[1] "ofn"        "-oTTHCA-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/THCA-TP/22507188/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/22542946/THCA-TP.mergedcluster.txt"

nPatients in clinical file=503, in cluster file=503, common to both=503
[1]  10 503
[1] "CN_CNMF"
[1] 3
  1   2   3 
132 138 229 
  1   2   3 
132 138 229 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
 46 149  85  42 181 
  1   2   3   4   5 
 46 149  85  42 181 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
64 64 43 51 
 1  2  3  4 
64 64 43 51 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
47 28 33 29 49 27  9 
 1  2  3  4  5  6  7 
47 28 33 29 49 27  9 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
158 169  59 115 
  1   2   3   4 
158 169  59 115 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
105 136  86  96  78 
  1   2   3   4   5 
105 136  86  96  78 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
166 147 120  69 
  1   2   3   4 
166 147 120  69 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
179 130 193 
  1   2   3 
179 130 193 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
133 126 108 105 
  1   2   3   4 
133 126 108 105 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
164 122 186 
  1   2   3 
164 122 186 
[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] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 503 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=16,	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=437,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'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 503 columns, 1 survival variables, and 16 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] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
143 166 169  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
143 166 169  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
143 166 169  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
143 166 169  23 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=29, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=62, 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 127   5
  subtype2 133   5
  subtype3 222   6
subtype1 subtype2 subtype3 
     132      138      228 
subtype1 subtype2 subtype3 
       5        5        6 
$subtype1
TCGA-DE-A0XZ TCGA-DJ-A13L TCGA-DJ-A3UU TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3CR 
       35.84         9.96        23.44        24.76        39.95         7.66 
TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-FK-A3SD TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0Z2 
      139.86        57.11         1.05        23.93         4.24        49.78 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A3PT 
       14.73        41.33        15.12        51.39        12.82        23.31 
TCGA-BJ-A45D TCGA-BJ-A45I TCGA-CE-A484 TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DJ-A13M 
       10.88        15.45        12.43        18.54        11.57        48.79 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QN 
       56.19        52.27        43.17        44.98        42.51        42.58 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PZ TCGA-DJ-A2Q7 TCGA-DJ-A2QA 
       17.56        10.09        26.20         8.42        35.11        33.53 
TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UR 
       35.18        36.92        32.42        31.46        16.41        36.33 
TCGA-DJ-A3VB TCGA-DJ-A3VJ TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DJ-A4V4 TCGA-DO-A2HM 
       22.92        36.43        27.62        34.78        15.81         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E1 TCGA-E8-A3X7 TCGA-E8-A432 TCGA-E8-A436 
       92.55        47.21        80.52        31.27        30.61        14.96 
TCGA-EL-A3CL TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GO TCGA-EL-A3GP 
       31.66       158.83        98.53        69.57        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GW TCGA-EL-A3GY TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3T2 
      115.10        50.20       101.13        83.57        57.63        32.48 
TCGA-EL-A3T9 TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZQ TCGA-EL-A4JZ 
        5.72        62.30        36.03        72.69        61.22        61.02 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EM-A1CS TCGA-EM-A1CW TCGA-EM-A22K TCGA-EM-A22L 
       44.15        47.84        26.86        18.05        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CP TCGA-EM-A2OZ TCGA-EM-A3AL 
       14.53        41.29        47.57         2.99        33.96        14.14 
TCGA-EM-A3AP TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FO TCGA-EM-A3FP 
        8.35        27.95        23.77        47.38        17.49        17.39 
TCGA-EM-A3O3 TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR 
       14.50         7.33        29.85        12.79        26.37        21.53 
TCGA-EM-A4FU TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A3BP 
       60.49        65.29         2.66        33.24       108.46        79.10 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A231 TCGA-FE-A237 
       43.73        62.83        43.99        37.48        31.59       112.80 
TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3R7 
       85.15        22.03         0.92         1.25        17.82        16.27 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A421 
       21.63        17.06        22.49        21.60        12.53        20.05 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-KS-A41I 
       16.90        31.10        25.64        43.17        31.82        15.98 
TCGA-KS-A4I3 TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A4N6 TCGA-QD-A8IV TCGA-E8-A418 
       43.69        32.45        84.72        36.10        12.89         3.02 

$subtype2
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-DJ-A2PR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3H8 
       30.21        22.88        27.45        45.53         4.18       150.48 
TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-J8-A4HW TCGA-BJ-A0YZ TCGA-BJ-A0Z3 
      178.29        29.72        50.40         2.60        24.79        16.34 
TCGA-BJ-A0ZA TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       18.87        16.73        25.48        42.15        21.04        35.54 
TCGA-BJ-A2N7 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-BJ-A45J TCGA-CE-A3MD 
       18.38        16.01        36.39        21.01        21.63        12.79 
TCGA-CE-A3ME TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       12.46        37.64        27.32        30.12        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13W TCGA-DJ-A1QF 
       14.70        14.27        38.17        18.58        52.37        30.61 
TCGA-DJ-A1QL TCGA-DJ-A1QO TCGA-DJ-A2PP TCGA-DJ-A2PY TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 
       17.59        47.41        30.58         8.78        37.74        33.93 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A4UP 
       19.20        23.21        21.27        18.97         9.60        30.12 
TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E8-A2EA TCGA-E8-A419 
       35.38        21.53        66.38        63.19        35.67        25.45 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CT TCGA-EL-A3CW TCGA-EL-A3CX 
       26.73       155.54        97.74        60.95        57.01       106.62 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
       65.39       136.01       147.75        43.36        49.71       139.00 
TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3ZK TCGA-EL-A3ZN 
      108.66        29.65       132.07        98.24        51.78        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KH 
       65.49        59.44        34.72        34.39        53.36        27.06 
TCGA-EM-A1CV TCGA-EM-A1YA TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CT TCGA-EM-A2CU 
       48.49        19.79        13.18        23.51        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3AO TCGA-EM-A3AR TCGA-EM-A3FR 
       22.16        17.59        14.60        44.52        37.25        15.02 
TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A4FM TCGA-ET-A25I TCGA-ET-A25J 
       15.06        12.53        27.02         5.33        81.70        77.56 
TCGA-ET-A2MX TCGA-ET-A2N0 TCGA-ET-A2N3 TCGA-ET-A39R TCGA-ET-A3BN TCGA-ET-A3BQ 
       88.41        52.60        83.34        94.13        28.24        76.64 
TCGA-ET-A3BT TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       87.62       116.78        94.59       166.62        24.72        46.26 
TCGA-ET-A4KN TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A4UB 
       33.17        81.83       106.36        85.68        78.77       116.09 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-H2-A2K9 
       16.57        18.08        23.87        19.04        14.04        21.67 
TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A41Y TCGA-J8-A3YE TCGA-J8-A3YF TCGA-KS-A41J 
       11.01        18.61        21.83        27.85        24.69        15.68 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-MK-A4N7 TCGA-MK-A4N9 
       87.39        35.28        33.24        40.37        32.45        30.21 

$subtype3
TCGA-BJ-A45K TCGA-CE-A13K TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-EL-A3GQ 
       23.18        12.66        59.57        42.54         3.12        50.24 
TCGA-EL-A3H2 TCGA-EL-A3MY TCGA-ET-A3BV TCGA-FY-A76V TCGA-J8-A3NZ TCGA-L6-A4ET 
       33.50        17.52        75.42         1.68        17.23        21.83 
TCGA-BJ-A0Z0 TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A190 
       13.78         4.01        11.57        42.08        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
        4.83        44.35        32.45        11.31        30.97        11.08 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3F0 TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.57        20.48        18.97        13.94        18.64         7.99 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
        3.45        23.84        28.44        19.43        23.47        12.30 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       11.38        10.68        15.02        12.66        21.63        50.17 
TCGA-DE-A4M9 TCGA-DE-A7U5 TCGA-DJ-A13P TCGA-DJ-A13S TCGA-DJ-A13X TCGA-DJ-A1QD 
       18.84         2.76       169.32         8.71         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PT 
      135.91        14.96         6.02         7.99        35.41        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       33.96        31.99        34.85        28.96        34.36        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC 
       40.24        37.48        36.46        39.09        35.90        39.95 
TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3US TCGA-DJ-A3V3 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       31.04        19.56        32.81        30.61        20.48        24.82 
TCGA-DJ-A3VD TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       40.70        35.67        23.44        30.87        33.04        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DO-A1JZ TCGA-E3-A3E3 TCGA-E8-A242 
       26.93        35.54         3.12        54.90        52.44        31.23 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A433 
       29.98        31.50        31.04        31.30        30.84        31.27 
TCGA-E8-A434 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CU 
       31.33        39.88        33.50        31.00        30.15       157.15 
TCGA-EL-A3CV TCGA-EL-A3CZ TCGA-EL-A3D6 TCGA-EL-A3GV TCGA-EL-A3GZ TCGA-EL-A3H1 
       37.94        79.50       108.36        50.37       139.99        49.32 
TCGA-EL-A3MZ TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       52.50       142.52       129.57        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A4JV 
       82.82        89.56        91.17        60.16         7.07        57.47 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG 
       45.96        31.04        30.51        41.13        43.59        24.30 
TCGA-EL-A4KI TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       23.90        18.18        20.91        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q 
       54.08        14.73        14.50        10.65        44.19        14.24 
TCGA-EM-A2CK TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       17.88         6.05        12.30        40.34        19.73        32.32 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AN 
       17.46        17.29        22.52        30.94        15.68        33.07 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FQ TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-EM-A3ST 
       21.01        12.07        16.18         9.24        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FN 
       29.95        13.51        84.59        29.33        21.34        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25K TCGA-ET-A25L 
       22.45        24.46        13.68        81.93        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       60.20        63.39        18.38        63.45        58.75        37.25 
TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39N 
       54.35        80.88       106.09       107.41        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BS TCGA-ET-A3BU 
      100.57        95.34        55.10        98.20         5.79        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A40R 
       46.65        52.47        84.85        80.58        66.84        44.38 
TCGA-ET-A40S TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 
       40.21        31.40        73.74        71.44        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 TCGA-FK-A3S3 
       68.22       117.40        66.77        39.95        33.63        71.08 
TCGA-FK-A3SB TCGA-FK-A3SH TCGA-FY-A3BL TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        4.11        48.10        20.42         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A4B0 
       13.91        15.68        23.31        17.36        15.16        13.81 
TCGA-H2-A26U TCGA-H2-A3RH TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A420 
       17.00        12.46        48.92        47.41        18.51         8.22 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.19        11.24        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-L6-A4EP TCGA-L6-A4EU 
      143.57       113.85        26.70        18.64        33.40         9.50 

subtype1 subtype2 subtype3 
    0.92     2.60     0.20 
subtype1 subtype2 subtype3 
  158.83   178.29   169.32 
subtype1 subtype2 subtype3 
  31.525   31.530   31.040 
[1] "0.9 - 158.8 (31.5)" "2.6 - 178.3 (31.5)" "0.2 - 169.3 (31.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      71        9        29        2        17         2
  subtype2      80       17        27        0        13         1
  subtype3     131       24        55        0        16         3
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         71       80      131
  STAGE II         9       17       24
  STAGE III       29       27       55
  STAGE IV         2        0        0
  STAGE IVA       17       13       16
  STAGE IVC        2        1        3
[1] 6 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 39 37 46 10
  subtype2 34 50 46  7
  subtype3 69 78 75  6
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       39       34       69
  T2       37       50       78
  T3       46       46       75
  T4       10        7        6
[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"
D1V5, binary
          cls
clus         0   1
  subtype1  58  63
  subtype2  60  66
  subtype3 107  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   63
  subtype2   60   66
  subtype3  107   95
   clus
vv  subtype1 subtype2 subtype3
  0       58       60      107
  1       63       66       95
[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"
D1V6, binary
          cls
clus         0   1
  subtype1  72   4
  subtype2  87   2
  subtype3 119   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    4
  subtype2   87    2
  subtype3  119    3
   clus
vv  subtype1 subtype2 subtype3
  0       72       87      119
  1        4        2        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"
D1V7, binary
          cls
clus         0   1
  subtype1  96  36
  subtype2 102  36
  subtype3 167  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96   36
  subtype2  102   36
  subtype3  167   62
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       96      102      167
  MALE         36       36       62
[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"
D1V8, binary
          cls
clus         0   1
  subtype1  40  85
  subtype2  53  83
  subtype3  87 135
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   85
  subtype2   53   83
  subtype3   87  135
     clus
vv    subtype1 subtype2 subtype3
  NO        40       53       87
  YES       85       83      135
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              4                                            90
  subtype2              1                                            99
  subtype3              2                                           167
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     30
  subtype2                                                                     24
  subtype3                                                                     46
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   8
  subtype2                                                                  14
  subtype3                                                                  14
D1V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                90
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       30
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           8
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                99
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          14
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               167
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       46
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          14
[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"
D1V10, binary
          cls
clus         0   1
  subtype1 114   3
  subtype2 113   6
  subtype3 193   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    3
  subtype2  113    6
  subtype3  193    8
     clus
vv    subtype1 subtype2 subtype3
  NO       114      113      193
  YES        3        6        8
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           35                       6   84                   1
  subtype2           42                       6   84                   0
  subtype3           55                       6  162                   0
D1V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  35       42       55
  MODERATE/ADVANCED (T4A)        6        6        6
  NONE                          84       84      162
  VERY ADVANCED (T4B)            1        0        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        R0  R1  R2  RX
  subtype1  94  16   2  13
  subtype2 110  10   2   6
  subtype3 179  25   0  11
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       94      110      179
  R1       16       10       25
  R2        2        2        0
  RX       13        6       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"
D1V13, continuous
D1V14, binary
          cls
clus         0   1
  subtype1  71  59
  subtype2  56  79
  subtype3  98 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71   59
  subtype2   56   79
  subtype3   98  126
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       71       56       98
  UNIFOCAL         59       79      126
[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"
D1V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    13                         9
  subtype2                                1     6                         6
  subtype3                                0    33                        12
          vv
clus       WHITE
  subtype1    82
  subtype2   106
  subtype3   141
D1V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  13        6       33
  BLACK OR AFRICAN AMERICAN               9        6       12
  WHITE                                  82      106      141
[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"
D1V17, binary
          cls
clus         0   1
  subtype1  11  92
  subtype2  14 100
  subtype3  13 168
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   92
  subtype2   14  100
  subtype3   13  168
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           11       14       13
  NOT HISPANIC OR LATINO       92      100      168
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1  44   2
  subtype2 144   5
  subtype3  80   5
  subtype4  41   0
  subtype5 177   4
subtype1 subtype2 subtype3 subtype4 subtype5 
      46      149       85       41      181 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        5        5        0        4 
$subtype1
TCGA-DJ-A3V4 TCGA-EL-A3CS TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A18Z TCGA-BJ-A28R 
       42.54        45.53         4.24        41.33        41.52        42.15 
TCGA-BJ-A3EZ TCGA-DE-A0Y2 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U 
       16.01        21.63        30.12        30.02        25.12        52.27 
TCGA-DJ-A1QO TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3VB TCGA-E8-A44K TCGA-EL-A3CM 
       47.41        19.20        23.21        22.92        31.00        26.73 
TCGA-EL-A3CN TCGA-EL-A3GS TCGA-EL-A3T6 TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZO 
      155.54        65.39        98.24        51.78        36.03        72.69 
TCGA-EL-A4JW TCGA-EM-A22O TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-ET-A25G TCGA-ET-A25R 
       34.72        44.19        29.95        12.79        81.93        63.45 
TCGA-ET-A2MX TCGA-ET-A39O TCGA-ET-A3DW TCGA-ET-A40Q TCGA-FE-A231 TCGA-FY-A3YR 
       88.41       100.57        24.72        46.26        31.59        17.36 
TCGA-FY-A40L TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A420 TCGA-J8-A3O1 TCGA-J8-A3YG 
       23.87        18.61        48.92         8.22        27.19        22.29 
TCGA-J8-A4HY TCGA-KS-A4I3 TCGA-KS-A4IB TCGA-L6-A4EU 
        0.20        43.69        84.72         9.50 

$subtype2
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-FK-A3SD 
       22.88        23.18        24.76        57.11        33.50         1.05 
TCGA-FY-A76V TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA 
        1.68        23.93        24.79        13.78        49.78        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 
       11.57        16.73        25.48        51.39        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       44.35        21.04        32.45        18.38        16.57        20.48 
TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F 
       12.82        13.94        23.31         7.99        10.88         3.45 
TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S 
       23.84        12.43        37.64        18.84        48.79         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP TCGA-DJ-A2PS 
       52.37        44.98        17.59         6.02        30.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3UX 
       34.36        43.96        35.18        16.41        36.33        11.34 
TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       40.96        35.67        23.44        27.62        34.78        47.21 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 TCGA-E8-A438 TCGA-EL-A3CZ 
       29.98        31.04        31.30        31.33        33.50        79.50 
TCGA-EL-A3D4 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T0 TCGA-EL-A3T2 
       69.57        64.87        50.20        49.32       142.52        32.48 
TCGA-EL-A3TA TCGA-EL-A3ZH TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       66.90        91.17        53.06        60.16        57.47        30.51 
TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       44.15        23.90        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       57.01        54.08        14.50        15.75        10.45        10.65 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        48.46        22.16        40.34        32.32 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL 
       17.29        22.52        14.14         8.35        37.25        47.38 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3OA 
       12.07        17.39        15.02        15.06        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR 
       38.66        38.86        13.51        29.33        21.34        21.53 
TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 
       60.49        13.68        81.70        18.38        54.35        83.34 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       80.88        33.24       108.46       123.32        66.84       166.62 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3I5 
       43.99        31.40        33.63         1.25        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA 
       29.10        16.14        16.27        16.57        21.63        17.06 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z 
       22.49        19.04        13.81        21.67        12.46        31.10 
TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-KS-A41I TCGA-KS-A41L TCGA-QD-A8IV 
       43.17        31.82        15.98       113.85        12.89 

$subtype3
TCGA-DJ-A13L TCGA-DJ-A3UW TCGA-EL-A3CY TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-ET-A3BV 
        9.96        59.57         4.18        17.52       178.29        75.42 
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        42.08        35.54        11.31        30.97        11.08 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-BJ-A45I TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 
       36.39        21.01        15.45        12.30        11.38        12.66 
TCGA-DE-A4M8 TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2PX 
       18.54         2.76        38.17        18.58        38.83        28.96 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A3UQ TCGA-DJ-A3US 
       37.74        40.24        37.48        35.90        19.56        32.81 
TCGA-DJ-A3V2 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4V0 
       20.22        40.70         9.60        30.12        27.06        35.54 
TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A414 
       35.38         2.33        31.23        35.67        11.70        31.50 
TCGA-E8-A419 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
       25.45        30.15        97.74        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3H3 TCGA-EL-A3H5 TCGA-EL-A3T1 
       57.01       108.36        49.51        43.36        83.57       129.57 
TCGA-EL-A3T9 TCGA-EL-A3ZS TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EM-A22M TCGA-EM-A22P 
        5.72         7.07        45.96        61.02        14.53        41.29 
TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AJ TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A3O9 
        2.99        17.46        30.94        16.18        14.50         9.24 
TCGA-EM-A4FO TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A3BS TCGA-ET-A3DO TCGA-ET-A3DQ 
       26.37        84.89        94.13         5.79       116.78        84.85 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A23A TCGA-FY-A3R6 
       43.73        62.83        40.21        33.17        81.83        13.91 
TCGA-FY-A3TY TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 TCGA-IM-A4EB TCGA-J8-A3YF 
       23.31        12.53        17.00        20.05        25.64        24.69 
TCGA-KS-A4ID 
       33.24 

$subtype4
TCGA-J8-A3NZ TCGA-BJ-A0Z5 TCGA-BJ-A3PU TCGA-BJ-A4O9 TCGA-CE-A3ME TCGA-CE-A483 
       17.23        14.73        18.64        23.47        12.46        15.02 
TCGA-DJ-A13P TCGA-DJ-A1QF TCGA-DJ-A2PZ TCGA-DJ-A3UR TCGA-DJ-A3UY TCGA-DJ-A3V8 
      169.32        30.61         8.42        36.33        35.87        21.27 
TCGA-DJ-A4V4 TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E8-A436 TCGA-EL-A3GV TCGA-EL-A3N2 
       15.81        21.53        80.52        14.96        50.37        29.65 
TCGA-EL-A3ZG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A2OZ TCGA-EM-A2P3 TCGA-ET-A25J 
       89.56        27.06        18.18        33.96        14.60        77.56 
TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BP TCGA-FE-A230 TCGA-FE-A232 
       52.60        95.34        98.20        79.10        71.44        79.69 
TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A238 TCGA-FY-A3BL TCGA-FY-A3RA TCGA-H2-A3RI 
       24.69        66.77        39.95        20.42        18.08        11.01 
TCGA-J8-A3YE TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4IC TCGA-MK-A4N6 
       27.85       143.57        15.68        35.28        36.10 

$subtype5
TCGA-BJ-A290 TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3VI 
       30.21        12.66        35.84        27.45        23.44         3.12 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3H8 TCGA-EM-A3AQ 
       39.95         7.66       139.86        50.24       150.48        29.72 
TCGA-ET-A3BO TCGA-J8-A4HW TCGA-L6-A4ET TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A2NA 
       50.40         2.60        21.83         4.01        15.12        18.97 
TCGA-BJ-A45H TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-CE-A3MD TCGA-CE-A482 TCGA-DE-A0Y3 
       28.44        21.63        19.43        12.79        10.68        50.17 
TCGA-DE-A3KN TCGA-DE-A4MB TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13T TCGA-DJ-A13V 
       27.32        11.57        14.70        14.27        56.19        43.17 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QN 
        8.32        48.07       135.91        42.51        14.96        42.58 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PV 
       17.56        10.09         7.99        35.41        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       34.85         8.78        33.93        36.46        35.11        39.09 
TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       33.53        39.95        36.92        31.04        32.42        31.46 
TCGA-DJ-A3V0 TCGA-DJ-A3V3 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DJ-A3VJ 
       36.99        30.61        20.48        24.82        18.97        36.43 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DO-A1JZ TCGA-E3-A3DY 
       30.87        33.04        26.93         3.12        54.90        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A432 
       66.38        63.19        52.44        31.27        30.84        30.61 
TCGA-E8-A433 TCGA-E8-A437 TCGA-EL-A3CL TCGA-EL-A3CP TCGA-EL-A3CX TCGA-EL-A3D1 
       31.27        39.88        31.66       158.83       106.62        98.53 
TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H4 
      115.10       136.01       147.75       101.13       139.99        49.71 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3T3 TCGA-EL-A3T7 
      139.00       108.66        57.63        52.50       132.07        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZL TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZT 
      107.47        82.82        62.30        65.49        61.22        59.44 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       31.04        34.39        53.36        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EM-A1CS TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A2CS 
       24.30        26.86        20.91        48.49        14.73        27.65 
TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P0 TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       13.15        19.73        17.59        15.68        33.07        44.52 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SX 
       27.95        23.77        21.01        17.49         7.33        29.85 
TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25K 
       84.59         5.33        26.37        22.45        24.46        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MY TCGA-ET-A2MZ 
       56.58        60.20        63.39        65.29        58.75        37.25 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BQ 
        2.66       106.09       107.41        55.10        28.24        76.64 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DR 
       87.62        77.82        46.65        52.47        94.59        80.58 
TCGA-ET-A40R TCGA-ET-A40T TCGA-FE-A22Z TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A237 
       44.38        37.48        73.74        68.22       117.40       112.80 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3ON TCGA-FY-A3R8 
       22.03         0.92        48.10       116.09        19.56        15.68 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       15.16        14.04        21.60        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-J8-A3O2 TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A4I1 TCGA-KS-A4I5 
       21.83        11.24         5.75         2.47        26.70        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45        87.39        33.40        40.37        32.45        30.21 
TCGA-E8-A418 
        3.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     1.05     2.33     8.42     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  155.54   166.62   178.29   169.32   158.83 
subtype1 subtype2 subtype3 subtype4 subtype5 
  33.155   23.930   30.970   29.650   33.960 
[1] "0.2 - 155.5 (33.2)" "1.1 - 166.6 (23.9)" "2.3 - 178.3 (31.0)"
[4] "8.4 - 169.3 (29.6)" "0.9 - 158.8 (34.0)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      19        1        16        0        10         0
  subtype2      86       29        26        1         4         2
  subtype3      51        2        22        1         8         1
  subtype4      25        4        11        0         2         0
  subtype5     103       15        36        0        23         3
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         19       86       51       25      103
  STAGE II         1       29        2        4       15
  STAGE III       16       26       22       11       36
  STAGE IV         0        1        1        0        0
  STAGE IVA       10        4        8        2       23
  STAGE IVC        0        2        1        0        3
[1] 6 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  4 10 26  6
  subtype2 52 57 39  1
  subtype3 29 24 27  4
  subtype4 10 15 17  0
  subtype5 48 60 60 12
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4       52       29       10       48
  T2       10       57       24       15       60
  T3       26       39       27       17       60
  T4        6        1        4        0       12
[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"
D2V5, binary
          cls
clus         0   1
  subtype1  15  30
  subtype2  98  25
  subtype3  34  47
  subtype4  16  21
  subtype5  64 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   30
  subtype2   98   25
  subtype3   34   47
  subtype4   16   21
  subtype5   64  103
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       15       98       34       16       64
  1       30       25       47       21      103
[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"
D2V6, binary
          cls
clus         0   1
  subtype1  28   0
  subtype2  69   3
  subtype3  55   1
  subtype4  25   0
  subtype5 103   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   69    3
  subtype3   55    1
  subtype4   25    0
  subtype5  103    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       28       69       55       25      103
  1        0        3        1        0        5
[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"
D2V7, binary
          cls
clus         0   1
  subtype1  32  14
  subtype2 108  41
  subtype3  61  24
  subtype4  33   9
  subtype5 134  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   14
  subtype2  108   41
  subtype3   61   24
  subtype4   33    9
  subtype5  134   47
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       32      108       61       33      134
  MALE         14       41       24        9       47
[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"
D2V8, binary
          cls
clus         0   1
  subtype1   9  37
  subtype2  54  88
  subtype3  32  49
  subtype4  19  22
  subtype5  67 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   37
  subtype2   54   88
  subtype3   32   49
  subtype4   19   22
  subtype5   67  110
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       54       32       19       67
  YES       37       88       49       22      110
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            34
  subtype2              2                                            70
  subtype3              1                                            68
  subtype4              0                                            37
  subtype5              4                                           149
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      0
  subtype2                                                                     77
  subtype3                                                                      7
  subtype4                                                                      3
  subtype5                                                                     15
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  12
  subtype2                                                                   0
  subtype3                                                                   9
  subtype4                                                                   2
  subtype5                                                                  13
D2V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                34
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          12
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                70
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                68
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           9
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                37
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
                                                                        clus
vv                                                                       subtype5
  OTHER, SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               149
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       15
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          13
[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"
D2V10, binary
          cls
clus         0   1
  subtype1  40   2
  subtype2 120   6
  subtype3  72   4
  subtype4  31   2
  subtype5 160   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    2
  subtype2  120    6
  subtype3   72    4
  subtype4   31    2
  subtype5  160    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        40      120       72       31      160
  YES        2        6        4        2        3
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           22                       6   17                   0
  subtype2           21                       0  119                   0
  subtype3           22                       3   55                   1
  subtype4           16                       0   24                   0
  subtype5           52                       9  118                   0
D2V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  MINIMAL (T3)                  22       21       22       16       52
  MODERATE/ADVANCED (T4A)        6        0        3        0        9
  NONE                          17      119       55       24      118
  VERY ADVANCED (T4B)            0        0        1        0        0
[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        R0  R1  R2  RX
  subtype1  33   9   1   2
  subtype2 118   8   0   8
  subtype3  62  10   1   5
  subtype4  36   1   0   1
  subtype5 136  24   2  14
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       33      118       62       36      136
  R1        9        8       10        1       24
  R2        1        0        1        0        2
  RX        2        8        5        1       14
[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"
D2V13, continuous
D2V14, binary
          cls
clus        0  1
  subtype1 18 28
  subtype2 69 77
  subtype3 38 45
  subtype4 13 27
  subtype5 89 89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   28
  subtype2   69   77
  subtype3   38   45
  subtype4   13   27
  subtype5   89   89
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  MULTIFOCAL       18       69       38       13       89
  UNIFOCAL         28       77       45       27       89
[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"
D2V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                         3
  subtype2                                0    11                         9
  subtype3                                0    10                         4
  subtype4                                0     4                         1
  subtype5                                0    22                        10
          vv
clus       WHITE
  subtype1    33
  subtype2    84
  subtype3    63
  subtype4    33
  subtype5   118
D2V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   5       11       10        4       22
  BLACK OR AFRICAN AMERICAN               3        9        4        1       10
  WHITE                                  33       84       63       33      118
[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"
D2V17, binary
          cls
clus         0   1
  subtype1   7  33
  subtype2   7  97
  subtype3   7  68
  subtype4   2  31
  subtype5  15 133
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   33
  subtype2    7   97
  subtype3    7   68
  subtype4    2   31
  subtype5   15  133
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            7        7        7        2       15
  NOT HISPANIC OR LATINO       33       97       68       31      133
[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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 58  6
  subtype2 62  2
  subtype3 41  2
  subtype4 47  4
subtype1 subtype2 subtype3 subtype4 
      64       64       43       51 
subtype1 subtype2 subtype3 subtype4 
       6        2        2        4 
$subtype1
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D5 TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       45.53         4.18        57.11        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 
       16.34        11.57        25.48        42.08        51.39        20.58 
TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QM 
       27.32        48.79        52.37         8.32        30.61         6.02 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 
       10.09         7.99        31.99         8.42        43.96        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EL-A3CL 
       35.11        35.90        33.53        39.95        47.21        31.66 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
      155.54        97.74       158.83       157.15        37.94        57.01 
TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EM-A1CW 
       79.50        69.57        50.37        50.20        49.32        18.05 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CN 
       57.01        54.08        10.45        47.57        17.88        23.51 
TCGA-EM-A2CQ TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN 
       12.30        13.15        22.16        30.94        14.14        33.07 
TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FP TCGA-ET-A2MZ TCGA-ET-A2N5 TCGA-ET-A39I 
        8.35        47.38        17.39        37.25        80.88        33.24 
TCGA-ET-A3BP TCGA-ET-A3DP TCGA-FY-A2QD TCGA-J8-A3O0 
       79.10        94.59         1.25        43.17 

$subtype2
TCGA-E3-A3E5 TCGA-EL-A3N3 TCGA-J8-A3NZ TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB 
       39.95       178.29        17.23        14.73        41.33         4.01 
TCGA-BJ-A0ZE TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       16.73        44.35        42.15        18.38        20.48        18.97 
TCGA-BJ-A3EZ TCGA-DE-A0Y2 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QD 
       16.01        21.63        38.17        18.58         8.71        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QG TCGA-DJ-A2PP TCGA-DJ-A2PY TCGA-DJ-A2Q0 TCGA-DJ-A2Q8 
      135.91        44.98        30.58         8.78        34.36        39.09 
TCGA-DJ-A2QB TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A2EA TCGA-EL-A3CM 
       35.18        21.53        80.52        52.44        35.67        26.73 
TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H5 
      108.36        65.39       136.01       101.13        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MZ TCGA-EM-A1CT TCGA-EM-A1YA TCGA-EM-A1YB 
      139.00       108.66        52.50        18.18        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A2CO TCGA-EM-A2OY 
       78.61        14.73        14.50        44.19         6.05        32.32 
TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O TCGA-ET-A2MY TCGA-ET-A2N0 
       81.93        56.58        60.20        65.29        58.75        52.60 
TCGA-ET-A39T TCGA-ET-A3BT TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A231 
       98.20        87.62       116.78        24.72        73.74        31.59 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FY-A3BL 
       66.77       112.80        81.83        20.42 

$subtype3
TCGA-BJ-A291 TCGA-CE-A13K TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-BJ-A0ZA TCGA-BJ-A18Z 
       22.88        12.66        33.50       150.48        18.87        41.52 
TCGA-BJ-A191 TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A2P4 
        4.83        21.04        35.54        32.45        11.31        12.82 
TCGA-BJ-A3F0 TCGA-CE-A27D TCGA-CE-A3MD TCGA-DE-A2OL TCGA-DJ-A1QI TCGA-DJ-A1QL 
       13.94        12.30        12.79        37.64        14.96        17.59 
TCGA-DJ-A1QN TCGA-DO-A1JZ TCGA-EL-A3CX TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GZ 
       42.58        54.90       106.62        64.87       115.10       139.99 
TCGA-EL-A3H3 TCGA-EM-A1CV TCGA-EM-A22Q TCGA-EM-A2CL TCGA-EM-A2CP TCGA-EM-A2CR 
       43.36        48.49        14.24        13.18         2.99        13.64 
TCGA-EM-A3AI TCGA-EM-A3AO TCGA-EM-A3FN TCGA-ET-A2N1 TCGA-ET-A39L TCGA-ET-A39M 
       22.52        44.52        12.07        54.35       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3DV TCGA-FE-A239 TCGA-H2-A2K9 TCGA-IM-A3ED 
      123.32        94.13       166.62        33.63        21.67        47.41 
TCGA-J8-A3O1 
       27.19 

$subtype4
TCGA-BJ-A290 TCGA-DJ-A2PR TCGA-EL-A3CR TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3MY 
       30.21        27.45         7.66       139.86        50.24        17.52 
TCGA-ET-A3BV TCGA-BJ-A28Z TCGA-CE-A3ME TCGA-DJ-A13V TCGA-DJ-A1QO TCGA-DJ-A2PQ 
       75.42        11.08        12.46        43.17        47.41        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       26.20        33.96        34.85        37.74        33.93        37.48 
TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E8-A2JQ TCGA-EL-A3CT TCGA-EL-A3D1 TCGA-EL-A3GP 
       92.55        66.38        11.70        60.95        98.53        49.51 
TCGA-EL-A3GX TCGA-EL-A3MX TCGA-EL-A3N2 TCGA-EM-A1CU TCGA-EM-A22M TCGA-EM-A2CS 
      147.75        57.63        29.65        20.91        14.53        27.65 
TCGA-EM-A2P1 TCGA-EM-A3FJ TCGA-EM-A3FO TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39P 
       17.46        27.95        17.49         2.66       106.09        95.34 
TCGA-ET-A3BN TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DS 
       28.24         5.79        77.82        46.65        52.47        66.84 
TCGA-ET-A3DT TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       43.73        71.44        79.69        24.69        68.22       117.40 
TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB 
       19.56        12.53        48.92 

subtype1 subtype2 subtype3 subtype4 
    1.25     4.01     2.99     2.66 
subtype1 subtype2 subtype3 subtype4 
  158.83   178.29   166.62   147.75 
subtype1 subtype2 subtype3 subtype4 
  35.505   41.740   33.500   37.480 
[1] "1.2 - 158.8 (35.5)" "4.0 - 178.3 (41.7)" "3.0 - 166.6 (33.5)"
[4] "2.7 - 147.8 (37.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      32       12        13         3         2
  subtype2      22       11        19        12         0
  subtype3      30        8         3         2         0
  subtype4      33        2        11         3         2
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         32       22       30       33
  STAGE II        12       11        8        2
  STAGE III       13       19        3       11
  STAGE IVA        3       12        2        3
  STAGE IVC        2        0        0        2
[1] 5 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 23 23 16  1
  subtype2 12 19 27  6
  subtype3  9 22 12  0
  subtype4  7 19 21  4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       23       12        9        7
  T2       23       19       22       19
  T3       16       27       12       21
  T4        1        6        0        4
[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"
D3V5, binary
          cls
clus        0  1
  subtype1 37 19
  subtype2 25 31
  subtype3 25 11
  subtype4 11 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   19
  subtype2   25   31
  subtype3   25   11
  subtype4   11   34
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       37       25       25       11
  1       19       31       11       34
[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"
D3V6, binary
          cls
clus        0  1
  subtype1 38  2
  subtype2 35  1
  subtype3 21  0
  subtype4 24  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    2
  subtype2   35    1
  subtype3   21    0
  subtype4   24    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       38       35       21       24
  1        2        1        0        2
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 44 20
  subtype2 47 17
  subtype3 32 11
  subtype4 31 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   20
  subtype2   47   17
  subtype3   32   11
  subtype4   31   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       44       47       32       31
  MALE         20       17       11       20
[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"
D3V8, binary
          cls
clus        0  1
  subtype1 31 31
  subtype2 24 40
  subtype3 20 22
  subtype4 15 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   31
  subtype2   24   40
  subtype3   20   22
  subtype4   15   35
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        31       24       20       15
  YES       31       40       22       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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            36
  subtype2              0                                            44
  subtype3              1                                            32
  subtype4              1                                            46
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     27
  subtype2                                                                     13
  subtype3                                                                     10
  subtype4                                                                      2
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                   7
  subtype3                                                                   0
  subtype4                                                                   2
D3V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                36
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       27
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                44
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           7
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                32
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                46
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
[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"
D3V10, binary
          cls
clus        0  1
  subtype1 55  4
  subtype2 55  3
  subtype3 29  2
  subtype4 45  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    4
  subtype2   55    3
  subtype3   29    2
  subtype4   45    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        55       55       29       45
  YES        4        3        2        2
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           12                       1   51
  subtype2           22                       6   34
  subtype3            5                       0   32
  subtype4           16                       3   32
D3V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  12       22        5       16
  MODERATE/ADVANCED (T4A)        1        6        0        3
  NONE                          51       34       32       32
[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       R0 R1 R2 RX
  subtype1 50  6  1  6
  subtype2 45 12  0  4
  subtype3 34  2  0  0
  subtype4 39  3  1  4
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       50       45       34       39
  R1        6       12        2        3
  R2        1        0        0        1
  RX        6        4        0        4
[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"
D3V13, continuous
D3V14, binary
          cls
clus        0  1
  subtype1 34 27
  subtype2 22 40
  subtype3 20 22
  subtype4 24 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   27
  subtype2   22   40
  subtype3   20   22
  subtype4   24   26
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       34       22       20       24
  UNIFOCAL         27       40       22       26
[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"
D3V15, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    36
  subtype2     3                         3    48
  subtype3     4                         1    28
  subtype4     6                         2    37
D3V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        3        4        6
  BLACK OR AFRICAN AMERICAN        7        3        1        2
  WHITE                           36       48       28       37
[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"
D3V17, binary
          cls
clus        0  1
  subtype1  3 45
  subtype2  5 49
  subtype3  5 31
  subtype4  3 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   45
  subtype2    5   49
  subtype3    5   31
  subtype4    3   43
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        5        5        3
  NOT HISPANIC OR LATINO       45       49       31       43
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 42  5
  subtype2 27  1
  subtype3 33  0
  subtype4 27  2
  subtype5 48  1
  subtype6 26  1
  subtype7  5  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      47       28       33       29       49       27        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       5        1        0        2        1        1        4 
$subtype1
TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA 
       57.11        33.50        24.79        13.78        49.78        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A28V 
       11.57        25.48        42.08        51.39        20.58        32.45 
TCGA-BJ-A2N9 TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A1QL TCGA-DJ-A2PO 
       20.48        37.64        48.79        52.37        17.59         7.99 
TCGA-DJ-A2Q2 TCGA-E3-A3DZ TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CW 
       43.96        47.21        97.74       158.83       157.15        57.01 
TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EM-A1CW TCGA-EM-A1YD 
       79.50        69.57        50.20        49.32        18.05        57.01 
TCGA-EM-A1YE TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CQ 
       54.08        10.45        47.57        17.88        13.18        12.30 
TCGA-EM-A2CR TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL 
       13.64        22.16        30.94        14.14         8.35        47.38 
TCGA-ET-A39I TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DV TCGA-FY-A2QD 
       33.24        79.10        94.59       166.62         1.25 

$subtype2
TCGA-EL-A3GQ TCGA-BJ-A0Z3 TCGA-DE-A3KN TCGA-DJ-A13O TCGA-DJ-A13X TCGA-DJ-A1QM 
       50.24        16.34        27.32        38.17         8.32         6.02 
TCGA-DJ-A2PN TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q6 
       10.09        35.41        26.20        31.99         8.42        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-EL-A3CL TCGA-EL-A3CV 
       35.11        35.90        33.53        39.95        31.66        37.94 
TCGA-EM-A1CT TCGA-EM-A2CU TCGA-EM-A3AN TCGA-EM-A3FJ TCGA-ET-A25M TCGA-ET-A2MZ 
       18.18        13.15        33.07        27.95        60.20        37.25 
TCGA-ET-A39P TCGA-FE-A232 TCGA-FE-A236 TCGA-J8-A3O0 
       95.34        79.69        66.77        43.17 

$subtype3
TCGA-BJ-A290 TCGA-J8-A3NZ TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A3EZ 
       30.21        17.23        14.73        41.33         4.01        16.01 
TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QO TCGA-DJ-A2PY 
       12.46        21.63        48.07       135.91        47.41         8.78 
TCGA-DJ-A2Q8 TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-EL-A3D6 TCGA-EL-A3GS 
       39.09        21.53        80.52        52.44       108.36        65.39 
TCGA-EL-A3GU TCGA-EL-A3GY TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3N2 
      136.01       101.13        83.57       139.00       108.66        29.65 
TCGA-EM-A22O TCGA-EM-A2P1 TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A3DO TCGA-ET-A3DW 
       44.19        17.46        81.93        56.58       116.78        24.72 
TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A23A 
       71.44        68.22        81.83 

$subtype4
TCGA-BJ-A291 TCGA-EL-A3CR TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-BJ-A0ZE TCGA-BJ-A28S 
       22.88         7.66         4.18       139.86        16.73        21.04 
TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-EL-A3CN TCGA-EL-A3GO 
       11.31        11.08        12.82        13.94       155.54        64.87 
TCGA-EL-A3H3 TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A3AI TCGA-EM-A3FN 
       43.36        14.24        23.51         2.99        22.52        12.07 
TCGA-EM-A3FP TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R 
       17.39        54.35        80.88       108.46       123.32        94.13 
TCGA-ET-A3BS TCGA-ET-A3DS TCGA-ET-A3DT TCGA-FE-A239 TCGA-H2-A2K9 
        5.79        66.84        43.73        33.63        21.67 

$subtype5
TCGA-CE-A13K TCGA-DJ-A2PR TCGA-EL-A3H8 TCGA-ET-A3BV TCGA-BJ-A18Z TCGA-BJ-A191 
       12.66        27.45       150.48        75.42        41.52         4.83 
TCGA-BJ-A28T TCGA-CE-A27D TCGA-CE-A3MD TCGA-DJ-A13V TCGA-DJ-A1QF TCGA-DJ-A1QI 
       35.54        12.30        12.79        43.17        30.61        14.96 
TCGA-DJ-A1QN TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       42.58        33.96        34.85        37.74        33.93        37.48 
TCGA-DO-A1JZ TCGA-E3-A3E0 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-EL-A3CX TCGA-EL-A3D1 
       54.90        66.38        35.67        11.70       106.62        98.53 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GZ TCGA-EL-A3MX 
       49.51       115.10        50.37       147.75       139.99        57.63 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A3AO TCGA-EM-A3FO 
       20.91        48.49        14.53        27.65        44.52        17.49 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39M TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BW 
        2.66       106.09        84.89        28.24        77.82        46.65 
TCGA-ET-A3BX TCGA-FE-A233 TCGA-FE-A235 TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB 
       52.47        24.69       117.40        19.56        12.53        48.92 
TCGA-IM-A3ED 
       47.41 

$subtype6
TCGA-BJ-A192 TCGA-BJ-A2N7 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP 
       44.35        18.38        18.58         8.71        44.98        30.58 
TCGA-DJ-A2Q0 TCGA-DJ-A2QB TCGA-E3-A3DY TCGA-EL-A3MZ TCGA-EM-A1YA TCGA-EM-A1YB 
       34.36        35.18        92.55        52.50        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A2CO TCGA-EM-A2OY TCGA-ET-A25O 
       78.61        14.73        14.50         6.05        32.32        65.29 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39T TCGA-ET-A3BT TCGA-FE-A22Z TCGA-FE-A231 
       58.75        52.60        98.20        87.62        73.74        31.59 
TCGA-FE-A237 TCGA-FY-A3BL TCGA-J8-A3O1 
      112.80        20.42        27.19 

$subtype7
TCGA-E3-A3E5 TCGA-EL-A3CS TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-BJ-A28R TCGA-BJ-A2NA 
       39.95        45.53        17.52       178.29        42.15        18.97 
TCGA-EL-A3CM TCGA-EL-A3CT TCGA-EL-A3H4 
       26.73        60.95        49.71 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1.25     6.02     4.01     2.99     2.66     6.05    17.52 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  166.62    95.34   139.00   155.54   150.48   112.80   178.29 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   37.64    34.32    48.07    22.52    41.52    34.36    42.15 
[1] "1.2 - 166.6 (37.6)"  "6.0 - 95.3 (34.3)"   "4.0 - 139.0 (48.1)" 
[4] "3.0 - 155.5 (22.5)"  "2.7 - 150.5 (41.5)"  "6.0 - 112.8 (34.4)" 
[7] "17.5 - 178.3 (42.1)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      26       11         6         1         1
  subtype2      16        3         7         2         0
  subtype3      13        4        11         5         0
  subtype4      17        4         7         0         1
  subtype5      35        3         6         4         1
  subtype6       9        7         7         4         0
  subtype7       1        1         2         4         1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         26       16       13       17       35        9        1
  STAGE II        11        3        4        4        3        7        1
  STAGE III        6        7       11        7        6        7        2
  STAGE IVA        1        2        5        0        4        4        4
  STAGE IVC        1        0        0        1        1        0        1
[1] 5 7
[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 16 22  9  0
  subtype2 11  9  8  0
  subtype3  3 11 17  2
  subtype4  4 11 12  1
  subtype5 11 21 16  1
  subtype6  5  9 11  2
  subtype7  1  0  3  5
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       16       11        3        4       11        5        1
  T2       22        9       11       11       21        9        0
  T3        9        8       17       12       16       11        3
  T4        0        0        2        1        1        2        5
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 28 11
  subtype2 13 13
  subtype3 10 22
  subtype4 17  9
  subtype5 16 26
  subtype6 11 10
  subtype7  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   11
  subtype2   13   13
  subtype3   10   22
  subtype4   17    9
  subtype5   16   26
  subtype6   11   10
  subtype7    3    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       28       13       10       17       16       11        3
  1       11       13       22        9       26       10        4
[1] 2 7
[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 21  1
  subtype2 19  0
  subtype3 21  1
  subtype4 13  1
  subtype5 26  1
  subtype6 11  0
  subtype7  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    1
  subtype2   19    0
  subtype3   21    1
  subtype4   13    1
  subtype5   26    1
  subtype6   11    0
  subtype7    7    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       21       19       21       13       26       11        7
  1        1        0        1        1        1        0        1
[1] 2 7
[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 31 16
  subtype2 18 10
  subtype3 25  8
  subtype4 21  8
  subtype5 33 16
  subtype6 20  7
  subtype7  6  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   16
  subtype2   18   10
  subtype3   25    8
  subtype4   21    8
  subtype5   33   16
  subtype6   20    7
  subtype7    6    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       31       18       25       21       33       20        6
  MALE         16       10        8        8       16        7        3
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus        0  1
  subtype1 21 24
  subtype2 14 14
  subtype3 13 20
  subtype4 11 17
  subtype5 20 28
  subtype6  8 19
  subtype7  3  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   24
  subtype2   14   14
  subtype3   13   20
  subtype4   11   17
  subtype5   20   28
  subtype6    8   19
  subtype7    3    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        21       14       13       11       20        8        3
  YES       24       14       20       17       28       19        6
[1] 2 7
[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       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            22
  subtype2              0                                            22
  subtype3              0                                            25
  subtype4              0                                            22
  subtype5              1                                            46
  subtype6              1                                            12
  subtype7              0                                             9
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     25
  subtype2                                                                      5
  subtype3                                                                      0
  subtype4                                                                      7
  subtype5                                                                      2
  subtype6                                                                     13
  subtype7                                                                      0
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                   1
  subtype3                                                                   8
  subtype4                                                                   0
  subtype5                                                                   0
  subtype6                                                                   1
  subtype7                                                                   0
D4V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                25
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           8
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype5
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                46
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype6
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                12
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype7
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                 9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus        0  1
  subtype1 39  3
  subtype2 26  0
  subtype3 29  0
  subtype4 22  2
  subtype5 39  2
  subtype6 23  3
  subtype7  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    3
  subtype2   26    0
  subtype3   29    0
  subtype4   22    2
  subtype5   39    2
  subtype6   23    3
  subtype7    6    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        39       26       29       22       39       23        6
  YES        3        0        0        2        2        3        1
[1] 2 7
[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       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1            4                       0   42
  subtype2            9                       0   19
  subtype3           15                       3   14
  subtype4            6                       1   18
  subtype5           12                       0   36
  subtype6            6                       2   19
  subtype7            3                       4    1
D4V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  MINIMAL (T3)                   4        9       15        6       12        6
  MODERATE/ADVANCED (T4A)        0        0        3        1        0        2
  NONE                          42       19       14       18       36       19
                         clus
vv                        subtype7
  MINIMAL (T3)                   3
  MODERATE/ADVANCED (T4A)        4
  NONE                           1
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 37  5  0  3
  subtype2 22  3  0  2
  subtype3 24  7  0  0
  subtype4 19  2  2  1
  subtype5 39  3  0  3
  subtype6 23  1  0  3
  subtype7  4  2  0  2
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       37       22       24       19       39       23        4
  R1        5        3        7        2        3        1        2
  R2        0        0        0        2        0        0        0
  RX        3        2        0        1        3        3        2
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
          cls
clus        0  1
  subtype1 27 17
  subtype2 12 16
  subtype3 12 20
  subtype4 12 17
  subtype5 25 22
  subtype6 10 16
  subtype7  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   17
  subtype2   12   16
  subtype3   12   20
  subtype4   12   17
  subtype5   25   22
  subtype6   10   16
  subtype7    2    7
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  MULTIFOCAL       27       12       12       12       25       10        2
  UNIFOCAL         17       16       20       17       22       16        7
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    25
  subtype2     2                         1    19
  subtype3     3                         0    28
  subtype4     2                         1    20
  subtype5     7                         2    33
  subtype6     1                         2    16
  subtype7     0                         1     8
D4V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        2        3        2        7
  BLACK OR AFRICAN AMERICAN        6        1        0        1        2
  WHITE                           25       19       28       20       33
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        0
  BLACK OR AFRICAN AMERICAN        2        1
  WHITE                           16        8
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V17, binary
          cls
clus        0  1
  subtype1  2 32
  subtype2  1 23
  subtype3  3 28
  subtype4  2 22
  subtype5  5 38
  subtype6  2 17
  subtype7  1  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   32
  subtype2    1   23
  subtype3    3   28
  subtype4    2   22
  subtype5    5   38
  subtype6    2   17
  subtype7    1    8
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        1        3        2        5        2
  NOT HISPANIC OR LATINO       32       23       28       22       38       17
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO        8
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 151   7
  subtype2 162   7
  subtype3  59   0
  subtype4 112   2
subtype1 subtype2 subtype3 subtype4 
     158      169       59      114 
subtype1 subtype2 subtype3 subtype4 
       7        7        0        2 
$subtype1
TCGA-DJ-A3VI TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 
        3.12         7.66        45.53       150.48        17.52       178.29 
TCGA-ET-A3BV TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB 
       75.42        17.23         2.60         4.24        41.33         4.01 
TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU 
       15.12        41.52        42.15        18.97        16.01        18.64 
TCGA-BJ-A4O8 TCGA-CE-A3ME TCGA-CE-A483 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MA 
       19.43        12.46        15.02        21.63        50.17        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A7U5 TCGA-DJ-A13U 
       11.57        30.02        25.12        14.70         2.76        52.27 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       48.07       135.91        42.51        47.41        17.56        10.09 
TCGA-DJ-A2PT TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3UQ 
       38.83         8.78         8.42        33.93        31.04        19.56 
TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VB TCGA-DJ-A3VF 
       36.99        19.20        23.21        21.27        22.92         9.60 
TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 
       36.43         3.12        35.38        21.53        80.52        52.44 
TCGA-E8-A242 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A44K 
       31.23        31.27        30.84        25.45        31.27        31.00 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CT TCGA-EL-A3D6 TCGA-EL-A3GR TCGA-EL-A3GS 
       26.73       155.54        60.95       108.36       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3MZ 
      136.01       147.75       101.13        49.71       139.00        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZK 
       29.65       129.57       132.07        98.24         5.72        51.78 
TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4K1 
       36.03        72.69        59.44        34.72        45.96        34.39 
TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22I TCGA-EM-A22O 
       53.36        24.30        18.18        20.91        14.73        44.19 
TCGA-EM-A2OZ TCGA-EM-A2P3 TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3SU 
       33.96        14.60        23.77        21.01        17.49        29.95 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-ET-A25G 
       12.79        84.59         5.33        26.37        22.45        81.93 
TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25R TCGA-ET-A2MX 
       77.56        56.58        60.20        63.39        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BN 
       58.75        52.60       100.57        95.34        98.20        28.24 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-ET-A40Q 
       87.62        77.82        52.47       116.78        24.72        46.26 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       33.17        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FK-A3SE 
       68.22        66.77       112.80        39.95        81.83        22.03 
TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40L 
       20.42        19.56        15.68        18.08        17.36        23.87 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       14.04        21.60        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O1 
       18.51        16.90        21.83         8.22        25.64        27.19 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4I9 TCGA-L6-A4EU 
       24.69        22.29        15.68        43.69        87.39         9.50 
TCGA-MK-A4N6 TCGA-E8-A418 
       36.10         3.02 

$subtype2
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-DJ-A3V4 TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-EL-A3H2 
       22.88        23.18        42.54        24.76        57.11        33.50 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
        1.05         1.68        23.93        24.79        13.78        49.78 
TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 
       18.87        11.57        16.73        25.48        51.39        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        4.83        44.35        21.04        32.45        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D 
       20.48        12.82        13.94        23.31         7.99        10.88 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-CE-A3MD TCGA-CE-A484 TCGA-DE-A2OL 
        3.45        23.84        28.44        12.79        12.43        37.64 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W 
       18.84        48.79        38.17        18.58         8.71        52.37 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       44.98        17.59         6.02        30.58        34.36        43.96 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX 
       33.53        35.18        16.41        32.81        36.33        11.34 
TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       40.96        35.67        23.44        27.62        33.04        34.78 
TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 
       35.54        15.81        47.21        31.04        31.30        31.33 
TCGA-E8-A437 TCGA-EL-A3CO TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 
       39.88        97.74        57.01       106.62        79.50        69.57 
TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3ZH 
       64.87        50.20        49.32       142.52        32.48        91.17 
TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD 
       53.06        60.16        57.47        30.51        44.15        43.59 
TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       23.90        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        48.46        22.16        40.34        32.32 
TCGA-EM-A2P0 TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP 
       17.59        17.29        22.52        30.94        14.14         8.35 
TCGA-EM-A3AR TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 
       37.25        47.38        12.07        17.39        15.02        15.06 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY 
       12.53         9.24        27.02        38.66        38.86        13.51 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I 
       29.33        21.34        21.53        60.49        13.68        81.70 
TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N 
       18.38        83.34        80.88        33.24       108.46       123.32 
TCGA-ET-A39S TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       55.10        84.85        80.58        66.84       166.62        43.99 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       31.40        33.63         1.25        17.82         7.82        29.10 
TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M 
       16.14        16.27        16.57        21.63        17.06        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
       19.04        13.81        21.67        12.46        31.10        43.17 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4ID 
       31.82        27.85         0.20        15.98       113.85        33.24 
TCGA-QD-A8IV 
       12.89 

$subtype3
TCGA-DJ-A13L TCGA-DJ-A3UW TCGA-EL-A3CY TCGA-ET-A3BO TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ 
        9.96        59.57         4.18        50.40        16.34        42.08 
TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A3PR TCGA-BJ-A45E 
       35.54        11.31        30.97        11.08        36.39        21.01 
TCGA-BJ-A45I TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DJ-A2PX 
       15.45        12.30        11.38        12.66        18.54        28.96 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UY TCGA-DJ-A3VD TCGA-DJ-A4UP 
       37.74        40.24        35.90        35.87        40.70        30.12 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DO-A2HM TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A413 
       27.06        26.93         2.33        35.67        11.70        29.98 
TCGA-E8-A414 TCGA-E8-A436 TCGA-E8-A44M TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3GP 
       31.50        14.96        30.15       157.15        37.94        49.51 
TCGA-EL-A3H3 TCGA-EL-A3H5 TCGA-EL-A3TA TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JZ 
       43.36        83.57        66.90        65.49         7.07        61.02 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2P1 TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FO 
       14.53        41.29        17.46        16.18        14.50        26.37 
TCGA-ET-A39R TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A3PB 
       94.13        43.73        62.83        44.38        40.21        85.15 
TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 TCGA-H2-A26U TCGA-J8-A3O2 
       13.91        23.31        12.53        17.00        11.24 

$subtype4
TCGA-BJ-A290 TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-E3-A3E5 
       30.21        12.66        35.84        27.45        23.44        39.95 
TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EM-A3AQ TCGA-L6-A4ET TCGA-BJ-A0Z5 TCGA-BJ-A45J 
      139.86        50.24        29.72        21.83        14.73        21.63 
TCGA-BJ-A4O9 TCGA-CE-A482 TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T 
       23.47        10.68        27.32        14.27       169.32        56.19 
TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO 
       43.17         8.32        30.61        14.96        42.58         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2Q5 
       35.41        26.20        33.96        31.99        34.85        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       36.46        35.11        39.95        36.92        32.42        31.46 
TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VE 
       36.33        20.22        30.61        20.48        24.82        18.97 
TCGA-DJ-A4UL TCGA-DO-A1JZ TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E8-A432 
       30.87        54.90        92.55        66.38        63.19        30.61 
TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3GV TCGA-EL-A3GZ 
       33.50        31.66       158.83        98.53        50.37       139.99 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG 
      108.66        57.63        41.29       107.47        82.82        89.56 
TCGA-EL-A3ZL TCGA-EL-A3ZQ TCGA-EL-A4K0 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KH 
       62.30        61.22        31.04        41.13        47.84        27.06 
TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A3AK 
       26.86        48.49        27.65        13.15        19.73        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-EM-A4FV 
       33.07        44.52        27.95         7.33        29.85        24.46 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K 
       70.42        65.29        37.25         2.66       106.09       107.41 
TCGA-ET-A39M TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW TCGA-ET-A3DP 
       84.89        79.10        76.64         5.79        46.65        94.59 
TCGA-ET-A40T TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       37.48       117.40       106.36        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K TCGA-H2-A3RI 
        4.11         0.92        48.10       116.09        15.16        11.01 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
        5.75         2.47       143.57        26.70        18.64        32.45 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N7 TCGA-MK-A4N9 
       84.72        35.28        33.40        40.37        32.45        30.21 

subtype1 subtype2 subtype3 subtype4 
    2.60     0.20     2.33     0.92 
subtype1 subtype2 subtype3 subtype4 
  178.29   166.62   157.15   169.32 
subtype1 subtype2 subtype3 subtype4 
   31.25    25.48    30.12    34.98 
[1] "2.6 - 178.3 (31.2)" "0.2 - 166.6 (25.5)" "2.3 - 157.2 (30.1)"
[4] "0.9 - 169.3 (35.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      78        6        44        1        27         2
  subtype2      99       29        31        1         6         2
  subtype3      41        1        12        0         5         0
  subtype4      65       15        23        0         9         2
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         78       99       41       65
  STAGE II         6       29        1       15
  STAGE III       44       31       12       23
  STAGE IV         1        1        0        0
  STAGE IVA       27        6        5        9
  STAGE IVC        2        2        0        2
[1] 6 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 26 42 75 15
  subtype2 57 61 48  2
  subtype3 26 15 15  2
  subtype4 33 47 31  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       26       57       26       33
  T2       42       61       15       47
  T3       75       48       15       31
  T4       15        2        2        4
[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"
D5V5, binary
          cls
clus         0   1
  subtype1  47  97
  subtype2 108  34
  subtype3  22  37
  subtype4  49  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   97
  subtype2  108   34
  subtype3   22   37
  subtype4   49   57
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       47      108       22       49
  1       97       34       37       57
[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"
D5V6, binary
          cls
clus        0  1
  subtype1 86  3
  subtype2 82  3
  subtype3 41  0
  subtype4 70  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86    3
  subtype2   82    3
  subtype3   41    0
  subtype4   70    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       86       82       41       70
  1        3        3        0        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1 115  43
  subtype2 119  50
  subtype3  44  15
  subtype4  88  27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115   43
  subtype2  119   50
  subtype3   44   15
  subtype4   88   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      115      119       44       88
  MALE         43       50       15       27
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1  49 106
  subtype2  64  96
  subtype3  24  33
  subtype4  43  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49  106
  subtype2   64   96
  subtype3   24   33
  subtype4   43   70
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        49       64       24       43
  YES      106       96       33       70
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           128
  subtype2              3                                            80
  subtype3              0                                            50
  subtype4              1                                            99
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      3
  subtype2                                                                     84
  subtype3                                                                      2
  subtype4                                                                     13
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  24
  subtype2                                                                   2
  subtype3                                                                   7
  subtype4                                                                   2
D5V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               128
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          24
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                80
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                50
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           7
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                99
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
[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"
D5V10, binary
          cls
clus         0   1
  subtype1 137   5
  subtype2 138   6
  subtype3  47   2
  subtype4  99   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  137    5
  subtype2  138    6
  subtype3   47    2
  subtype4   99    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       137      138       47       99
  YES        5        6        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           65                      14   74                   1
  subtype2           27                       1  132                   0
  subtype3           13                       2   41                   0
  subtype4           28                       1   84                   0
D5V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  65       27       13       28
  MODERATE/ADVANCED (T4A)       14        1        2        1
  NONE                          74      132       41       84
  VERY ADVANCED (T4B)            1        0        0        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 119  26   1   8
  subtype2 134  10   0   9
  subtype3  40   7   1   5
  subtype4  90   9   2   8
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      119      134       40       90
  R1       26       10        7        9
  R2        1        0        1        2
  RX        8        9        5        8
[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"
D5V13, continuous
D5V14, binary
          cls
clus        0  1
  subtype1 60 96
  subtype2 79 87
  subtype3 29 28
  subtype4 58 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   96
  subtype2   79   87
  subtype3   29   28
  subtype4   58   54
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       60       79       29       58
  UNIFOCAL         96       87       28       54
[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"
D5V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    14                        11
  subtype2                                0    13                         9
  subtype3                                0    10                         1
  subtype4                                0    14                         6
          vv
clus       WHITE
  subtype1   114
  subtype2    98
  subtype3    43
  subtype4    76
D5V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                  14       13       10       14
  BLACK OR AFRICAN AMERICAN              11        9        1        6
  WHITE                                 114       98       43       76
[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"
D5V17, binary
          cls
clus         0   1
  subtype1  23 113
  subtype2   9 108
  subtype3   3  51
  subtype4   3  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23  113
  subtype2    9  108
  subtype3    3   51
  subtype4    3   88
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           23        9        3        3
  NOT HISPANIC OR LATINO      113      108       51       88
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 100   5
  subtype2 130   6
  subtype3  85   1
  subtype4  93   2
  subtype5  76   2
subtype1 subtype2 subtype3 subtype4 subtype5 
     105      136       86       95       78 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        6        1        2        2 
$subtype1
TCGA-DJ-A13L TCGA-EL-A3CR TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-ET-A3BO TCGA-ET-A3BV 
        9.96         7.66        17.52       178.29        50.40        75.42 
TCGA-J8-A3NZ TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28R 
       17.23         4.24        41.33         4.01        41.52        42.15 
TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       18.64        15.45        19.43        30.12        11.57        30.02 
TCGA-DE-A69J TCGA-DE-A7U5 TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A2PT TCGA-DJ-A2PY 
       14.70         2.76       135.91        42.51        38.83         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q6 TCGA-DJ-A3UQ TCGA-DJ-A3V0 TCGA-DJ-A3V5 
        8.42        37.74        36.46        19.56        36.99        19.20 
TCGA-DJ-A3VB TCGA-DJ-A3VF TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       22.92         9.60        31.23        35.67        11.70        31.27 
TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CU 
       25.45        31.27        31.00        26.73       155.54       157.15 
TCGA-EL-A3CV TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 
       37.94       108.36        49.51       136.01        83.57       139.00 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZM 
       52.50        29.65       129.57        98.24         5.72        36.03 
TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG 
       72.69        45.96        61.02        34.39        53.36        24.30 
TCGA-EM-A22I TCGA-EM-A2P3 TCGA-EM-A3FM TCGA-EM-A3O3 TCGA-EM-A3SU TCGA-EM-A3SZ 
       14.73        14.60        21.01        14.50        29.95        12.79 
TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FQ TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L 
       84.59         5.33        22.45        81.93        77.56        56.58 
TCGA-ET-A25M TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P 
       60.20        63.45        58.75        52.60       100.57        95.34 
TCGA-ET-A3BT TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN 
       87.62       116.78        62.83        24.72        46.26        33.17 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
       73.74        71.44        68.22       112.80        81.83        85.15 
TCGA-FY-A3R8 TCGA-FY-A3YR TCGA-FY-A40L TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 
       15.68        17.36        23.87        12.53        17.00        20.05 
TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3YF 
       48.92        18.51        16.90         8.22        25.64        24.69 
TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39         9.50        36.10 

$subtype2
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-FK-A3SD 
       22.88        23.18        24.76        57.11        33.50         1.05 
TCGA-FY-A76V TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA 
        1.68        23.93        24.79        13.78        49.78        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 
       11.57        16.73        25.48        51.39        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       44.35        21.04        32.45        18.38        16.57        20.48 
TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F 
       12.82        13.94        23.31         7.99        10.88         3.45 
TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S 
       23.84        12.43        37.64        18.84        48.79         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       52.37        44.98        17.59        30.58        34.36        43.96 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.18        16.41        36.33        35.67        23.44        27.62 
TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A416 TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CZ 
       34.78        47.21        31.30        97.74       106.62        79.50 
TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR 
       64.87        50.20        49.32        32.48        91.17        60.16 
TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA 
       57.47        30.51        44.15        23.90        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        54.08        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.45        10.65        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV 
       23.51         6.05        12.30        13.64        48.46        22.16 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL 
       40.34        32.32        17.29        22.52        30.94        14.14 
TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 
        8.35        47.38        12.07        17.39        15.02        15.06 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY 
       12.53         9.24        27.02        38.66        38.86        13.51 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I 
       29.33        21.34        21.53        60.49        13.68        81.70 
TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N 
       18.38        83.34        80.88        33.24       108.46       123.32 
TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FY-A2QD 
       66.84       166.62        43.99        31.40        33.63         1.25 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA 
        7.82        29.10        16.14        16.57        21.63        17.06 
TCGA-FY-A40M TCGA-FY-A4B0 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
       22.49        13.81        21.67        12.46        31.10        43.17 
TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L TCGA-QD-A8IV 
        0.20        15.98       113.85        12.89 

$subtype3
TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-EL-A3CY 
       35.84        27.45        23.44        59.57        42.54         4.18 
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        42.08        35.54        11.31        30.97        11.08 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-BJ-A45H TCGA-CE-A27D TCGA-CE-A485 TCGA-DE-A4M8 
       36.39        21.01        28.44        12.30        12.66        18.54 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A1QM TCGA-DJ-A2PS TCGA-DJ-A2PX TCGA-DJ-A2Q3 
       38.17        18.58         6.02        26.20        28.96        40.24 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3US TCGA-DJ-A3UX TCGA-DJ-A3UY 
       37.48        35.90        33.53        32.81        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3VD TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       40.96        20.22        30.61        40.70        30.12        33.04 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM 
       27.06        26.93        35.54        15.81        35.38         2.33 
TCGA-E3-A3E2 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A434 TCGA-E8-A436 
       63.19        29.98        31.50        31.04        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A44M TCGA-EL-A3CW TCGA-EL-A3D4 TCGA-EL-A3H3 TCGA-EL-A3T0 
       39.88        30.15        57.01        69.57        43.36       142.52 
TCGA-EL-A3TA TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EM-A22M 
       66.90        53.06        65.49        61.22         7.07        14.53 
TCGA-EM-A22P TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A4FO 
       41.29         2.99        17.46        37.25        16.18        26.37 
TCGA-EM-A4FV TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A3BS TCGA-ET-A3DQ 
       24.46        84.89        94.13        55.10         5.79        84.85 
TCGA-ET-A3DT TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-FE-A232 TCGA-FY-A3R6 
       43.73        44.38        40.21        37.48        79.69        13.91 
TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A40N TCGA-IM-A3ED TCGA-J8-A3O2 TCGA-J8-A3YD 
       16.27        23.31        19.04        47.41        11.24        31.82 
TCGA-J8-A42S TCGA-KS-A4ID 
        2.47        33.24 

$subtype4
TCGA-BJ-A290 TCGA-CE-A13K TCGA-E3-A3E5 TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EM-A3AQ 
       30.21        12.66        39.95       139.86        50.24        29.72 
TCGA-L6-A4ET TCGA-BJ-A0Z5 TCGA-BJ-A45J TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A482 
       21.83        14.73        21.63        12.79        11.38        10.68 
TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13X 
       27.32        14.27       169.32        56.19        43.17         8.32 
TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.61        14.96        42.58        35.41        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       34.85        35.11        39.95        36.92        32.42        31.46 
TCGA-DJ-A3UR TCGA-DJ-A3V9 TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DO-A1JZ TCGA-E3-A3E0 
       36.33        20.48        18.97        30.87        54.90        66.38 
TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3GV 
       30.61        33.50        31.66       158.83        98.53        50.37 
TCGA-EL-A3GZ TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB 
      139.99       108.66        57.63        41.29       107.47        82.82 
TCGA-EL-A3ZL TCGA-EL-A4K0 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH 
       62.30        31.04        41.13        47.84        43.59        27.06 
TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A3AK 
       26.86        48.49        27.65        13.15        19.73        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SX 
       33.07        44.52        27.95        17.49         7.33        29.85 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K 
       70.42        65.29        37.25         2.66       106.09       107.41 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A235 TCGA-FE-A3PA 
       79.10        76.64        46.65        94.59       117.40       106.36 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       78.77        71.08         4.11         0.92        48.10       116.09 
TCGA-FY-A40K TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.16         5.75       143.57        26.70        18.64        32.45 
TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N7 TCGA-MK-A4N9 
       84.72        33.40        40.37        32.45        30.21 

$subtype5
TCGA-DJ-A3VI TCGA-EL-A3CS TCGA-EL-A3H8 TCGA-J8-A4HW TCGA-BJ-A0ZH TCGA-BJ-A2NA 
        3.12        45.53       150.48         2.60        15.12        18.97 
TCGA-BJ-A3EZ TCGA-BJ-A4O9 TCGA-CE-A3ME TCGA-CE-A483 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       16.01        23.47        12.46        15.02        21.63        50.17 
TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       25.12        52.27        48.07        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VA 
        7.99        33.93        31.04        23.21        21.27        24.82 
TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E3 
       36.43         3.12        21.53        92.55        80.52        52.44 
TCGA-E8-A417 TCGA-EL-A3CT TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GX TCGA-EL-A3GY 
       30.84        60.95       115.10        65.39       147.75       101.13 
TCGA-EL-A3H4 TCGA-EL-A3T3 TCGA-EL-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZT TCGA-EL-A4JW 
       49.71       132.07        89.56        51.78        59.44        34.72 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22O TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3FK 
       18.18        20.91        44.19        33.96        17.59        23.77 
TCGA-EM-A4FN TCGA-ET-A25N TCGA-ET-A2MX TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BU 
       26.37        63.39        88.41        98.20        28.24        77.82 
TCGA-ET-A3BX TCGA-ET-A3DR TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A238 
       52.47        80.58        31.59        24.69        66.77        39.95 
TCGA-FE-A3PC TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3RA 
       85.68        22.03        20.42        17.82        19.56        18.08 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A41Y TCGA-J8-A3O1 
       14.04        21.60        11.01        18.61        21.83        27.19 
TCGA-J8-A3YE TCGA-J8-A3YG TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-E8-A418 
       27.85        22.29        15.68        43.69        35.28         3.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.76     0.20     2.33     0.92     2.60 
subtype1 subtype2 subtype3 subtype4 subtype5 
  178.29   166.62   142.52   169.32   150.48 
subtype1 subtype2 subtype3 subtype4 subtype5 
  34.390   23.475   31.415   34.850   28.045 
[1] "2.8 - 178.3 (34.4)" "0.2 - 166.6 (23.5)" "2.3 - 142.5 (31.4)"
[4] "0.9 - 169.3 (34.9)" "2.6 - 150.5 (28.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      46        2        39        1        16         1
  subtype2      77       29        22        1         4         2
  subtype3      57        3        18        0         8         0
  subtype4      54       12        19        0         8         2
  subtype5      49        5        12        0        11         1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         46       77       57       54       49
  STAGE II         2       29        3       12        5
  STAGE III       39       22       18       19       12
  STAGE IV         1        1        0        0        0
  STAGE IVA       16        4        8        8       11
  STAGE IVC        1        2        0        2        1
[1] 6 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 17 21 57 10
  subtype2 43 55 36  2
  subtype3 38 22 23  1
  subtype4 26 41 25  4
  subtype5 18 26 28  6
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       17       43       38       26       18
  T2       21       55       22       41       26
  T3       57       36       23       25       28
  T4       10        2        1        4        6
[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"
D6V5, binary
          cls
clus        0  1
  subtype1 29 68
  subtype2 91 19
  subtype3 38 45
  subtype4 43 45
  subtype5 25 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   68
  subtype2   91   19
  subtype3   38   45
  subtype4   43   45
  subtype5   25   48
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       29       91       38       43       25
  1       68       19       45       45       48
[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"
D6V6, binary
          cls
clus        0  1
  subtype1 56  1
  subtype2 57  3
  subtype3 60  0
  subtype4 58  3
  subtype5 48  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    1
  subtype2   57    3
  subtype3   60    0
  subtype4   58    3
  subtype5   48    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       56       57       60       58       48
  1        1        3        0        3        2
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 84 21
  subtype2 96 40
  subtype3 61 25
  subtype4 74 22
  subtype5 51 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84   21
  subtype2   96   40
  subtype3   61   25
  subtype4   74   22
  subtype5   51   27
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       84       96       61       74       51
  MALE         21       40       25       22       27
[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"
D6V8, binary
          cls
clus        0  1
  subtype1 30 74
  subtype2 47 83
  subtype3 38 43
  subtype4 37 57
  subtype5 28 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   74
  subtype2   47   83
  subtype3   38   43
  subtype4   37   57
  subtype5   28   48
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        30       47       38       37       28
  YES       74       83       43       57       48
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              1                                            79
  subtype2              2                                            57
  subtype3              1                                            69
  subtype4              0                                            83
  subtype5              3                                            69
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      2
  subtype2                                                                     77
  subtype3                                                                     10
  subtype4                                                                     11
  subtype5                                                                      2
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  23
  subtype2                                                                   0
  subtype3                                                                   6
  subtype4                                                                   2
  subtype5                                                                   4
D6V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                79
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          23
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                57
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                69
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                83
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
                                                                        clus
vv                                                                       subtype5
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                69
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
[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"
D6V10, binary
          cls
clus         0   1
  subtype1  95   3
  subtype2 111   5
  subtype3  66   6
  subtype4  85   1
  subtype5  64   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    3
  subtype2  111    5
  subtype3   66    6
  subtype4   85    1
  subtype5   64    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        95      111       66       85       64
  YES        3        5        6        1        2
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           53                      10   38                   1
  subtype2           16                       1  110                   0
  subtype3           20                       1   62                   0
  subtype4           22                       1   71                   0
  subtype5           22                       5   50                   0
D6V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  MINIMAL (T3)                  53       16       20       22       22
  MODERATE/ADVANCED (T4A)       10        1        1        1        5
  NONE                          38      110       62       71       50
  VERY ADVANCED (T4B)            1        0        0        0        0
[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        R0  R1  R2  RX
  subtype1  70  23   2   6
  subtype2 104  10   0   8
  subtype3  70   4   0   6
  subtype4  76   8   2   6
  subtype5  63   7   0   4
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       70      104       70       76       63
  R1       23       10        4        8        7
  R2        2        0        0        2        0
  RX        6        8        6        6        4
[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"
D6V13, continuous
D6V14, binary
          cls
clus        0  1
  subtype1 39 66
  subtype2 64 69
  subtype3 43 41
  subtype4 47 46
  subtype5 33 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   66
  subtype2   64   69
  subtype3   43   41
  subtype4   47   46
  subtype5   33   43
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  MULTIFOCAL       39       64       43       47       33
  UNIFOCAL         66       69       41       46       43
[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"
D6V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        11
  subtype2                                0     7                         8
  subtype3                                0    17                         1
  subtype4                                0    12                         6
  subtype5                                0    11                         1
          vv
clus       WHITE
  subtype1    77
  subtype2    75
  subtype3    61
  subtype4    60
  subtype5    58
D6V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   4        7       17       12       11
  BLACK OR AFRICAN AMERICAN              11        8        1        6        1
  WHITE                                  77       75       61       60       58
[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"
D6V17, binary
          cls
clus        0  1
  subtype1 15 77
  subtype2  9 82
  subtype3  3 72
  subtype4  3 71
  subtype5  8 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   77
  subtype2    9   82
  subtype3    3   72
  subtype4    3   71
  subtype5    8   58
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           15        9        3        3        8
  NOT HISPANIC OR LATINO       77       82       72       71       58
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 157   9
  subtype2 143   4
  subtype3 118   1
  subtype4  67   2
subtype1 subtype2 subtype3 subtype4 
     166      147      119       69 
subtype1 subtype2 subtype3 subtype4 
       9        4        1        2 
$subtype1
TCGA-BJ-A291 TCGA-DJ-A13L TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-EL-A3CR 
       22.88         9.96        23.44        59.57        42.54         7.66 
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3MY TCGA-ET-A3BV 
       45.53         4.18       139.86        50.24        17.52        75.42 
TCGA-J8-A4HW TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28X 
        2.60         4.24         4.01        41.52        35.54        30.97 
TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D 
       23.31        21.01        28.44        15.45        19.43        12.30 
TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MA TCGA-DE-A4MB 
       12.79        11.38        12.66        18.54        30.12        11.57 
TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
        2.76        38.17        48.07       135.91        30.61        42.51 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV 
        6.02        47.41        17.56        26.20        38.83        31.99 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        8.78         8.42        37.74        40.24        37.48        36.46 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UX TCGA-DJ-A3UY 
       39.09        35.90        31.04        19.56        11.34        35.87 
TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       36.99        19.20        21.27        20.48        40.70         9.60 
TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V4 TCGA-DO-A2HM 
       36.43        33.04        27.06        26.93        15.81         2.33 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        35.67        11.70        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       31.04        31.30        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CP 
       39.88        31.00        30.15        26.73        97.74       158.83 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
      157.15        37.94        57.01        98.53        69.57        49.51 
TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GZ TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX 
      115.10       136.01       139.99        83.57       139.00        57.63 
TCGA-EL-A3MZ TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       52.50         5.72        66.90        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW TCGA-EL-A4JZ 
       53.06        72.69        65.49         7.07        34.72        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P 
       31.04        34.39        53.36        20.91        57.01        41.29 
TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ 
       13.15        19.73        17.46        14.60        37.25        16.18 
TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M 
       14.50         5.33        26.37        81.93        56.58        60.20 
TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU 
       52.60        95.34        55.10        28.24        87.62        77.82 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       84.85        80.58        46.26        37.48        33.17        73.74 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3I5 
      112.80        85.15        22.03        48.10        17.82         7.82 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       13.91        16.27        23.31        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 
       22.49        14.04        12.53        17.00        18.51         8.22 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       25.64        11.24        31.82        24.69        22.29         2.47 
TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU TCGA-MK-A4N6 
       43.69        35.28         9.50        36.10 

$subtype2
TCGA-BJ-A45K TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-FK-A3SD TCGA-MK-A84Z TCGA-BJ-A0YZ 
       23.18        24.76        57.11         1.05        23.93        24.79 
TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       13.78        49.78        18.87        11.57        16.73        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
       42.08        51.39        20.58         4.83        44.35        21.04 
TCGA-BJ-A28V TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A45C 
       32.45        18.38        16.57        20.48        12.82         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A3KN 
       10.88         3.45        23.84        12.43        37.64        27.32 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A13X 
       18.84        48.79        18.58         8.71        52.37         8.32 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2PX TCGA-DJ-A2QA TCGA-DJ-A2QB 
       44.98        17.59        30.58        28.96        33.53        35.18 
TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL 
       16.41        32.81        36.33        40.96        35.67        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UP TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-DO-A1JZ TCGA-E3-A3DZ 
       27.62        30.12        34.78        35.54        54.90        47.21 
TCGA-E3-A3E0 TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T0 
       66.38       106.62        79.50        50.20        49.32       142.52 
TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4K2 
       32.48        91.17        60.16        59.44        57.47        30.51 
TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CW TCGA-EM-A1YA 
       44.15        43.59        23.90        26.86        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        78.61        54.08        14.50        15.75        10.45 
TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       10.65        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OW 
        6.05         2.99        12.30        13.64        48.46        40.34 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AL TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP 
       17.29        22.52        14.14        47.38        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.02        15.06        12.53        27.02        38.66        38.86 
TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 
       13.51        29.33        21.34        21.53        60.49        13.68 
TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N3 
       81.70        18.38        88.41        37.25        54.35        83.34 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3BQ 
       80.88        33.24       106.09       108.46       123.32        76.64 
TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R 
       46.65        94.59        66.84       166.62        43.99        44.38 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FY-A2QD TCGA-FY-A3NM 
       31.40        33.63        78.77        71.08         1.25        29.10 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B0 TCGA-H2-A2K9 
       16.14        16.57        21.63        17.06        13.81        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB 
       12.46        31.10        43.17        15.98       113.85        84.72 
TCGA-KS-A4ID TCGA-MK-A4N7 TCGA-QD-A8IV 
       33.24        32.45        12.89 

$subtype3
TCGA-BJ-A290 TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3VI TCGA-EL-A3H8 
       30.21        12.66        35.84        27.45         3.12       150.48 
TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-FY-A76V TCGA-J8-A3NZ TCGA-L6-A4ET TCGA-BJ-A0Z3 
       29.72        50.40         1.68        17.23        21.83        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A28Z TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A482 TCGA-CE-A483 
       14.73        11.08        21.63        23.47        10.68        15.02 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P 
       21.63        50.17        30.02        14.70        14.27       169.32 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PW 
       14.96        42.58         7.99        35.41        33.96        34.85 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       33.93        35.11        39.95        36.92        32.42        31.46 
TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       36.33        20.22        30.61        24.82        22.92        18.97 
TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E8-A417 TCGA-E8-A438 
       30.87         3.12        35.38        21.53        30.84        33.50 
TCGA-EL-A3CL TCGA-EL-A3MW TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3T8 
       31.66       108.66       129.57       132.07        41.29       107.47 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 
       82.82        89.56        61.22        45.96        41.13        47.84 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O 
       24.30        27.06        48.49        14.73        14.53        44.19 
TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FJ 
       27.65        33.96        15.68        33.07        44.52        27.95 
TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       21.01        17.49         7.33        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25K TCGA-ET-A25O 
       84.59        26.37        22.45        24.46        70.42        65.29 
TCGA-ET-A2MY TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A3BP TCGA-ET-A3BS TCGA-ET-A3DO 
       58.75       107.41       100.57        79.10         5.79       116.78 
TCGA-ET-A40S TCGA-FE-A232 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A3PA TCGA-FK-A3SB 
       40.21        79.69        68.22       117.40       106.36         4.11 
TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3RA TCGA-FY-A40N TCGA-FY-A4B4 
        0.92       116.09        20.42        18.08        19.04        21.60 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3YE TCGA-J8-A3YH 
       20.05        18.61        16.90        21.83        27.85         5.75 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
        0.20       143.57        15.68        26.70        18.64        32.45 
TCGA-KS-A4I9 TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N9 TCGA-E8-A418 
       87.39        33.40        40.37        30.21         3.02 

$subtype4
TCGA-E3-A3E5 TCGA-EL-A3H2 TCGA-EL-A3N3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A28R 
       39.95        33.50       178.29        41.33        15.12        42.15 
TCGA-BJ-A28W TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       11.31        18.97        16.01        13.94        36.39        18.64 
TCGA-CE-A3ME TCGA-DE-A4MD TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A2PN TCGA-DJ-A2Q0 
       12.46        25.12        56.19        52.27        10.09        34.36 
TCGA-DJ-A2Q2 TCGA-DJ-A3V7 TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       43.96        23.21        92.55        80.52        63.19        52.44 
TCGA-E8-A419 TCGA-EL-A3CN TCGA-EL-A3CT TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GS 
       25.45       155.54        60.95       108.36        64.87        65.39 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3N2 
       50.37       147.75       101.13        43.36        49.71        29.65 
TCGA-EL-A3T6 TCGA-EM-A1CT TCGA-EM-A2OV TCGA-EM-A2OY TCGA-EM-A2P0 TCGA-EM-A3AJ 
       98.24        18.18        22.16        32.32        17.59        30.94 
TCGA-EM-A3AP TCGA-EM-A3FK TCGA-EM-A3O9 TCGA-ET-A25J TCGA-ET-A25N TCGA-ET-A25R 
        8.35        23.77         9.24        77.56        63.39        63.45 
TCGA-ET-A2N4 TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BX TCGA-ET-A3DT 
        2.66        84.89        94.13        98.20        52.47        43.73 
TCGA-ET-A3DU TCGA-ET-A3DW TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 
       62.83        24.72        71.44        31.59        24.69        66.77 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PC TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-H2-A3RI 
       39.95        81.83        85.68        19.56        15.68        11.01 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-J8-A3O1 
       48.92        47.41        27.19 

subtype1 subtype2 subtype3 subtype4 
    2.33     1.05     0.20     2.66 
subtype1 subtype2 subtype3 subtype4 
  158.83   166.62   169.32   178.29 
subtype1 subtype2 subtype3 subtype4 
   31.25    29.10    30.02    42.15 
[1] "2.3 - 158.8 (31.2)" "1.1 - 166.6 (29.1)" "0.2 - 169.3 (30.0)"
[4] "2.7 - 178.3 (42.1)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      80        4        53        1        25         2
  subtype2      92       23        24        1         4         2
  subtype3      72       15        21        0        10         2
  subtype4      39        9        13        0         8         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         80       92       72       39
  STAGE II         4       23       15        9
  STAGE III       53       24       21       13
  STAGE IV         1        1        0        0
  STAGE IVA       25        4       10        8
  STAGE IVC        2        2        2        0
[1] 6 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 51 34 65 14
  subtype2 45 62 39  1
  subtype3 35 45 35  5
  subtype4 12 25 29  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       51       45       35       12
  T2       34       62       45       25
  T3       65       39       35       29
  T4       14        1        5        3
[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"
D7V5, binary
          cls
clus         0   1
  subtype1  57 103
  subtype2  93  26
  subtype3  47  63
  subtype4  30  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57  103
  subtype2   93   26
  subtype3   47   63
  subtype4   30   33
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       57       93       47       30
  1      103       26       63       33
[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"
D7V6, binary
          cls
clus         0   1
  subtype1 113   2
  subtype2  65   3
  subtype3  69   3
  subtype4  32   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    2
  subtype2   65    3
  subtype3   69    3
  subtype4   32    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      113       65       69       32
  1        2        3        3        1
[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"
D7V7, binary
          cls
clus         0   1
  subtype1 121  45
  subtype2 106  41
  subtype3  89  31
  subtype4  51  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  121   45
  subtype2  106   41
  subtype3   89   31
  subtype4   51   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      121      106       89       51
  MALE         45       41       31       18
[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"
D7V8, binary
          cls
clus         0   1
  subtype1  55 103
  subtype2  52  90
  subtype3  46  71
  subtype4  28  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55  103
  subtype2   52   90
  subtype3   46   71
  subtype4   28   41
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        55       52       46       28
  YES      103       90       71       41
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           130
  subtype2              2                                            66
  subtype3              1                                           107
  subtype4              1                                            54
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      8
  subtype2                                                                     79
  subtype3                                                                      6
  subtype4                                                                      9
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   0
  subtype3                                                                   6
  subtype4                                                                   5
D7V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               130
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                66
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       79
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               107
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                54
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           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"
D7V10, binary
          cls
clus         0   1
  subtype1 140   5
  subtype2 124   4
  subtype3  99   5
  subtype4  59   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  140    5
  subtype2  124    4
  subtype3   99    5
  subtype4   59    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       140      124       99       59
  YES        5        4        5        3
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           57                      13   89                   1
  subtype2           22                       0  118                   0
  subtype3           33                       3   81                   0
  subtype4           20                       2   45                   0
D7V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  57       22       33       20
  MODERATE/ADVANCED (T4A)       13        0        3        2
  NONE                          89      118       81       45
  VERY ADVANCED (T4B)            1        0        0        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 119  24   2  12
  subtype2 116   9   0  10
  subtype3  94  13   1   5
  subtype4  55   6   1   3
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      119      116       94       55
  R1       24        9       13        6
  R2        2        0        1        1
  RX       12       10        5        3
[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"
D7V13, continuous
D7V14, binary
          cls
clus        0  1
  subtype1 77 88
  subtype2 62 80
  subtype3 65 52
  subtype4 22 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   88
  subtype2   62   80
  subtype3   65   52
  subtype4   22   46
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       77       62       65       22
  UNIFOCAL         88       80       52       46
[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"
D7V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    24                         8
  subtype2                                0     9                        10
  subtype3                                1    16                         8
  subtype4                                0     3                         1
          vv
clus       WHITE
  subtype1   119
  subtype2    84
  subtype3    70
  subtype4    58
D7V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                  24        9       16        3
  BLACK OR AFRICAN AMERICAN               8       10        8        1
  WHITE                                 119       84       70       58
[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"
D7V17, binary
          cls
clus         0   1
  subtype1  12 131
  subtype2   9  94
  subtype3   7  85
  subtype4  10  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  131
  subtype2    9   94
  subtype3    7   85
  subtype4   10   51
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           12        9        7       10
  NOT HISPANIC OR LATINO      131       94       85       51
[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(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 169  10
  subtype2 125   5
  subtype3 191   1
subtype1 subtype2 subtype3 
     179      130      192 
subtype1 subtype2 subtype3 
      10        5        1 
$subtype1
TCGA-DJ-A13L TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-EL-A3CR TCGA-EL-A3CS 
        9.96        23.44        59.57        42.54         7.66        45.53 
TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-ET-A3BV 
        4.18       139.86        50.24        17.52       178.29        75.42 
TCGA-J8-A4HW TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A18Z TCGA-BJ-A28T 
        2.60         4.24         4.01        25.48        41.52        35.54 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E 
       11.31        30.97        18.97        36.39        23.31        21.01 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 
       28.44        15.45        19.43        12.30        11.38        12.66 
TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE 
       18.54        11.57         2.76        38.17        48.07       135.91 
TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS 
       42.51         6.02        47.41        17.56        10.09        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
       38.83        31.99         8.78         8.42        37.74        40.24 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ 
       36.46        39.09        35.90        33.53        31.04        19.56 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       11.34        35.87        40.96        36.99        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       20.48        40.70         9.60        36.43        30.12        33.04 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 
       27.06        26.93        35.54        15.81         2.33        80.52 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       31.23        35.67        11.70        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       31.04        31.30        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       39.88        31.00        30.15        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D1 
      158.83        60.95       157.15        37.94        57.01        98.53 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GZ TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.51       115.10       136.01       139.99        83.57       139.00 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T9 TCGA-EL-A3TA 
       57.63        52.50       142.52       129.57         5.72        66.90 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
        7.07        59.44        34.72        61.02        31.04        34.39 
TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX 
       53.36        24.30        57.01        41.29        13.15        19.73 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 TCGA-EM-A4FF 
       17.59        17.46        14.60        37.25        14.50        84.59 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R 
        5.33        26.37        81.93        56.58        60.20        63.45 
TCGA-ET-A2N0 TCGA-ET-A39J TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT 
       52.60       106.09        95.34        55.10        28.24        87.62 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       84.85        80.58        46.26        37.48        33.17        73.74 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
      112.80        85.15         4.11        22.03        48.10        17.82 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
       13.91        16.27        15.68        23.31        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 
       23.87        14.04        12.53        17.00        18.51         8.22 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       25.64        11.24        31.82        24.69        22.29         2.47 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4IC TCGA-L6-A4EU TCGA-MK-A4N6 
       43.69        18.64        35.28         9.50        36.10 

$subtype2
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-FK-A3SD TCGA-MK-A84Z 
       22.88        23.18        57.11        33.50         1.05        23.93 
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        49.78        18.87        11.57        16.73 
TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V 
       51.39        20.58         4.83        44.35        21.04        32.45 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C 
       18.38        16.57        20.48        12.82        13.94         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 
       10.88         3.45        23.84        12.43        37.64        18.84 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL 
       48.79        18.58         8.71        52.37        44.98        17.59 
TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT 
       30.58        34.36        43.96        35.18        16.41        36.33 
TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-EL-A3CZ 
       35.67        23.44        27.62        34.78        47.21        79.50 
TCGA-EL-A3D4 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T2 TCGA-EL-A3ZH 
       69.57        64.87        50.20        49.32        32.48        91.17 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW 
       60.16        57.47        30.51        44.15        23.90        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        78.61        54.08        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.45        10.65        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        13.64        48.46 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ 
       22.16        40.34        32.32        17.29        22.52        30.94 
TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR 
       14.14         8.35        47.38        12.07        17.39        15.02 
TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 
       13.51        29.33        21.34        21.53        60.49        13.68 
TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N 
       81.70        18.38        83.34        80.88        33.24       123.32 
TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FY-A2QD 
       66.84       166.62        43.99        31.40        33.63         1.25 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA 
        7.82        29.10        16.14        16.57        21.63        17.06 
TCGA-FY-A4B0 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 
       13.81        21.67        12.46        31.10        43.17        27.19 
TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4ID TCGA-QD-A8IV 
       15.98       113.85        33.24        12.89 

$subtype3
TCGA-BJ-A290 TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3VI TCGA-DJ-A3VK 
       30.21        12.66        35.84        27.45         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3H8 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-FY-A76V TCGA-J8-A3NZ 
       39.95       150.48        29.72        50.40         1.68        17.23 
TCGA-L6-A4ET TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
       21.83        16.34        14.73        41.33        15.12        42.08 
TCGA-BJ-A28R TCGA-BJ-A28Z TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 
       42.15        11.08        16.01        18.64        21.63        23.47 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       12.79        12.46        10.68        15.02        21.63        50.17 
TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       27.32        30.12        30.02        25.12        14.70        14.27 
TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI 
      169.32        56.19        52.27         8.32        30.61        14.96 
TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX 
       42.58         7.99        35.41        33.96        34.85        28.96 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       33.93        37.48        35.11        39.95        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 
       31.46        36.33        32.81        20.22        30.61        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       24.82        22.92        18.97        30.87         3.12        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 
       54.90        21.53        92.55        66.38        63.19        52.44 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CX TCGA-EL-A3D6 
       30.84        25.45        33.50        31.66       106.62       108.36 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 
       65.39        50.37       147.75       101.13        43.36        49.71 
TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      108.66        29.65       132.07        98.24        41.29       107.47 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 
       82.82        89.56        61.22        45.96        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       43.59        27.06        26.86        18.18        20.91        48.49 
TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK 
       14.73        14.53        44.19        27.65        33.96        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO 
       33.07        44.52        27.95        23.77        21.01        17.49 
TCGA-EM-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FN 
       16.18         7.33        29.95        29.85        12.79        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O 
       22.45        24.46        77.56        70.42        63.39        65.29 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K 
       88.41        58.75        37.25        54.35         2.66       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BP 
      108.46        84.89       100.57        94.13        98.20        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       76.64         5.79        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40R TCGA-ET-A40S 
       94.59        43.73        62.83        24.72        44.38        40.21 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       66.77        39.95        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3RA 
       71.08         0.92       116.09        20.42        19.56        18.08 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       22.49        19.04        21.60        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3YE TCGA-J8-A3YH 
       48.92        47.41        16.90        21.83        27.85         5.75 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I7 TCGA-KS-A4I9 
        0.20       143.57        15.68        26.70        32.45        87.39 
TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-E8-A418 
       84.72        33.40        40.37        32.45        30.21         3.02 

subtype1 subtype2 subtype3 
    2.33     1.05     0.20 
subtype1 subtype2 subtype3 
  178.29   166.62   169.32 
subtype1 subtype2 subtype3 
  31.500   23.310   33.235 
[1] "2.3 - 178.3 (31.5)" "1.1 - 166.6 (23.3)" "0.2 - 169.3 (33.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      88        5        57        1        25         2
  subtype2      75       27        20        1         4         2
  subtype3     120       19        34        0        18         2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         88       75      120
  STAGE II         5       27       19
  STAGE III       57       20       34
  STAGE IV         1        1        0
  STAGE IVA       25        4       18
  STAGE IVC        2        2        2
[1] 6 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 55 36 71 15
  subtype2 41 53 35  1
  subtype3 47 77 62  7
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55       41       47
  T2       36       53       77
  T3       71       35       62
  T4       15        1        7
[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"
D8V5, binary
          cls
clus         0   1
  subtype1  66 103
  subtype2  86  19
  subtype3  75 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66  103
  subtype2   86   19
  subtype3   75  103
   clus
vv  subtype1 subtype2 subtype3
  0       66       86       75
  1      103       19      103
[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"
D8V6, binary
          cls
clus         0   1
  subtype1 124   2
  subtype2  55   3
  subtype3 100   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  124    2
  subtype2   55    3
  subtype3  100    4
   clus
vv  subtype1 subtype2 subtype3
  0      124       55      100
  1        2        3        4
[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 135  44
  subtype2  92  38
  subtype3 140  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135   44
  subtype2   92   38
  subtype3  140   53
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      135       92      140
  MALE         44       38       53
[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, binary
          cls
clus         0   1
  subtype1  68 104
  subtype2  44  80
  subtype3  69 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68  104
  subtype2   44   80
  subtype3   69  121
     clus
vv    subtype1 subtype2 subtype3
  NO        68       44       69
  YES      104       80      121
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           141
  subtype2              2                                            51
  subtype3              2                                           165
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      9
  subtype2                                                                     77
  subtype3                                                                     16
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   0
  subtype3                                                                  10
D8V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               141
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          26
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                51
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               165
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       16
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          10
[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"
D8V10, binary
          cls
clus         0   1
  subtype1 153   6
  subtype2 107   5
  subtype3 162   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  153    6
  subtype2  107    5
  subtype3  162    6
     clus
vv    subtype1 subtype2 subtype3
  NO       153      107      162
  YES        6        5        6
[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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           67                      14   91                   1
  subtype2           15                       0  107                   0
  subtype3           50                       4  135                   0
D8V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  67       15       50
  MODERATE/ADVANCED (T4A)       14        0        4
  NONE                          91      107      135
  VERY ADVANCED (T4B)            1        0        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        R0  R1  R2  RX
  subtype1 129  26   3  13
  subtype2 101   9   0   7
  subtype3 154  17   1  10
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      129      101      154
  R1       26        9       17
  R2        3        0        1
  RX       13        7       10
[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"
D8V13, continuous
D8V14, binary
          cls
clus         0   1
  subtype1  76 101
  subtype2  61  67
  subtype3  89  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76  101
  subtype2   61   67
  subtype3   89   98
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       76       61       89
  UNIFOCAL        101       67       98
[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"
D8V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    26                         7
  subtype2                                0     6                         8
  subtype3                                1    20                        12
          vv
clus       WHITE
  subtype1   131
  subtype2    71
  subtype3   129
D8V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  26        6       20
  BLACK OR AFRICAN AMERICAN               7        8       12
  WHITE                                 131       71      129
[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"
D8V17, binary
          cls
clus         0   1
  subtype1  13 143
  subtype2   8  76
  subtype3  17 142
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  143
  subtype2    8   76
  subtype3   17  142
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        8       17
  NOT HISPANIC OR LATINO      143       76      142
[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 123  10
  subtype2 121   5
  subtype3 108   0
  subtype4 103   1
subtype1 subtype2 subtype3 subtype4 
     133      126      108      104 
subtype1 subtype2 subtype3 subtype4 
      10        5        0        1 
$subtype1
TCGA-BJ-A291 TCGA-DJ-A13L TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-EL-A3CR 
       22.88         9.96        23.44        59.57        42.54         7.66 
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3MY TCGA-EL-A3N3 
       45.53         4.18       139.86        50.24        17.52       178.29 
TCGA-ET-A3BV TCGA-4C-A93U TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
       75.42         4.24        41.52        35.54        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A4O8 
       11.08        18.97        36.39        23.31        21.01        19.43 
TCGA-CE-A27D TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13O 
       12.30        12.66        18.54        11.57         2.76        38.17 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PT 
       48.07       135.91         6.02        47.41        17.56        38.83 
TCGA-DJ-A2PV TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A3UM 
       31.99        37.74        40.24        39.09        35.90        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       19.56        11.34        35.87        36.99        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UT TCGA-DJ-A4UW 
       20.48        40.70         9.60        36.43        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       35.54        15.81         2.33        31.23        35.67        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 
       31.27        29.98        31.50        31.04        31.30        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CT 
       31.27        31.33        14.96        26.73        97.74        60.95 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GU 
       37.94        57.01        98.53        49.51       115.10       136.01 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3T0 TCGA-EL-A3T9 
       83.57       139.00        57.63        52.50       142.52         5.72 
TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       66.90        51.78        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZS TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K4 TCGA-EM-A22P TCGA-EM-A2CR 
        7.07        34.72        61.02        53.36        41.29        13.64 
TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FO 
       17.46        14.60        37.25        16.18        14.50        26.37 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A39S TCGA-ET-A3BU TCGA-ET-A3DO TCGA-ET-A3DQ 
       56.58        60.20        55.10        77.82       116.78        84.85 
TCGA-ET-A3DR TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       80.58        62.83        46.26        37.48        33.17        73.74 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FY-A3I4 TCGA-FY-A3I5 
      112.80        85.15         4.11        22.03        17.82         7.82 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A40K TCGA-GE-A2C6 TCGA-H2-A26U 
       13.91        16.27        23.31        15.16        12.53        17.00 
TCGA-IM-A3U2 TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       18.51        25.64        11.24        24.69        22.29         2.47 
TCGA-L6-A4EU 
        9.50 

$subtype2
TCGA-BJ-A45K TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-FK-A3SD TCGA-MK-A84Z 
       23.18        24.76        57.11        33.50         1.05        23.93 
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       24.79        13.78        49.78        11.57        16.73        25.48 
TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V 
       51.39        20.58         4.83        44.35        21.04        32.45 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C 
       18.38        16.57        20.48        12.82        13.94         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 
       10.88         3.45        23.84        12.43        37.64        18.84 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP 
      169.32        18.58         8.71        44.98        17.59        30.58 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UN TCGA-DJ-A3UP TCGA-DJ-A3UR 
       34.36        43.96        35.18        32.42        16.41        36.33 
TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR 
       36.33        40.96        35.67        23.44        27.62        34.78 
TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T2 
       54.90        47.21        64.87        50.20        49.32        32.48 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 
       89.56        91.17        60.16        57.47        30.51        44.15 
TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       43.59        23.90        48.49        18.05        19.79        19.46 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       57.01        54.08        14.50        15.75        10.45        10.65 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2P2 
        2.99        12.30        48.46        22.16        40.34        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FN TCGA-EM-A3FP 
       22.52        30.94        14.14         8.35        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        15.06        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A4FH TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25P TCGA-ET-A2N3 
       38.86        29.33        60.49        13.68        18.38        83.34 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV 
       80.88        33.24       123.32        94.59        66.84       166.62 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3S3 TCGA-FY-A2QD TCGA-FY-A3NM 
       43.99        31.40        33.63        71.08         1.25        29.10 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B0 TCGA-H2-A2K9 
       16.14        16.57        21.63        17.06        13.81        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-KS-A41I TCGA-QD-A8IV 
       12.46        31.10        43.17        31.82        15.98        12.89 

$subtype3
TCGA-DJ-A2PR TCGA-E3-A3E5 TCGA-EM-A3AQ TCGA-BJ-A0Z3 TCGA-BJ-A0ZB TCGA-BJ-A0ZH 
       27.45        39.95        29.72        16.34         4.01        15.12 
TCGA-BJ-A28R TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0Y2 
       42.15        16.01        18.64        12.79        12.46        21.63 
TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QH 
       50.17        27.32        56.19         8.32        30.61        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       14.96        42.58        10.09        24.82        22.92        18.97 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       21.53        92.55        66.38        80.52        63.19        52.44 
TCGA-E8-A417 TCGA-E8-A419 TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3D6 TCGA-EL-A3GV 
       30.84        25.45       155.54       158.83       108.36        50.37 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3MW 
      147.75       101.13       139.99        43.36        49.71       108.66 
TCGA-EL-A3N2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3ZL TCGA-EL-A3ZQ 
       29.65        98.24        41.29       107.47        62.30        61.22 
TCGA-EL-A3ZT TCGA-EM-A1CS TCGA-EM-A1CU TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       59.44        26.86        20.91        19.73        33.96        17.59 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FK TCGA-EM-A3O7 TCGA-ET-A25G 
       15.68        33.07        44.52        23.77         7.33        81.93 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX 
       77.56        70.42        63.39        65.29        63.45        88.41 
TCGA-ET-A2MZ TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       37.25       107.41        84.89       100.57        95.34        94.13 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW TCGA-ET-A3BX 
       98.20        28.24        76.64         5.79        46.65        52.47 
TCGA-ET-A3DT TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       43.73        44.38        40.21        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A 
       24.69        68.22       117.40        66.77        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 
      106.36        85.68        78.77        20.42        19.56        15.68 
TCGA-FY-A3RA TCGA-FY-A40N TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       18.08        19.04        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A420 TCGA-J8-A3O1 TCGA-KS-A41F TCGA-KS-A41J TCGA-E8-A418 
       47.41         8.22        27.19       143.57        15.68         3.02 

$subtype4
TCGA-BJ-A290 TCGA-DE-A0XZ TCGA-DJ-A3VI TCGA-EL-A3H8 TCGA-ET-A3BO TCGA-FY-A76V 
       30.21        35.84         3.12       150.48        50.40         1.68 
TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       17.23         2.60        21.83        28.44        15.45        21.63 
TCGA-BJ-A4O9 TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A4MA TCGA-DE-A4MC 
       23.47        11.38        10.68        15.02        30.12        30.02 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PU 
       14.70        14.27         7.99        35.41        26.20        33.96 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.85        28.96         8.78         8.42        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UO 
       36.46        35.11        33.53        39.95        36.92        31.46 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4V2 
       20.22        30.61        30.87        30.12        33.04         3.12 
TCGA-DJ-A4V5 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       35.38        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CU TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3TB TCGA-EL-A4JX TCGA-EL-A4K0 
      157.15       129.57       132.07        82.82        45.96        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A22I 
       34.39        41.13        47.84        24.30        27.06        14.73 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A3FJ TCGA-EM-A3FM 
       14.53        44.19        27.65        13.15        27.95        21.01 
TCGA-EM-A3FO TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN 
       17.49        29.95        12.79        84.59         5.33        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       22.45        21.53        24.46        58.75        52.60        54.35 
TCGA-ET-A39J TCGA-ET-A3BP TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3YR 
      106.09        79.10         0.92        48.10       116.09        17.36 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-IM-A3U3 TCGA-IM-A41Y 
       23.87        22.49        14.04        21.60        16.90        21.83 
TCGA-J8-A3YE TCGA-J8-A3YH TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       27.85         5.75        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 
       87.39        35.28        33.24        33.40        40.37        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45        30.21 

subtype1 subtype2 subtype3 subtype4 
    2.33     1.05     3.02     0.92 
subtype1 subtype2 subtype3 subtype4 
  178.29   169.32   158.83   157.15 
subtype1 subtype2 subtype3 subtype4 
  31.300   24.345   42.545   30.135 
[1] "2.3 - 178.3 (31.3)" "1.1 - 169.3 (24.3)" "3.0 - 158.8 (42.5)"
[4] "0.9 - 157.2 (30.1)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      70        4        38        1        18         2
  subtype2      71       26        22        1         3         2
  subtype3      72       11        13        0        10         1
  subtype4      54        8        31        0        11         1
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         70       71       72       54
  STAGE II         4       26       11        8
  STAGE III       38       22       13       31
  STAGE IV         1        1        0        0
  STAGE IVA       18        3       10       11
  STAGE IVC        2        2        1        1
[1] 6 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 39 28 51 14
  subtype2 38 51 36  1
  subtype3 26 44 33  5
  subtype4 33 33 36  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       39       38       26       33
  T2       28       51       44       33
  T3       51       36       33       36
  T4       14        1        5        2
[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"
D9V5, binary
          cls
clus        0  1
  subtype1 49 79
  subtype2 83 19
  subtype3 43 54
  subtype4 38 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49   79
  subtype2   83   19
  subtype3   43   54
  subtype4   38   60
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       49       83       43       38
  1       79       19       54       60
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 91  2
  subtype2 55  3
  subtype3 48  3
  subtype4 69  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91    2
  subtype2   55    3
  subtype3   48    3
  subtype4   69    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       91       55       48       69
  1        2        3        3        1
[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"
D9V7, binary
          cls
clus        0  1
  subtype1 99 34
  subtype2 87 39
  subtype3 80 28
  subtype4 79 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   99   34
  subtype2   87   39
  subtype3   80   28
  subtype4   79   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       99       87       80       79
  MALE         34       39       28       26
[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"
D9V8, binary
          cls
clus        0  1
  subtype1 50 77
  subtype2 46 75
  subtype3 41 66
  subtype4 35 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   77
  subtype2   46   75
  subtype3   41   66
  subtype4   35   66
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        50       46       41       35
  YES       77       75       66       66
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                           105
  subtype2              1                                            54
  subtype3              1                                            93
  subtype4              3                                            89
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      6
  subtype2                                                                     71
  subtype3                                                                      8
  subtype4                                                                      7
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  20
  subtype2                                                                   0
  subtype3                                                                   6
  subtype4                                                                   6
D9V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               105
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          20
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                54
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       71
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                93
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
                                                                        clus
vv                                                                       subtype4
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                89
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
[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"
D9V10, binary
          cls
clus         0   1
  subtype1 113   3
  subtype2 101   7
  subtype3  89   6
  subtype4  94   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    3
  subtype2  101    7
  subtype3   89    6
  subtype4   94    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       113      101       89       94
  YES        3        7        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           46                      12   68                   1
  subtype2           21                       0   98                   0
  subtype3           26                       3   77                   0
  subtype4           32                       2   69                   0
D9V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  46       21       26       32
  MODERATE/ADVANCED (T4A)       12        0        3        2
  NONE                          68       98       77       69
  VERY ADVANCED (T4B)            1        0        0        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 96 20  1  7
  subtype2 96  9  0  8
  subtype3 85  8  2  9
  subtype4 83 12  1  5
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       96       96       85       83
  R1       20        9        8       12
  R2        1        0        2        1
  RX        7        8        9        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"
D9V13, continuous
D9V14, binary
          cls
clus        0  1
  subtype1 62 70
  subtype2 59 64
  subtype3 41 64
  subtype4 53 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   70
  subtype2   59   64
  subtype3   41   64
  subtype4   53   51
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       62       59       41       53
  UNIFOCAL         70       64       64       51
[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"
D9V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    19                         4
  subtype2                                0     7                        10
  subtype3                                0     8                         4
  subtype4                                1    15                         8
          vv
clus       WHITE
  subtype1    99
  subtype2    69
  subtype3    81
  subtype4    64
D9V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                  19        7        8       15
  BLACK OR AFRICAN AMERICAN               4       10        4        8
  WHITE                                  99       69       81       64
[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"
D9V17, binary
          cls
clus         0   1
  subtype1   9 111
  subtype2   7  79
  subtype3  11  82
  subtype4   8  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  111
  subtype2    7   79
  subtype3   11   82
  subtype4    8   71
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            9        7       11        8
  NOT HISPANIC OR LATINO      111       79       82       71
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 154  10
  subtype2 117   5
  subtype3 184   1
subtype1 subtype2 subtype3 
     164      122      185 
subtype1 subtype2 subtype3 
      10        5        1 
$subtype1
TCGA-BJ-A291 TCGA-DJ-A13L TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-EL-A3CR 
       22.88         9.96        23.44        59.57        42.54         7.66 
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ TCGA-EL-A3MY TCGA-EL-A3N3 
       45.53         4.18       139.86        50.24        17.52       178.29 
TCGA-ET-A3BV TCGA-J8-A4HW TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T 
       75.42         2.60         4.24         4.01        41.52        35.54 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT 
       11.31        30.97        11.08        18.97        36.39        23.31 
TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 
       21.01        28.44        15.45        19.43        12.30        11.38 
TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD 
       12.66        18.54        11.57         2.76        38.17        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PS 
      135.91        42.51         6.02        47.41        17.56        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
       38.83        31.99         8.78         8.42        37.74        40.24 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ 
       36.46        39.09        35.90        33.53        31.04        19.56 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       11.34        35.87        40.96        36.99        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       20.48        40.70         9.60        36.43        30.12        33.04 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E8-A242 
       27.06        26.93        35.54        15.81         2.33        31.23 
TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       35.67        11.70        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       31.30        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CT TCGA-EL-A3CU 
       31.00        30.15        26.73        97.74        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GU 
       37.94        57.01        98.53        49.51       115.10       136.01 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3T0 TCGA-EL-A3T9 
       83.57       139.00        57.63        52.50       142.52         5.72 
TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       66.90        51.78        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZS TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 
        7.07        34.72        61.02        31.04        34.39        53.36 
TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR 
       57.01        41.29        13.15        17.46        14.60        37.25 
TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M 
       14.50         5.33        26.37        81.93        56.58        60.20 
TCGA-ET-A25R TCGA-ET-A2N0 TCGA-ET-A39M TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN 
       63.45        52.60        84.89        95.34        55.10        28.24 
TCGA-ET-A3BX TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q 
       52.47        84.85        80.58        43.73        62.83        46.26 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE 
       37.48        33.17        73.74       112.80        85.15        22.03 
TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY 
       48.10        17.82        13.91        16.27        15.68        23.31 
TCGA-FY-A3YR TCGA-FY-A40L TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 
       17.36        23.87        14.04        12.53        17.00        18.51 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       25.64        11.24        31.82        24.69        22.29         2.47 
TCGA-KS-A4IC TCGA-L6-A4EU 
       35.28         9.50 

$subtype2
TCGA-BJ-A45K TCGA-DJ-A3VK TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-FK-A3SD TCGA-FY-A76V 
       23.18        24.76        57.11        33.50         1.05         1.68 
TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       23.93        24.79        13.78        49.78        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
       25.48        51.39        20.58         4.83        44.35        21.04 
TCGA-BJ-A28V TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 
       32.45        18.38        16.57        20.48        12.82        13.94 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-CE-A484 TCGA-DE-A2OL 
        7.99        10.88         3.45        23.84        12.43        37.64 
TCGA-DE-A4M9 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP 
       18.84        18.58         8.71        44.98        17.59        30.58 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3V3 
       34.36        43.96        35.18        16.41        36.33        30.61 
TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-EL-A3GO 
       35.67        27.62        34.78        54.90        47.21        64.87 
TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV 
       50.20        49.32        32.48        91.17        60.16        57.47 
TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA 
       30.51        44.15        43.59        23.90        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       19.46        54.08        14.50        15.75        10.45        10.65 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        13.64        48.46        22.16        40.34 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FN 
       17.29        22.52        30.94        14.14         8.35        12.07 
TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       17.39        15.02        15.06        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A4FH TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 
       38.66        38.86        29.33        21.53        60.49        13.68 
TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N 
       18.38        54.35        83.34        80.88        33.24       123.32 
TCGA-ET-A3BW TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 
       46.65        66.84       166.62        43.99        31.40        33.63 
TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 
        1.25         7.82        29.10        16.14        16.57        21.63 
TCGA-FY-A3WA TCGA-FY-A4B0 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
       17.06        13.81        21.67        12.46        31.10        43.17 
TCGA-KS-A41I TCGA-QD-A8IV 
       15.98        12.89 

$subtype3
TCGA-BJ-A290 TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3VI TCGA-E3-A3E5 TCGA-EL-A3H8 
       30.21        35.84        27.45         3.12        39.95       150.48 
TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-J8-A3NZ TCGA-L6-A4ET TCGA-BJ-A0Z3 TCGA-BJ-A0ZH 
       29.72        50.40        17.23        21.83        16.34        15.12 
TCGA-BJ-A28R TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A3MD 
       42.15        16.01        18.64        21.63        23.47        12.79 
TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       12.46        10.68        15.02        21.63        50.17        27.32 
TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T 
       30.12        30.02        14.70        14.27       169.32        56.19 
TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PO 
        8.32        30.61        14.96        42.58        10.09         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       35.41        33.96        34.85        28.96        33.93        37.48 
TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR 
       35.11        39.95        36.92        32.42        31.46        36.33 
TCGA-DJ-A3V2 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VL TCGA-DJ-A4UL 
       20.22        24.82        22.92        18.97        23.44        30.87 
TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 
        3.12        35.38        21.53        92.55        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL 
       63.19        52.44        30.84        25.45        33.50        31.66 
TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3D6 TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      155.54       158.83       108.36        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T1 
      139.99        43.36        49.71       108.66        29.65       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG 
      132.07        98.24        41.29       107.47        82.82        89.56 
TCGA-EL-A3ZL TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 
       62.30        61.22        59.44        45.96        41.13        47.84 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I 
       24.30        27.06        26.86        20.91        48.49        14.73 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       14.53        44.19        27.65        19.73        33.96        17.59 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       15.68        33.07        44.52        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF 
       17.49        16.18         7.33        29.95        12.79        84.59 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N 
       26.37        22.45        24.46        77.56        70.42        63.39 
TCGA-ET-A25O TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A39J TCGA-ET-A39K 
       65.29        88.41        58.75        37.25       106.09       107.41 
TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
      100.57        94.13        98.20        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 
       77.82       116.78        94.59        44.38        40.21        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       39.95        81.83       106.36        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3RA 
        4.11         0.92       116.09        20.42        19.56        18.08 
TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 
       15.16        22.49        19.04        21.60        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        16.90        21.83         8.22 
TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 
       27.19        27.85         5.75       143.57        15.68        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4ID TCGA-L6-A4EP 
       43.69        18.64        32.45        87.39        33.24        33.40 
TCGA-L6-A4EQ TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-E8-A418 
       40.37        36.10        32.45        30.21         3.02 

subtype1 subtype2 subtype3 
    2.33     1.05     0.92 
subtype1 subtype2 subtype3 
  178.29   166.62   169.32 
subtype1 subtype2 subtype3 
  31.415   22.850   33.240 
[1] "2.3 - 178.3 (31.4)" "1.1 - 166.6 (22.9)" "0.9 - 169.3 (33.2)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      77        4        58        1        22         2
  subtype2      67       27        21        1         3         2
  subtype3     123       18        25        0        17         2
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         77       67      123
  STAGE II         4       27       18
  STAGE III       58       21       25
  STAGE IV         1        1        0
  STAGE IVA       22        3       17
  STAGE IVC        2        2        2
[1] 6 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 47 33 67 15
  subtype2 34 53 34  1
  subtype3 55 70 55  6
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       47       34       55
  T2       33       53       70
  T3       67       34       55
  T4       15        1        6
[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"
D10V5, binary
          cls
clus        0  1
  subtype1 58 97
  subtype2 79 18
  subtype3 76 97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   97
  subtype2   79   18
  subtype3   76   97
   clus
vv  subtype1 subtype2 subtype3
  0       58       79       76
  1       97       18       97
[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"
D10V6, binary
          cls
clus         0   1
  subtype1 113   2
  subtype2  49   3
  subtype3 101   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    2
  subtype2   49    3
  subtype3  101    4
   clus
vv  subtype1 subtype2 subtype3
  0      113       49      101
  1        2        3        4
[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 124  40
  subtype2  83  39
  subtype3 138  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  124   40
  subtype2   83   39
  subtype3  138   48
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      124       83      138
  MALE         40       39       48
[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, binary
          cls
clus         0   1
  subtype1  60  97
  subtype2  40  75
  subtype3  72 112
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   97
  subtype2   40   75
  subtype3   72  112
     clus
vv    subtype1 subtype2 subtype3
  NO        60       40       72
  YES       97       75      112
[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"
          vv
clus       OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           129
  subtype2              2                                            51
  subtype3              2                                           161
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     69
  subtype3                                                                     16
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   0
  subtype3                                                                   7
D10V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER, SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               129
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
                                                                        clus
vv                                                                       subtype2
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                51
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       69
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER, SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               161
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       16
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           7
[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"
D10V10, binary
          cls
clus         0   1
  subtype1 137   6
  subtype2 100   5
  subtype3 160   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  137    6
  subtype2  100    5
  subtype3  160    5
     clus
vv    subtype1 subtype2 subtype3
  NO       137      100      160
  YES        6        5        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           63                      14   80                   1
  subtype2           16                       0   99                   0
  subtype3           46                       3  133                   0
D10V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  63       16       46
  MODERATE/ADVANCED (T4A)       14        0        3
  NONE                          80       99      133
  VERY ADVANCED (T4B)            1        0        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        R0  R1  R2  RX
  subtype1 116  25   2  11
  subtype2  93   9   0   8
  subtype3 151  15   2  10
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      116       93      151
  R1       25        9       15
  R2        2        0        2
  RX       11        8       10
[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"
D10V13, continuous
D10V14, binary
          cls
clus        0  1
  subtype1 71 92
  subtype2 58 61
  subtype3 86 96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71   92
  subtype2   58   61
  subtype3   86   96
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       71       58       86
  UNIFOCAL         92       61       96
[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"
D10V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    24                         5
  subtype2                                0     8                         9
  subtype3                                1    17                        12
          vv
clus       WHITE
  subtype1   123
  subtype2    65
  subtype3   125
D10V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  24        8       17
  BLACK OR AFRICAN AMERICAN               5        9       12
  WHITE                                 123       65      125
[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"
D10V17, binary
          cls
clus         0   1
  subtype1  11 135
  subtype2   7  76
  subtype3  17 132
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  135
  subtype2    7   76
  subtype3   17  132
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           11        7       17
  NOT HISPANIC OR LATINO      135       76      132
[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"
