10        3        2
  T3+T4       13       10        3        5       15       14
[1] 3 6
[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  9  3  1
  subtype2 10  2  0
  subtype3  8  0  0
  subtype4 11  1  0
  subtype5  6  9  0
  subtype6  4  8  3
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        9       10        8       11        6        4
  N1        3        2        0        1        9        8
  N2        1        0        0        0        0        3
[1] 3 6
[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 17  1
  subtype2 17  1
  subtype3 15  0
  subtype4 17  1
  subtype5  8  2
  subtype6 11  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    1
  subtype2   17    1
  subtype3   15    0
  subtype4   17    1
  subtype5    8    2
  subtype6   11    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       17       17       15       17        8       11
  1        1        1        0        1        2        3
[1] 2 6
[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 11 45
  subtype2 12 31
  subtype3 12 47
  subtype4 12 47
  subtype5  8 21
  subtype6 18 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   45
  subtype2   12   31
  subtype3   12   47
  subtype4   12   47
  subtype5    8   21
  subtype6   18   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       11       12       12       12        8       18
  MALE         45       31       47       47       21       11
[1] 2 6
[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
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18        8       16       17       10        2 
 [1] "subtype2" "subtype3" "subtype5" "subtype5" "subtype3" "subtype4"
 [7] "subtype1" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
[13] "subtype2" "subtype3" "subtype5" "subtype2" "subtype1" "subtype4"
[19] "subtype5" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[25] "subtype1" "subtype5" "subtype2" "subtype4" "subtype1" "subtype2"
[31] "subtype5" "subtype1" "subtype3" "subtype4" "subtype1" "subtype1"
[37] "subtype1" "subtype3" "subtype4" "subtype5" "subtype4" "subtype5"
[43] "subtype3" "subtype3" "subtype1" "subtype4" "subtype4" "subtype1"
[49] "subtype4" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[55] "subtype2" "subtype5" "subtype3" "subtype4" "subtype4" "subtype5"
[61] "subtype4" "subtype4" "subtype1" "subtype4" "subtype3" "subtype1"
[67] "subtype3" "subtype1" "subtype3"
D2V10, continuous
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12        6       13       13        7        2 
 [1] "subtype2" "subtype3" "subtype4" "subtype2" "subtype4" "subtype2"
 [7] "subtype3" "subtype5" "subtype3" "subtype4" "subtype5" "subtype1"
[13] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype5"
[19] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype4"
[25] "subtype5" "subtype4" "subtype5" "subtype3" "subtype3" "subtype1"
[31] "subtype4" "subtype4" "subtype3" "subtype3" "subtype4" "subtype2"
[37] "subtype5" "subtype3" "subtype4" "subtype4" "subtype5" "subtype4"
[43] "subtype4" "subtype1" "subtype4" "subtype3" "subtype1" "subtype1"
[49] "subtype3" "subtype1" "subtype3"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                        10
  subtype2                                1     0                         7
  subtype3                                0     1                        14
  subtype4                                1     0                         7
  subtype5                                0     0                         7
  subtype6                                0     3                         9
          vv
clus       WHITE
  subtype1    39
  subtype2    34
  subtype3    41
  subtype4    47
  subtype5    22
  subtype6    15
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        1        0
  ASIAN                                   2        0        1        0        0
  BLACK OR AFRICAN AMERICAN              10        7       14        7        7
  WHITE                                  39       34       41       47       22
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   3
  BLACK OR AFRICAN AMERICAN               9
  WHITE                                  15
[1] 4 6
[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 44
  subtype2  4 34
  subtype3  4 52
  subtype4  2 50
  subtype5  0 25
  subtype6  1 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   44
  subtype2    4   34
  subtype3    4   52
  subtype4    2   50
  subtype5    0   25
  subtype6    1   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        4        4        2        0        1
  NOT HISPANIC OR LATINO       44       34       52       50       25       22
[1] 2 6
[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 71 12
  subtype3 49  7
subtype1 subtype2 subtype3 
      75       83       56 
subtype1 subtype2 subtype3 
      13       12        7 
$subtype1
TCGA-A4-7584 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       21.37        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-DW-7837 TCGA-DW-7838 
       11.87        19.23        13.25        44.84        37.55        24.46 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6134 TCGA-IA-A83W TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.75        14.63        61.02        67.17        19.73        17.75 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       21.60        15.91         7.04        75.55       100.27        56.91 
TCGA-2Z-A9JI TCGA-A4-7583 TCGA-A4-8517 TCGA-AL-3473 TCGA-AL-7173 TCGA-B3-8121 
       51.52         0.10        19.63        62.66        67.73        12.46 
TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       43.99        17.23        17.49         8.88        22.92        21.63 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
       25.35        10.82        40.77        79.86        80.88        74.60 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6795 
       24.89        10.68        13.08         0.43         4.01        39.25 
TCGA-G7-6796 TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NH 
       71.44        12.92        12.43        12.89        11.21        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       11.84        56.75        73.25        25.22        16.80         2.04 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-8537 TCGA-P4-A5E6 TCGA-P4-A5EA TCGA-P4-A5ED 
       96.69        22.26        10.55        99.78         6.61        92.58 
TCGA-SX-A71U TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-UZ-A9PL TCGA-V9-A7HT 
       44.61        19.00        16.31        26.47       103.63        31.73 
TCGA-WN-A9G9 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        18.64        18.05 

$subtype2
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-A4-7734 
       75.42        39.88        33.07        25.58        12.26         0.89 
TCGA-B9-5155 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7842 
       21.86        48.85        13.61       129.86        13.78         3.02 
TCGA-UZ-A9PR TCGA-Y8-A8RZ TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       86.37         6.74        58.22         4.57        91.73        56.81 
TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9KF TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
        0.13        49.58        27.78         0.23        16.64        30.48 
TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 TCGA-B1-7332 
       23.97         0.76        14.33         8.48        66.71        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5885 TCGA-BQ-5891 
       36.49        20.25        22.06         0.16        30.28         0.95 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 
       61.28        50.40         3.81        51.19        34.19        19.00 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        2.40         1.18        90.90        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-8500 TCGA-HE-7129 TCGA-IZ-8196 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       27.65        81.93        21.34        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5E8 
       29.10        11.41        27.78        20.25        87.09        42.94 
TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.01        47.90        41.62        53.10        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       65.13       110.73        18.64        25.28         6.02 

$subtype3
TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-A4-7288 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7055 
       34.85        22.49        61.05        11.97        96.92        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A8JU 
       20.12        11.28        84.89        16.34        12.13        12.49 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y 
       41.33        62.83        31.20        29.36        12.82        11.57 
TCGA-5P-A9KE TCGA-A4-7585 TCGA-A4-8098 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI 
       27.09        35.18        29.46        41.13        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 
       86.76        63.72        43.20        47.80        40.83         7.66 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 
        7.92         2.76       123.62        93.34        49.84         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-7130 TCGA-IA-A40X TCGA-MH-A560 TCGA-P4-A5EB TCGA-P4-AAVK 
       16.31        58.19        19.99        30.38        99.12        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PM TCGA-UZ-A9PN 
       50.60        78.90        14.07        11.93       125.29        37.35 
TCGA-UZ-A9Q1 TCGA-Y8-A8S1 
       51.35        13.28 

subtype1 subtype2 subtype3 
    0.10     0.13     1.05 
subtype1 subtype2 subtype3 
  103.63   194.79   125.29 
subtype1 subtype2 subtype3 
   21.63    25.84    29.41 
[1] "0.1 - 103.6 (21.6)" "0.1 - 194.8 (25.8)" "1.1 - 125.3 (29.4)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      42        8        18        4
  subtype2      57        7        11        5
  subtype3      30        3        17        5
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         42       57       30
  STAGE II         8        7        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 59 14    10
  subtype3 32  3    22
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          46       59       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 20  6  0
  subtype3  9  8  1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18       20        9
  N1        7        6        8
  N2        2        0        1
[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 26  3
  subtype3 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    2
  subtype2   26    3
  subtype3   23    3
   clus
vv  subtype1 subtype2 subtype3
  0       24       26       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 62
  subtype3 17 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   57
  subtype2   21   62
  subtype3   17   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       21       17
  MALE         57       62       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     3                        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        3        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 76
  subtype3  4 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    2   76
  subtype3    4   43
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        4
  NOT HISPANIC OR LATINO       58       76       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 58  9
  subtype3 46 19
  subtype4 41  3
subtype1 subtype2 subtype3 subtype4 
      38       67       65       44 
subtype1 subtype2 subtype3 subtype4 
       1        9       19        3 
$subtype1
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5888 
       21.67        27.68        21.07        10.16        19.23        13.25 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7841 TCGA-DZ-6134 TCGA-PJ-A5Z9 TCGA-UZ-A9PZ 
       37.55        24.46        14.63        61.02        17.75        21.60 
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-B9-5156 TCGA-B9-A8YH TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DZ-6132 TCGA-EV-5903 
       43.99        17.49         7.63         3.81        80.88        24.89 
TCGA-G7-7502 TCGA-GL-7773 TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NL TCGA-IA-A40Y 
       25.84        12.92        12.89        26.01        25.22         2.04 
TCGA-KV-A6GD TCGA-P4-A5E7 TCGA-SX-A71U TCGA-SX-A7SP TCGA-UZ-A9PK TCGA-UZ-A9PS 
       18.41        87.09        44.61        16.31       117.40        71.24 
TCGA-V9-A7HT TCGA-WN-A9G9 
       31.73        26.01 

$subtype2
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-A4-7734 TCGA-B9-5155 TCGA-DW-5560 
       33.07        25.58        12.26         0.89        21.86        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7842 TCGA-UZ-A9PR TCGA-Y8-A8RZ 
       13.61       129.86        13.78         3.02        86.37         6.74 
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-4A-A93W TCGA-5P-A9JY 
       58.22         4.57        91.73        56.81         0.13        49.58 
TCGA-5P-A9KF TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 
       27.78        16.64        30.48        23.97         0.76        14.33 
TCGA-A4-A57E TCGA-AL-3472 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-7268 
        8.48        66.71        37.51        36.49        20.25        22.06 
TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5891 TCGA-BQ-7051 TCGA-DZ-6133 TCGA-EV-5901 
        0.16        63.72         0.95        50.40        51.19        34.19 
TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       19.00         2.40        90.90        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-HE-7129 
       17.98        23.08        80.65       194.79        27.65        81.93 
TCGA-HE-A5NI TCGA-IZ-8196 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 
       11.84        21.34        29.10        11.41        27.78        20.25 
TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A7SQ TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PP 
       16.01        47.90        41.62        18.02        26.20        98.96 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A8RY 
       30.67        47.47        65.13       110.73        18.64        25.28 
TCGA-Y8-A8S0 
        6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JT TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5892 
       75.42        39.88        22.49        49.25        11.87        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7056 TCGA-DW-7840 TCGA-IA-A83W TCGA-PJ-A5Z8 
       96.92        44.84        20.12         3.75        67.17        19.73 
TCGA-Y8-A895 TCGA-A4-7915 TCGA-AL-3473 TCGA-AL-7173 TCGA-B3-8121 TCGA-B9-A5W8 
       15.91         0.23        62.66        67.73        12.46        17.23 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
        8.88        22.92        21.63        30.28        25.35        10.82 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-DZ-6131 TCGA-DZ-6135 
        7.92         2.76        61.28        49.84        79.86        74.60 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 
       10.68        13.08         1.18         0.43         4.01        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A59R TCGA-HE-7130 
       39.25        71.44        16.90         3.68        12.43        58.19 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83V TCGA-J7-6720 
       56.75        73.25        16.80        19.99        96.69        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       10.55        10.09        99.78        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS 
       92.58        14.07        11.93        19.00        26.47        53.10 
TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A896 TCGA-Y8-A897 
      103.63        37.35        86.27        18.64        18.05 

$subtype4
TCGA-2Z-A9JD TCGA-A4-7288 TCGA-A4-7584 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-HE-A5NF 
       34.85        61.05        21.37        26.27        11.28        84.89 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-2Z-A9JO 
       16.34        12.13        12.49        41.33        62.83        31.20 
TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9KE TCGA-A4-7585 TCGA-A4-8098 
       29.36        12.82        11.57        27.09        35.18        29.46 
TCGA-A4-8517 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 
       19.63        41.13        14.86        12.30        86.76        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7060 
       47.80        40.83         7.66       123.62        93.34         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-IZ-8195 TCGA-MH-A560 TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-UZ-A9PM 
       22.26        30.38        52.27        50.60        78.90       125.29 
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 
  24.675   25.280   20.120   29.920 
[1] "0.1 - 117.4 (24.7)" "0.1 - 194.8 (25.3)" "0.2 - 103.6 (20.1)"
[4] "1.1 - 125.3 (29.9)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      30        4         4        0
  subtype2      47        5         8        4
  subtype3      25        5        24        9
  subtype4      27        4        10        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         30       47       25       27
  STAGE II         4        5        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 28  7    30
  subtype4 29  4    11
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          31       49       28       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 18 14  3
  subtype4  8  3  0
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        7       14       18        8
  N1        1        3       14        3
  N2        0        0        3        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"
D4V6, binary
          cls
clus        0  1
  subtype1 10  0
  subtype2 19  2
  subtype3 28  6
  subtype4 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    0
  subtype2   19    2
  subtype3   28    6
  subtype4   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       10       19       28       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 42
  subtype4  9 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   31
  subtype2   16   51
  subtype3   23   42
  subtype4    9   35
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        8       16       23        9
  MALE         31       51       42       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     6                        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        6        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 49
  subtype4  2 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    1   59
  subtype3    4   49
  subtype4    2   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        4        2
  NOT HISPANIC OR LATINO       33       59       49       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 24  5
  subtype2 80 11
  subtype3 65  6
  subtype4 26  6
  subtype5 48 16
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       91       71       32       64 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       11        6        6       16 
$subtype1
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-DW-7838 TCGA-GL-A59T TCGA-IA-A83W 
       21.67        27.68        21.07        24.46        17.95        67.17 
TCGA-IZ-A6M8 TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J5 TCGA-A4-7997 TCGA-B3-8121 
       16.34        15.62         7.04       100.27        30.48        12.46 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-BQ-7045 TCGA-BQ-7059 
       28.18         0.46        43.99        17.23        48.26         7.63 
TCGA-DZ-6132 TCGA-GL-A9DD TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83T TCGA-IA-A83V 
       80.88        11.21        25.22        16.80        88.24        96.69 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-V9-A7HT 
       12.36        18.41        16.31       125.29        31.73 

$subtype2
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-5155 
       33.07        25.58        16.18        76.64        10.16        21.86 
TCGA-B9-A5W7 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7840 
       19.23        48.85        13.61        35.93        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       14.63         3.02        17.75        35.38        86.37        21.60 
TCGA-Y8-A895 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM 
       15.91        75.55        58.22         4.57        56.81        30.71 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9K4 
        5.29         0.13        49.58        90.21        78.64        71.80 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 
        0.10        19.13        23.97        23.31         0.76        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU 
       16.96        16.31        12.46        49.32        66.71         2.20 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-7268 
       36.49        20.25        50.50        26.40         1.15        22.06 
TCGA-B9-A8YH TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 
       17.49        51.19        19.00         2.40        39.25        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-HE-7129 
       25.25        17.98        27.65        12.43        12.89        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-MH-A55W TCGA-MH-A55Z 
       26.01        11.84        56.75        21.34        34.29        27.78 
TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A71S 
       20.25        17.62        15.48        16.01        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       44.61        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-A9PU 
       43.76        26.20       117.40       103.63        98.96        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       47.47        65.13       110.73        18.64        18.05        25.28 
TCGA-Y8-A8S0 
        6.02 

$subtype3
TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-B9-A44B 
       34.85        22.49        12.26        61.05        21.37        11.87 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-7837 TCGA-HE-A5NF 
       26.04        11.97        96.92        11.28        37.55        84.89 
TCGA-MH-A855 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-Y8-A8RZ TCGA-2Z-A9J2 TCGA-2Z-A9J6 
       12.13        41.33        62.83         6.74        59.01        56.91 
TCGA-2Z-A9J8 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K0 TCGA-5P-A9K6 
       91.73        29.36        12.82       106.55        22.26        62.93 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-7996 
       12.39        27.09        27.78        18.21        35.18        16.64 
TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5XZ 
       25.64        19.63        19.73        12.46         8.48        15.75 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 
       62.66        41.13        37.51        16.77        20.32        30.58 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5890 
       12.30        19.27        43.20        47.80        26.04         7.66 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       61.28        50.40         7.04         7.17         3.81        40.77 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6796 TCGA-GL-6846 TCGA-GL-A9DE TCGA-IA-A40X 
        0.43        51.78        71.44       194.79        16.31        19.99 
TCGA-IA-A83S TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVK 
       85.78        29.10        11.41        99.78        99.12        52.27 
TCGA-P4-AAVM TCGA-SX-A71V TCGA-SX-A7SM TCGA-UZ-A9Q1 TCGA-WN-A9G9 
       50.60        28.80        11.93        51.35        26.01 

$subtype4
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-5P-A9JV TCGA-A4-7734 TCGA-BQ-7049 TCGA-DW-7834 
       75.42        39.88        67.17         0.89        44.84       129.86 
TCGA-DZ-6134 TCGA-2Z-A9JK TCGA-4A-A93Y TCGA-5P-A9KA TCGA-A4-7287 TCGA-A4-7828 
       61.02        38.99        11.57        12.99        19.63         7.82 
TCGA-B3-3925 TCGA-B3-4104 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5889 TCGA-BQ-5894 
       33.83        34.49        22.92        40.83        10.82         2.76 
TCGA-BQ-7053 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-7502 
       49.84        74.60        34.19        24.89        90.90        25.84 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-J7-6720 TCGA-MH-A561 TCGA-MH-A856 TCGA-P4-A5E7 
       80.65        12.92        12.76        27.65        31.13        87.09 
TCGA-P4-A5EA TCGA-UZ-A9PN 
        6.61        37.35 

$subtype5
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-MH-A857 
       12.99        49.25        13.25        26.27        20.12        29.26 
TCGA-PJ-A5Z8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-5P-A9K3 
       19.73        54.64        51.52        24.33        31.20        15.48 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KH TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
       43.04        19.36        67.43         0.23        29.46        23.28 
TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-7173 TCGA-B3-3926 TCGA-B9-4116 
        8.28         9.63        70.19        67.73        29.03        20.61 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5882 
        0.16        14.86        86.76         8.88        63.72        21.63 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7048 
       30.28        25.35         0.95         7.92       123.62        93.34 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
       79.86        10.68        13.08         1.18         4.01        11.05 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-7130 
       20.52        23.08        16.90         3.68         1.05        58.19 
TCGA-HE-A5NK TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 
       73.25         2.04        22.26        10.55        10.09        30.38 
TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       42.94        92.58        78.90        14.07        18.02        86.27 
TCGA-UZ-A9PS TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8S1 
       71.24        39.06        18.64        13.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.46     0.10     0.43     0.89     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  125.29   117.40   194.79   129.86   123.62 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.670   25.250   27.090   34.010   21.945 
[1] "0.5 - 125.3 (21.7)" "0.1 - 117.4 (25.2)" "0.4 - 194.8 (27.1)"
[4] "0.9 - 129.9 (34.0)" "0.2 - 123.6 (21.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      20        5         3        0
  subtype2      69        6         6        2
  subtype3      41        5        12        4
  subtype4      20        2         6        2
  subtype5      22        3        25        7
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         20       69       41       20       22
  STAGE II         5        6        5        2        3
  STAGE III        3        6       12        6       25
  STAGE IV         0        2        4        2        7
[1] 4 5
[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 21  7     3
  subtype2 75 11     5
  subtype3 49  6    15
  subtype4 22  2     8
  subtype5 26  7    31
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T1          21       75       49       22       26
  T2           7       11        6        2        7
  T3+T4        3        5       15        8       31
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  7  1  0
  subtype2 13  0  0
  subtype3 16  6  0
  subtype4  2  4  0
  subtype5 12 13  4
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        7       13       16        2       12
  N1        1        0        6        4       13
  N2        0        0        0        0        4
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 25  1
  subtype3 26  2
  subtype4 13  2
  subtype5 22  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   25    1
  subtype3   26    2
  subtype4   13    2
  subtype5   22    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0        9       25       26       13       22
  1        0        1        2        2        4
[1] 2 5
[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 28
  subtype2 16 75
  subtype3 13 58
  subtype4 12 20
  subtype5 31 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   28
  subtype2   16   75
  subtype3   13   58
  subtype4   12   20
  subtype5   31   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        4       16       13       12       31
  MALE         28       75       58       20       33
[1] 2 5
[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     0                         8
  subtype2                                1     0                        19
  subtype3                                1     1                        14
  subtype4                                0     1                         6
  subtype5                                0     4                        14
          vv
clus       WHITE
  subtype1    21
  subtype2    65
  subtype3    54
  subtype4    23
  subtype5    43
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0        0
  ASIAN                                   0        0        1        1        4
  BLACK OR AFRICAN AMERICAN               8       19       14        6       14
  WHITE                                  21       65       54       23       43
[1] 4 5
[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 27
  subtype2  3 81
  subtype3  3 61
  subtype4  4 22
  subtype5  1 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   27
  subtype2    3   81
  subtype3    3   61
  subtype4    4   22
  subtype5    1   51
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        3        3        4        1
  NOT HISPANIC OR LATINO       27       81       61       22       51
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  98  19
  subtype2 112  12
  subtype3  33  13
subtype1 subtype2 subtype3 
     117      124       46 
subtype1 subtype2 subtype3 
      19       12       13 
$subtype1
TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       34.85        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5892 
       12.99        49.25        27.68        11.87        26.04        11.97 
TCGA-BQ-7046 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7838 TCGA-DZ-6134 TCGA-GL-A59T 
       96.92        20.12        11.28        24.46        61.02        17.95 
TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-Y8-A8RZ 
       84.89        16.34        12.13        41.33        62.83         6.74 
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
        7.04        59.01       100.27        91.73        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       38.99        31.20        29.36        12.82        11.57       106.55 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-5P-A9KE 
       22.26        15.48        62.93        19.36        12.39        27.09 
TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-8518 
       18.21        35.18        29.46        25.64        19.63        19.73 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 
       12.46         8.48         8.28         9.63        62.66        41.13 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B9-4117 TCGA-B9-A5W8 TCGA-B9-A5W9 
       16.77        20.32        30.58         0.46        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       14.86        12.30        86.76        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 
       47.80        21.63        26.04        30.28        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 
        0.95       123.62        93.34        61.28        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-F9-A97G 
        7.04         7.17         3.81        40.77        79.86         0.43 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM TCGA-GL-A9DD 
       71.44        20.52        16.90       194.79         1.05        11.21 
TCGA-GL-A9DE TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.31        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 TCGA-P4-A5E6 TCGA-P4-A5EB 
       22.26        10.55        18.41        30.38        99.78        99.12 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SM 
       52.27        50.60        78.90        14.07        28.80        11.93 
TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       16.31       125.29        86.27        71.24        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A8S1 
       26.01        39.06        13.28 

$subtype2
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M 
       33.07        25.58        16.18         0.89        76.64        21.67 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-DW-5560 TCGA-DW-5561 
       21.07        10.16        21.86        19.23        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        35.93        37.55        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-IA-A83W TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PR TCGA-UZ-A9PZ 
        3.02        67.17        17.75        35.38        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       15.91        15.62        75.55        58.22        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ 
       56.81        30.71         5.29         0.13        49.58        90.21 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9KA TCGA-5P-A9KF TCGA-A4-7583 TCGA-A4-7732 
       78.64        71.80        12.99        27.78         0.10        19.13 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 
       16.64        30.48        23.97        23.31         0.76        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.96        16.31        15.75        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
       66.71         2.20        37.51        36.49        20.25        33.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       50.50        28.18        26.40         1.15        43.99        22.06 
TCGA-B9-A8YH TCGA-BQ-7045 TCGA-BQ-7051 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       17.49        48.26        50.40        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       19.00        24.89         2.40        51.78        90.90        39.25 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 
       25.15        25.84        25.25        17.98        80.65        27.65 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        12.89        81.93        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE 
       25.22        16.80        21.34        12.36        12.76        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       11.41        34.29        27.78        27.65        20.25        17.62 
TCGA-O9-A75Z TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN 
       15.48        47.90        49.45        44.61        27.06        19.00 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
      103.63        98.96        30.67        47.47        65.13       110.73 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.05        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-MH-A857 
       75.42        39.88        13.25        44.84        26.27        29.26 
TCGA-PJ-A5Z8 TCGA-2Z-A9JN TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7828 
       19.73        24.33        43.04        67.43        19.63         7.82 
TCGA-A4-7915 TCGA-A4-8312 TCGA-AL-7173 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
        0.23        23.28        67.73        29.03        34.49        12.46 
TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5889 TCGA-BQ-5893 
       20.61         8.88        22.92        40.83        10.82         7.92 
TCGA-BQ-5894 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 
        2.76        80.88        10.68        13.08         1.18         4.01 
TCGA-G7-6793 TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7130 TCGA-HE-A5NK 
       11.05        23.08        12.92         3.68        58.19        73.25 
TCGA-J7-A8I2 TCGA-MH-A856 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       10.09        31.13        87.09        42.94         6.61        92.58 
TCGA-P4-AAVL TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-Y8-A896 
       16.01        18.02        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 
  25.640   26.105   21.765 
[1] "0.2 - 194.8 (25.6)" "0.1 - 129.9 (26.1)" "0.2 - 92.6 (21.8)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      56       10        34        5
  subtype2      93        9         8        2
  subtype3      23        2        10        8
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         56       93       23
  STAGE II        10        9        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  25   4    18
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          65      103       25
  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  1
  subtype2 20  0  0
  subtype3  5 10  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       25       20        5
  N1       14        0       10
  N2        1        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 18  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    3
  subtype2   36    1
  subtype3   18    5
   clus
vv  subtype1 subtype2 subtype3
  0       41       36       18
  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  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   89
  subtype2   22  103
  subtype3   25   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       22       25
  MALE         89      103       22
[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     3                        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        3
  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  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  100
  subtype2    4  109
  subtype3    4   33
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        4
  NOT HISPANIC OR LATINO      100      109       33
[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 27  2
  subtype2 35  3
  subtype3 56 10
  subtype4 37  6
  subtype5 61 19
  subtype6 28  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      29       38       66       43       80       32 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        3       10        6       19        4 
$subtype1
TCGA-2Z-A9JT TCGA-B1-A47O TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7055 TCGA-IZ-A6M8 
       22.49        27.68        13.25        96.92        26.27        16.34 
TCGA-MH-A855 TCGA-Y8-A898 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9JR 
       12.13        15.62         7.04        75.55       100.27         5.29 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A6HP TCGA-B1-5398 
       27.09        67.43        14.33        12.46        12.46        41.13 
TCGA-B9-A69E TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7062 TCGA-G7-6796 TCGA-HE-7130 
       14.86         7.66        48.26         3.81        71.44        58.19 
TCGA-IA-A83T TCGA-IZ-A6M9 TCGA-SX-A7SN TCGA-UZ-A9PM TCGA-Y8-A897 
       88.24        12.36        19.00       125.29        18.05 

$subtype2
TCGA-2Z-A9JD TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-BQ-5886 TCGA-BQ-5892 
       34.85        12.26        61.05        21.37        26.04        11.97 
TCGA-BQ-7058 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-Y8-A8RZ TCGA-2Z-A9J2 
       11.28        12.49        41.33        62.83         6.74        59.01 
TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY 
       56.91        91.73        54.64        12.82       106.55        49.58 
TCGA-5P-A9K0 TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 
       22.26        27.78        18.21        29.46        25.64        19.63 
TCGA-B1-A655 TCGA-B9-5156 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
       16.77        43.99        17.49        12.30        86.76        63.72 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-G7-7501 TCGA-P4-AAVM 
       47.80        26.04        50.40         7.04        20.52        50.60 
TCGA-P4-AAVO TCGA-UZ-A9Q1 
       78.90        51.35 

$subtype3
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-DW-7842 
       25.58        16.18        76.64        10.16        21.86         3.02 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-2Z-A9J3 TCGA-2Z-A9J7 
       84.89        17.75        86.37        21.60        58.22         4.57 
TCGA-2Z-A9JE TCGA-5P-A9K2 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 
       56.81        78.64         0.10        19.13        16.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-AL-3471 TCGA-AT-A5NU 
       23.31         0.76        16.96        16.31        49.32         2.20 
TCGA-B3-3926 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5893 
       29.03        50.50         1.15        22.06         0.16         7.92 
TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6797 TCGA-G7-A8LB TCGA-GL-7773 
       51.19        19.00         2.40        25.15        17.98        12.92 
TCGA-GL-8500 TCGA-GL-A59R TCGA-HE-7129 TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y 
       27.65        12.43        81.93        11.84        16.80         2.04 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-MH-A854 
       29.10        11.41        34.29        27.78        20.25        17.62 
TCGA-MH-A856 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SQ 
       31.13        47.90        44.61        28.80        27.06        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PS TCGA-UZ-A9PU 
       26.47        53.10        18.02        26.20        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       47.47        65.13       110.73        18.64        25.28         6.02 

$subtype4
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-DW-7839 
       75.42        39.88        12.99        49.25        11.87        13.78 
TCGA-GL-A59T TCGA-2Z-A9JI TCGA-2Z-A9JO TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 
       17.95        51.52        31.20        90.21        15.48        43.04 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3467 TCGA-B1-7332 TCGA-B9-4114 TCGA-B9-4116 
        8.48         8.28        70.19        37.51        28.18        20.61 
TCGA-B9-4117 TCGA-B9-A5W8 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7044 
        0.46        17.23        21.63        30.28         0.95       123.62 
TCGA-BQ-7050 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6795 
       61.28         7.17        79.86        13.08         1.18        39.25 
TCGA-G7-A8LC TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-MH-A560 
       23.08        12.89        16.31        73.25        19.99        30.38 
TCGA-MH-A561 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-UZ-A9PQ TCGA-WN-AB4C 
       27.65        99.12        92.58        52.27        86.27        39.06 
TCGA-Y8-A896 
       18.64 

$subtype5
TCGA-5P-A9JV TCGA-A4-7734 TCGA-B1-A47M TCGA-B1-A657 TCGA-BQ-7049 TCGA-BQ-7056 
       67.17         0.89        21.67        21.07        44.84        20.12 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6134 
       48.85        13.61       129.86        35.93        24.46        61.02 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A71W TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       29.26        19.73        35.38        38.99        30.71        24.33 
TCGA-2Z-A9JP TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-A4-7287 
       29.36         0.13        11.57        62.93        19.36        19.63 
TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-A4-8518 TCGA-AL-3472 
       35.18         7.82         0.23        23.28        19.73        66.71 
TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-4103 TCGA-B3-4104 
       67.73        36.49        20.25        20.32        30.58        34.49 
TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5883 
       12.46        19.27         8.88        22.92        43.20        40.83 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-DZ-6132 
       25.35        10.82         2.76        93.34        49.84        80.88 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 
       34.19        24.89        10.68         4.01        51.78        11.05 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
       25.84        16.90        80.65       194.79         3.68         1.05 
TCGA-HE-A5NJ TCGA-IA-A83S TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-6720 
       56.75        85.78        96.69        22.26        21.34        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL 
       10.55        10.09        18.41        87.09         6.61        16.01 
TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PN 
       14.07        49.45        11.93        43.76       117.40        37.35 
TCGA-UZ-A9PP TCGA-Y8-A8S1 
       98.96        13.28 

$subtype6
TCGA-2Z-A9JL TCGA-B9-A5W7 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-IA-A83W 
       33.07        19.23        37.55         3.75        14.63        67.17 
TCGA-Y8-A895 TCGA-5P-A9K4 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7997 TCGA-A4-A5XZ 
       15.91        71.80        12.99        12.39        30.48        15.75 
TCGA-AL-3466 TCGA-AL-3473 TCGA-B3-3925 TCGA-B9-4115 TCGA-BQ-7059 TCGA-DW-7963 
        9.63        62.66        33.83        26.40         7.63        40.77 
TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-A4TM TCGA-GL-A9DD TCGA-HE-A5NH 
       74.60         0.43        90.90        25.25        11.21        26.01 
TCGA-HE-A5NL TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-SX-A7SP TCGA-UZ-A9PL 
       25.22        15.48        99.78        42.94        16.31       103.63 
TCGA-V9-A7HT TCGA-WN-A9G9 
       31.73        26.01 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3.81     6.74     0.10     0.46     0.13     0.43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  125.29   106.55   110.73   123.62   194.79   103.63 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  19.000   28.620   23.640   28.180   24.395   26.010 
[1] "3.8 - 125.3 (19.0)" "6.7 - 106.5 (28.6)" "0.1 - 110.7 (23.6)"
[4] "0.5 - 123.6 (28.2)" "0.1 - 194.8 (24.4)" "0.4 - 103.6 (26.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      18        4         4        0
  subtype2      23        1         7        1
  subtype3      47        6         7        3
  subtype4      19        2        12        2
  subtype5      45        4        18        8
  subtype6      21        4         4        1
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         18       23       47       19       45       21
  STAGE II         4        1        6        2        4        4
  STAGE III        4        7        7       12       18        4
  STAGE IV         0        1        3        2        8        1
[1] 4 6
[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 20  4     4
  subtype2 28  2     9
  subtype3 50  9     7
  subtype4 23  8    12
  subtype5 48  5    27
  subtype6 25  5     3
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1          20       28       50       23       48       25
  T2           4        2        9        8        5        5
  T3+T4        4        9        7       12       27        3
[1] 3 6
[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  8  0  0
  subtype2  6  3  0
  subtype3  9  2  0
  subtype4  9  4  0
  subtype5 13 12  4
  subtype6  5  3  0
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0        8        6        9        9       13        5
  N1        0        3        2        4       12        3
  N2        0        0        0        0        4        0
[1] 3 6
[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 11  0
  subtype2 12  0
  subtype3 19  2
  subtype4 11  2
  subtype5 34  4
  subtype6  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    0
  subtype2   12    0
  subtype3   19    2
  subtype4   11    2
  subtype5   34    4
  subtype6    8    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       11       12       19       11       34        8
  1        0        0        2        2        4        1
[1] 2 6
[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  6 23
  subtype2  9 30
  subtype3 12 54
  subtype4 19 24
  subtype5 28 53
  subtype6  3 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   23
  subtype2    9   30
  subtype3   12   54
  subtype4   19   24
  subtype5   28   53
  subtype6    3   30
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        6        9       12       19       28        3
  MALE         23       30       54       24       53       30
[1] 2 6
[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     0                         5
  subtype2                                1     0                         6
  subtype3                                1     0                        11
  subtype4                                0     2                        11
  subtype5                                0     3                        17
  subtype6                                0     1                        11
          vv
clus       WHITE
  subtype1    23
  subtype2    31
  subtype3    50
  subtype4    28
  subtype5    57
  subtype6    18
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0        0
  ASIAN                                   0        0        0        2        3
  BLACK OR AFRICAN AMERICAN               5        6       11       11       17
  WHITE                                  23       31       50       28       57
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   1
  BLACK OR AFRICAN AMERICAN              11
  WHITE                                  18
[1] 4 6
[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  0 24
  subtype2  1 32
  subtype3  2 58
  subtype4  4 35
  subtype5  4 65
  subtype6  1 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   24
  subtype2    1   32
  subtype3    2   58
  subtype4    4   35
  subtype5    4   65
  subtype6    1   29
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        2        4        4        1
  NOT HISPANIC OR LATINO       24       32       58       35       65       29
[1] 2 6
[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  71   9
  subtype3  71  18
subtype1 subtype2 subtype3 
     119       80       89 
subtype1 subtype2 subtype3 
      17        9       18 
$subtype1
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-A4-7584 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       34.85        33.07        12.26        21.37        12.99        49.25 
TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-5561 
       11.87        26.04        11.97        96.92        11.28        13.61 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-IA-A83W TCGA-IZ-A6M8 
       37.55        13.78         3.75        14.63        67.17        16.34 
TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A8RZ 
       12.13        12.49        41.33        62.83        86.37         6.74 
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-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93X 
       56.81        54.64        38.99        29.36         5.29        12.82 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 
      106.55        90.21        22.26        15.48        71.80        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7585 
       19.36        12.99        12.39        27.09        18.21        35.18 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D 
       30.48        29.46        25.64         0.76        14.33        12.46 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
        8.48         8.28         9.63        70.19        62.66        41.13 
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-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.46        43.99        17.49        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5890 
       63.72        43.20        47.80        21.63        30.28         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
        0.95       123.62        61.28        50.40         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A97G 
        7.17         3.81        40.77        74.60        19.00         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       51.78        90.90        20.52        12.89        11.21        16.31 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-KV-A6GE TCGA-KV-A74V 
       25.22        19.99        85.78        88.24        29.10        11.41 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM 
       27.78        30.38        20.25        99.12        52.27        50.60 
TCGA-P4-AAVO TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SP TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       78.90        27.06        11.93        16.31        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PS TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-WN-A9G9 
      125.29        71.24        65.13        51.35        26.01 

$subtype2
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-AL-3468 TCGA-B1-A47O TCGA-B1-A657 
       16.18        22.49        61.05        76.64        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-7055 TCGA-GL-A59T 
       10.16        21.86        19.23        13.25        26.27        17.95 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-2Z-A9J3 
       84.89        17.75        21.60        15.91        15.62        58.22 
TCGA-2Z-A9J7 TCGA-2Z-A9JI TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9KF TCGA-5P-A9KH 
        4.57        51.52        49.58        78.64        27.78        67.43 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
        0.10        19.13        16.64        23.97        23.31        19.63 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AT-A5NU 
       16.96        16.31        15.75        12.46        49.32         2.20 
TCGA-B1-A47N TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-7268 
       36.49        29.03        30.58        50.50         1.15        22.06 
TCGA-B9-A5W8 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6796 TCGA-G7-6797 
       17.23        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-HE-7129 
       25.84        17.98        23.08        27.65        12.43        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-IA-A40U TCGA-IZ-A6M9 TCGA-MH-A55W 
       26.01        11.84        73.25        16.80        12.36        34.29 
TCGA-MH-A854 TCGA-P4-A5E6 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       17.62        99.78        47.90        44.61        28.80        19.00 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PU 
       41.62        26.47        53.10        43.76        18.02        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       47.47       110.73        31.73        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-5P-A9JV TCGA-A4-7734 TCGA-B1-A47M 
       75.42        39.88        25.58        67.17         0.89        21.67 
TCGA-BQ-7049 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       44.84        20.12        48.85       129.86        35.93        24.46 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A71W TCGA-2Z-A9JM 
        3.02        61.02        29.26        19.73        35.38        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9K6 TCGA-A4-7287 
       24.33        31.20         0.13        11.57        62.93        19.63 
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-A654 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A5W9 TCGA-B9-A69E 
       20.25        20.32        34.49        12.46         0.16        14.86 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 
        8.88        22.92        40.83        26.04        25.35        10.82 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-DZ-6131 
        7.92         2.76        48.26        93.34        49.84        79.86 
TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 
       80.88        34.19        24.89        10.68         1.18         4.01 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       11.05        39.25        25.25        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-7130 TCGA-HE-A5NJ TCGA-IA-A40Y 
       12.92         3.68         1.05        58.19        56.75         2.04 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 
       18.41        27.65        31.13        15.48        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-UZ-A9PK 
        6.61        92.58        16.01        14.07        49.45       117.40 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A8S1 
       37.35        98.96        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 
  27.060   23.195   24.890 
[1] "0.4 - 125.3 (27.1)" "0.1 - 110.7 (23.2)" "0.1 - 194.8 (24.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      67        9        23        4
  subtype2      54        8         9        2
  subtype3      52        4        20        9
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         67       54       52
  STAGE II         9        8        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 55  7    27
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          77       62       55
  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  1
  subtype2 12  2  0
  subtype3 15 14  3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       23       12       15
  N1        8        2       14
  N2        1        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 33  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    3
  subtype2   24    1
  subtype3   33    5
   clus
vv  subtype1 subtype2 subtype3
  0       38       24       33
  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 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   94
  subtype2   16   65
  subtype3   34   55
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       16       34
  MALE         94       65       55
[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     4                        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        4
  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  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  103
  subtype2    2   71
  subtype3    6   69
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        6
  NOT HISPANIC OR LATINO      103       71       69
[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  8
  subtype2 70  5
  subtype3 53 24
subtype1 subtype2 subtype3 
      70       75       77 
subtype1 subtype2 subtype3 
       8        5       24 
$subtype1
TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-BQ-5886 
       34.85        22.49        61.05        12.99        27.68        26.04 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-MH-A855 TCGA-SX-A7SO 
       11.97        96.92        26.27        11.28        12.13        41.33 
TCGA-UZ-A9PO TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 
       62.83         6.74         7.04        75.55        59.01       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-2Z-A9JO TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K0 
       56.91        51.52        31.20        12.82       106.55        22.26 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7585 TCGA-A4-7996 
       62.93        43.04        27.09        18.21        35.18        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5XZ 
       30.48        29.46        19.63        19.73         8.48        15.75 
TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A69E 
        8.28        62.66        41.13         0.46        43.99        14.86 
TCGA-B9-A8YI TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5890 
       12.30        43.20        47.80        21.63        26.04         7.66 
TCGA-BQ-7050 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6131 TCGA-F9-A97G 
       61.28         7.63         7.04         3.81        79.86         0.43 
TCGA-G7-6790 TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL 
       51.78        71.44        20.52        11.21        16.31        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-P4-A5E6 TCGA-P4-AAVK TCGA-P4-AAVM TCGA-SX-A7SP 
       16.80        19.99        99.78        52.27        50.60        16.31 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A897 
       31.73        26.01        39.06        18.05 

$subtype2
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-B1-A657 TCGA-B9-5155 TCGA-DW-5560 TCGA-DW-5561 
       33.07        25.58        21.07        21.86        48.85        13.61 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-GL-A59T TCGA-PJ-A5Z9 
       37.55        13.78         3.75         3.02        17.95        17.75 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-2Z-A9J3 TCGA-2Z-A9JG TCGA-2Z-A9JP TCGA-2Z-A9JR 
       86.37        21.60        58.22        54.64        29.36         5.29 
TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9KF TCGA-A4-8310 TCGA-A4-8515 
        0.13        49.58        90.21        27.78        25.64        23.31 
TCGA-A4-8516 TCGA-A4-8630 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 
        0.76        14.33        66.71         2.20        36.49        20.25 
TCGA-B9-4115 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5878 TCGA-BQ-5891 TCGA-BQ-7044 
       26.40         0.16        17.49        63.72         0.95       123.62 
TCGA-BQ-7051 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6792 
       50.40        51.19        74.60        19.00        13.08        90.90 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-8500 
       39.25        25.25        17.98        23.08        12.92        27.65 
TCGA-GL-A9DC TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE 
       12.89        56.75         2.04        21.34        12.36        29.10 
TCGA-KV-A74V TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-SX-A71R TCGA-SX-A71S 
       11.41        17.62        31.13        15.48        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       44.61        27.06        19.00        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV 
       26.20       117.40       103.63        98.96        30.67        47.47 
TCGA-UZ-A9PX TCGA-Y8-A8RY TCGA-Y8-A8S0 
       65.13        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-5P-A9JV TCGA-A4-7734 TCGA-B9-A44B TCGA-BQ-5888 
       75.42        39.88        67.17         0.89        11.87        13.25 
TCGA-BQ-7049 TCGA-BQ-7056 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6134 
       44.84        20.12       129.86        35.93        24.46        61.02 
TCGA-IA-A83W TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A71W TCGA-Y8-A898 TCGA-2Z-A9JK 
       67.17        29.26        19.73        35.38        15.62        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-4A-A93Y TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       30.71        24.33        11.57        19.36        12.99        12.39 
TCGA-A4-7287 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-AL-3466 TCGA-AL-7173 
       19.63         7.82         0.23        23.28         9.63        67.73 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 
       20.32        33.83        34.49        12.46        19.27         8.88 
TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       22.92        40.83        25.35        10.82         7.92         2.76 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7061 TCGA-DZ-6132 TCGA-EV-5901 
       48.26        93.34        49.84         7.17        80.88        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 
       24.89        10.68         1.18         4.01        11.05        25.84 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-7130 
       16.90        80.65       194.79         3.68         1.05        58.19 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-6720 TCGA-J7-8537 
       85.78        88.24        96.69        22.26        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVL 
       10.09        18.41        87.09        42.94         6.61        16.01 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       14.07        11.93        37.35        86.27        13.28 

subtype1 subtype2 subtype3 
    0.43     0.13     0.23 
subtype1 subtype2 subtype3 
  106.55   123.62   194.79 
subtype1 subtype2 subtype3 
   26.04    26.20    22.26 
[1] "0.4 - 106.5 (26.0)" "0.1 - 123.6 (26.2)" "0.2 - 194.8 (22.3)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      38        6        16        2
  subtype2      58        4         8        1
  subtype3      37        4        19       11
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         38       58       37
  STAGE II         6        4        4
  STAGE III       16        8       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 46  8    17
  subtype2 61  7     8
  subtype3 40  6    29
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          46       61       40
  T2           8        7        6
  T3+T4       17        8       29
[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  6  0
  subtype2 12  2  0
  subtype3 12 15  4
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       12       12
  N1        6        2       15
  N2        0        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 23  1
  subtype2 23  0
  subtype3 30  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    1
  subtype2   23    0
  subtype3   30    7
   clus
vv  subtype1 subtype2 subtype3
  0       23       23       30
  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 17 54
  subtype2 15 61
  subtype3 30 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   54
  subtype2   15   61
  subtype3   30   47
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       15       30
  MALE         54       61       47
[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                        12
  subtype2                                1     1                        11
  subtype3                                0     4                        17
          vv
clus       WHITE
  subtype1    54
  subtype2    59
  subtype3    53
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        1        4
  BLACK OR AFRICAN AMERICAN              12       11       17
  WHITE                                  54       59       53
[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 59
  subtype2  4 64
  subtype3  3 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   59
  subtype2    4   64
  subtype3    3   61
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        4        3
  NOT HISPANIC OR LATINO       59       64       61
[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 85  6
  subtype2 68 31
  subtype3 32  0
subtype1 subtype2 subtype3 
      91       99       32 
subtype1 subtype2 subtype3 
       6       31        0 
$subtype1
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JT TCGA-A4-7288 TCGA-B1-A47O TCGA-B1-A657 
       34.85        33.07        22.49        61.05        27.68        21.07 
TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-GL-A59T 
       26.04        96.92        37.55        13.78         3.75        17.95 
TCGA-IA-A83W TCGA-MH-A855 TCGA-UZ-A9PO TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       67.17        12.13        62.83         6.74         7.04        75.55 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JR 
       58.22       100.27        56.91        54.64        51.52         5.29 
TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9KA 
       12.82       106.55        49.58        90.21        22.26        12.99 
TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       27.09        27.78        18.21        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A5XZ 
       25.64        23.31         0.76        19.63        14.33        15.75 
TCGA-A4-A5Y0 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 
        8.28        41.13        33.83        26.40         0.46        43.99 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 
       17.49        12.30        63.72         7.66         0.95       123.62 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6133 TCGA-DZ-6135 
       50.40         7.63         7.04         3.81        51.19        74.60 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6792 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 
       19.00        13.08        90.90        17.98        23.08        27.65 
TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       12.89        16.31        25.22        16.80        19.99         2.04 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-AAVM TCGA-SX-A71R 
       12.36        29.10        11.41        99.78        50.60        47.90 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PJ 
       44.61        27.06        19.00        26.47        53.10        26.20 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-V9-A7HT TCGA-WN-A9G9 
      103.63        98.96        30.67        47.47        31.73        26.01 
TCGA-Y8-A897 
       18.05 

$subtype2
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5888 
       75.42        39.88        67.17        12.99        11.87        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7834 
       11.97        44.84        26.27        20.12        11.28       129.86 
TCGA-DW-7838 TCGA-DZ-6134 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A898 
       24.46        61.02        29.26        19.73        41.33        15.62 
TCGA-2Z-A9J2 TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y 
       59.01        38.99        30.71        24.33        31.20        11.57 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7585 
       62.93        43.04        19.36        12.39        19.63        35.18 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-AL-3466 
        7.82         0.23        23.28        19.73         8.48         9.63 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A69E 
       62.66        67.73        20.32        34.49        12.46        14.86 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       40.83        26.04        25.35        10.82         7.92         2.76 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7061 TCGA-DZ-6131 
       48.26        93.34        61.28        49.84         7.17        79.86 
TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       80.88        34.19        24.89        10.68         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
        4.01        51.78        11.05        39.25        71.44        20.52 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A9DD 
       25.84        16.90       194.79         3.68         1.05        11.21 
TCGA-HE-7130 TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-6720 
       58.19        85.78        88.24        96.69        22.26        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK 
       10.55        10.09        18.41        42.94         6.61        52.27 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SP TCGA-UZ-A9PK TCGA-UZ-A9PN 
       16.01        14.07        11.93        16.31       117.40        37.35 
TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A8S1 
       86.27        39.06        13.28 

$subtype3
TCGA-2Z-A9JQ TCGA-A4-7734 TCGA-B9-5155 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 
       25.58         0.89        21.86        48.85        13.61        35.93 
TCGA-DW-7842 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-2Z-A9JP 
        3.02        17.75        35.38        86.37        21.60        29.36 
TCGA-4A-A93W TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-A5W9 
        0.13        66.71         2.20        36.49        20.25         0.16 
TCGA-G7-A4TM TCGA-G7-A8LE TCGA-GL-7773 TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-MH-A854 
       25.25        80.65        12.92        56.75        21.34        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-SX-A71S TCGA-SX-A7SU TCGA-UZ-A9PX 
       31.13        15.48        87.09        49.45        43.76        65.13 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

subtype1 subtype2 subtype3 
    0.46     0.23     0.13 
subtype1 subtype2 subtype3 
  123.62   194.79    87.09 
subtype1 subtype2 subtype3 
  26.200   23.280   25.265 
[1] "0.5 - 123.6 (26.2)" "0.2 - 194.8 (23.3)" "0.1 - 87.1 (25.3)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      58        9        13        2
  subtype2      47        5        28       12
  subtype3      28        0         2        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         58       47       28
  STAGE II         9        5        0
  STAGE III       13       28        2
  STAGE IV         2       12        0
[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 67 12    14
  subtype2 51  8    38
  subtype3 29  1     2
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          67       51       29
  T2          12        8        1
  T3+T4       14       38        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"
          vv
clus       N0 N1 N2
  subtype1 16  4  0
  subtype2 22 19  4
  subtype3  3  0  0
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       16       22        3
  N1        4       19        0
  N2        0        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"
D10V6, binary
          cls
clus        0  1
  subtype1 26  0
  subtype2 40  8
  subtype3 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    0
  subtype2   40    8
  subtype3   10    0
   clus
vv  subtype1 subtype2 subtype3
  0       26       40       10
  1        0        8        0
[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"
D10V7, binary
          cls
clus        0  1
  subtype1 18 75
  subtype2 36 63
  subtype3  8 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   75
  subtype2   36   63
  subtype3    8   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       36        8
  MALE         75       63       24
[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"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        15
  subtype2                                0     5                        20
  subtype3                                0     0                         5
          vv
clus       WHITE
  subtype1    71
  subtype2    70
  subtype3    25
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   1        5        0
  BLACK OR AFRICAN AMERICAN              15       20        5
  WHITE                                  71       70       25
[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"
D10V12, binary
          cls
clus        0  1
  subtype1  2 80
  subtype2  5 76
  subtype3  3 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    5   76
  subtype3    3   28
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        3
  NOT HISPANIC OR LATINO       80       76       28
[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"
