[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/19775590/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/20140899/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 
 56 360  83 
  1   2   3 
 56 360  83 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
277 156  70 
  1   2   3 
277 156  70 
[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 
168 157  59 117 
  1   2   3   4 
168 157  59 117 
[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 
182 153 167 
  1   2   3 
182 153 167 
[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 
161 165 146 
  1   2   3 
161 165 146 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
165 128 179 
  1   2   3 
165 128 179 
[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=434,	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  52   3
  subtype2 347  12
  subtype3  82   1
subtype1 subtype2 subtype3 
      55      359       83 
subtype1 subtype2 subtype3 
       3       12        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0ZB TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A290 
        4.24        24.79         4.01        20.58        44.35        30.21 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DE-A4MB TCGA-DE-A4MD TCGA-DJ-A1QE 
       16.57        20.48        21.01        11.57        25.12       135.91 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP 
       33.96        31.99        34.36         2.33        30.61        49.51 
TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A3ZO 
      136.01        83.57        57.63         5.72        36.03        47.38 
TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YC 
       45.96        41.13        47.84        23.90        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI 
       57.01        54.08        10.65         6.05        32.32        22.52 
TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SU TCGA-EM-A3SY TCGA-ET-A25L TCGA-ET-A2MZ 
       14.50         9.24        29.95        13.51        56.58        37.25 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BV TCGA-ET-A40S TCGA-FE-A231 TCGA-FE-A239 
       84.89       123.32        75.42        40.21        31.59        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-J8-A3YG 
        7.82         0.99        17.06        48.92        18.51        22.29 
TCGA-L6-A4EU 
        9.50 

$subtype2
TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       13.78        16.34        41.33        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       25.48        42.08        41.52         4.83        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A291 
       35.54        32.45        11.31        30.97        11.08        22.88 
TCGA-BJ-A2N7 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       18.38        18.97        16.01        13.94        36.39        18.64 
TCGA-BJ-A45C TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
        7.99        23.84        28.44        15.45        21.63        23.18 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       19.43        23.47        12.66        12.30        12.79        12.46 
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-A2OL TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K 
       37.64        18.84        30.12        30.02        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76         9.96        38.17       169.32        18.58         8.71 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QF 
       23.38        43.17        52.37         8.32        11.01        30.61 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59         6.02        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PW 
        7.82        30.58        35.41        27.45        38.83        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
       28.96         8.78         8.42         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM 
       37.48        36.46        39.09        35.90        15.88        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       36.43        17.23        30.87        21.34        33.04        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
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-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
        0.72         0.26         3.02        25.45         0.16        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        33.50         0.39         0.39        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D6 
       37.94        57.01       106.62         4.18        79.50       108.36 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
       50.24       115.10        65.39        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
      139.99        49.32        33.50        43.36        49.71       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      150.48       108.66        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      142.52       129.57       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        89.56        78.97        51.78        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4K0 
       65.49        61.22         7.07        59.44        34.72        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       34.39        30.51        53.36        43.59        24.30        27.06 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A22I 
       18.18        20.91        48.49        18.05        19.79        14.73 
TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       14.50        44.19        14.24        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR 
       15.68        14.14        33.07        13.38        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP 
       27.95        23.77        47.38        21.01        12.07        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        15.06         7.33         0.49        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       38.66        38.86        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       26.37        22.45        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R 
       77.56        70.42        60.20        63.39        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 
       88.41        58.75        52.60        54.35        83.34        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       33.24       106.09       107.41       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        50.40        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       84.85        80.58        43.73        62.83       166.62        24.72 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       46.26        44.38        33.17        31.40        73.74        71.44 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 
       79.69        24.69        68.22       117.40        66.77        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83       106.36        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
        1.05        13.28        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       17.82        19.56        13.91        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
        0.30        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.35         1.68        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB 
       20.05        18.61        47.41        21.83         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A42S 
       17.23        27.19        11.24        27.85        24.69         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        2.60         0.20       143.57        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       43.69        18.64        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83        36.10        32.45        30.21 

$subtype3
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A3PT 
       49.78        14.73        15.12        51.39         7.04        23.31 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DE-A4M8 
       10.88         3.45        12.43        35.84        15.85        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QN TCGA-DJ-A2PS 
       48.79        56.19        44.98        42.51        42.58        26.20 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       37.74        35.11        33.53        35.18        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VK TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       31.46        16.41        24.76        27.62        34.78        47.21 
TCGA-E3-A3E5 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       39.95         0.23        31.66       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       57.11        64.87        50.20        32.48        62.30        60.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       57.47        37.94        44.15        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OX TCGA-EM-A3AP TCGA-EM-A3FO 
       14.53        41.29        47.57        19.73         8.35        17.49 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25O 
       29.85        12.79        26.37        21.53        60.49        65.29 
TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T 
        2.66       108.46        79.10        66.84        43.99        37.48 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SG TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A4B4 
      112.80        85.15         0.92        16.27         0.76        21.60 
TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH 
       12.53        16.90        31.10        43.17        31.82         5.75 
TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       15.98        32.45        84.72        23.93        12.89 

subtype1 subtype2 subtype3 
    0.99     0.16     0.23 
subtype1 subtype2 subtype3 
  136.01   169.32   139.86 
subtype1 subtype2 subtype3 
   30.61    30.02    32.45 
[1] "1.0 - 136.0 (30.6)" "0.2 - 169.3 (30.0)" "0.2 - 139.9 (32.5)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      14       14        16        1        10         1
  subtype2     219       31        78        0        26         4
  subtype3      49        5        17        1        10         1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         14      219       49
  STAGE II        14       31        5
  STAGE III       16       78       17
  STAGE IV         1        0        1
  STAGE IVA       10       26       10
  STAGE IVC        1        4        1
[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   8  21  22   5
  subtype2 109 115 119  15
  subtype3  25  29  26   3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8      109       25
  T2       21      115       29
  T3       22      119       26
  T4        5       15        3
[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  24  23
  subtype2 162 162
  subtype3  39  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   23
  subtype2  162  162
  subtype3   39   39
   clus
vv  subtype1 subtype2 subtype3
  0       24      162       39
  1       23      162       39
[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  24   1
  subtype2 209   6
  subtype3  45   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2  209    6
  subtype3   45    2
   clus
vv  subtype1 subtype2 subtype3
  0       24      209       45
  1        1        6        2
[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  37  19
  subtype2 267  93
  subtype3  61  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   19
  subtype2  267   93
  subtype3   61   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37      267       61
  MALE         19       93       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1  21  30
  subtype2 142 204
  subtype3  22  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   30
  subtype2  142  204
  subtype3   22   56
     clus
vv    subtype1 subtype2 subtype3
  NO        21      142       22
  YES       30      204       56
[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              0                                            40
  subtype2              7                                           257
  subtype3              1                                            58
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     12
  subtype2                                                                     67
  subtype3                                                                     21
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   4
  subtype2                                                                  29
  subtype3                                                                   3
D1V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                40
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       12
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               257
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       67
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          29
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                58
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       21
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
[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  49   3
  subtype2 299  12
  subtype3  72   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    3
  subtype2  299   12
  subtype3   72    2
     clus
vv    subtype1 subtype2 subtype3
  NO        49      299       72
  YES        3       12        2
[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           15                       4   34                   1
  subtype2           99                      13  237                   0
  subtype3           18                       1   59                   0
D1V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  15       99       18
  MODERATE/ADVANCED (T4A)        4       13        1
  NONE                          34      237       59
  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  38   9   0   6
  subtype2 284  35   3  16
  subtype3  61   7   1   8
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       38      284       61
  R1        9       35        7
  R2        0        3        1
  RX        6       16        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
          cls
clus         0   1
  subtype1  21  35
  subtype2 159 193
  subtype3  45  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   35
  subtype2  159  193
  subtype3   45   36
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       21      159       45
  UNIFOCAL         35      193       36
[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     1                         4
  subtype2                                1    41                        18
  subtype3                                0    10                         5
          vv
clus       WHITE
  subtype1    39
  subtype2   237
  subtype3    52
D1V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1       41       10
  BLACK OR AFRICAN AMERICAN               4       18        5
  WHITE                                  39      237       52
[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   4  37
  subtype2  27 265
  subtype3   7  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   37
  subtype2   27  265
  subtype3    7   57
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4       27        7
  NOT HISPANIC OR LATINO       37      265       57
[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 270   7
  subtype2 149   5
  subtype3  66   4
subtype1 subtype2 subtype3 
     277      154       70 
subtype1 subtype2 subtype3 
       7        5        4 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z 
        4.24        14.73        41.33         4.01        15.12        41.52 
TCGA-BJ-A28R TCGA-BJ-A290 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45H 
       42.15        30.21        18.97        16.01        18.64        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.66        12.79 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       10.68        15.02        35.84        21.63        50.17        15.85 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X 
        2.76       169.32        56.19        23.38        43.17         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QN 
       11.01       135.91        30.61        42.51        14.96        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       47.41        17.56        10.09         7.82        35.41        27.45 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2QA TCGA-DJ-A2QC 
       33.93        36.46        35.11        39.09        33.53        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UU 
       36.92        31.04        32.42        31.46        19.56        17.69 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VI 
       21.27        20.48        24.82        22.92        18.97         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       36.43        30.87        33.04        26.93         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 
       35.38        54.90        21.53        92.55        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 
       63.19        52.44        39.95        31.27         0.26         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       30.61         0.16        14.96         7.69        33.50         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       31.66        26.73       155.54       158.83         7.66        45.53 
TCGA-EL-A3CU TCGA-EL-A3CX TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP 
      157.15       106.62       139.86        98.53       108.36        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      101.13       139.99        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZK 
      129.57       132.07        41.29       107.47        82.82        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZT 
       62.30        36.03        47.38        65.49        61.22        59.44 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4K7 
       34.72        37.94        31.04        34.39        53.36        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU 
       20.91        48.49        14.73        44.19        27.65        13.15 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AN 
       19.73        33.96        17.59        14.60        15.68        33.07 
TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO 
       13.38        29.72        27.95        23.77        21.01        17.49 
TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM 
        7.33        29.95        29.85        12.79        84.59         5.33 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K 
       26.37        22.45        24.46        81.93        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX 
       56.58        60.20        63.39        65.29        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K 
       58.75        37.25        52.60         2.66       106.09       107.41 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
      100.57        95.34        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R 
       52.47        94.59        80.58        24.72        46.26        44.38 
TCGA-ET-A40T TCGA-FE-A22Z TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       37.48        73.74        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PA TCGA-FE-A3PB 
      117.40        66.77       112.80        39.95       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA 
       48.10       116.09        20.42        19.56        15.68        18.08 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI 
       17.36        15.16         6.58         1.35        21.60         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       20.05        18.61        47.41        18.51        16.90        21.83 
TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG 
        8.22        17.23        27.19        11.24        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
        5.75         2.47         2.60         0.20       143.57        15.68 
TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       26.70        18.64        32.45        87.39        84.72        35.28 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 
       30.21 

$subtype2
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-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-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
       32.45        22.88        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         7.99        10.88         3.45        23.84 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M 
       23.18        12.46        12.43        37.64        18.84        48.79 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        52.37        44.98        17.59         6.02        30.58 
TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UR 
       26.20        34.36         6.77        35.18        16.41        36.33 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VK 
       36.33        11.34        35.87        40.96        35.67        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A413 TCGA-E8-A415 
       17.23        27.62        34.78        47.21        29.98        31.04 
TCGA-E8-A416 TCGA-E8-A434 TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO 
        0.72         0.23        79.50        69.57        57.11        64.87 
TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3TA 
       50.20        49.32        33.50       142.52        32.48        66.90 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       89.56        78.97        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-A3O9 
       12.07        17.39        15.02        15.06         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
       13.91        38.66        38.86        13.51        29.33        21.34 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N1 
       21.53        60.49        13.68        81.70        18.38        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS 
       83.34        80.88        33.24       108.46       123.32        66.84 
TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD 
      166.62        43.99        31.40        33.63         1.05         1.25 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 
       17.82         7.82         0.99        16.14        16.27        16.57 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A76V TCGA-H2-A2K9 
        0.76        17.06        22.49        19.04         1.68        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-KS-A41I 
       12.46        31.10        43.17        31.82        27.85        15.98 
TCGA-KS-A41L TCGA-KS-A4I3 TCGA-MK-A84Z TCGA-QD-A8IV 
      113.85        43.69        23.93        12.89 

$subtype3
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-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
       36.39        21.01        12.30        11.38        12.66        18.54 
TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
        9.96        38.17        18.58        38.83        37.74        40.24 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A3US TCGA-DJ-A3UW TCGA-DJ-A3VD TCGA-DJ-A3VF 
       37.48        35.90        32.81        59.57        21.01         7.76 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4V0 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA 
       21.34        27.06        35.54         2.33        31.23        35.67 
TCGA-E8-A2JQ TCGA-E8-A414 TCGA-E8-A419 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CT 
       11.70        31.50        25.45         0.39        97.74        60.95 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3N3 TCGA-EL-A3T6 TCGA-EL-A3T9 
       37.94        57.01         4.18       147.42        98.24         5.72 
TCGA-EL-A3ZS TCGA-EL-A4JX TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CP TCGA-EM-A2P1 
        7.07        45.96        14.53        41.29         2.99        17.46 
TCGA-EM-A3AJ TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FO TCGA-ET-A39M TCGA-ET-A39R 
       30.94        16.18        14.50        26.37        84.89        94.13 
TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40S 
       75.42       116.78        84.85        43.73        62.83        40.21 
TCGA-ET-A4KN TCGA-FE-A230 TCGA-FE-A23A TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 
       33.17        71.44        81.83        13.91         0.30        12.53 
TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A4EB TCGA-KS-A4ID 
       17.00        48.92        25.64        33.24 

subtype1 subtype2 subtype3 
    0.16     0.23     0.30 
subtype1 subtype2 subtype3 
  169.32   166.62   147.42 
subtype1 subtype2 subtype3 
  31.990   23.410   31.365 
[1] "0.2 - 169.3 (32.0)" "0.2 - 166.6 (23.4)" "0.3 - 147.4 (31.4)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1     148       19        68        0        37         4
  subtype2      90       30        28        1         4         2
  subtype3      46        2        15        1         6         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        148       90       46
  STAGE II        19       30        2
  STAGE III       68       28       15
  STAGE IV         0        1        1
  STAGE IVA       37        4        6
  STAGE IVC        4        2        0
[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  65  88 103  20
  subtype2  53  58  44   1
  subtype3  25  20  22   2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       65       53       25
  T2       88       58       20
  T3      103       44       22
  T4       20        1        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1  96 160
  subtype2 101  29
  subtype3  30  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96  160
  subtype2  101   29
  subtype3   30   37
   clus
vv  subtype1 subtype2 subtype3
  0       96      101       30
  1      160       29       37
[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"
D2V6, binary
          cls
clus         0   1
  subtype1 165   6
  subtype2  74   3
  subtype3  41   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  165    6
  subtype2   74    3
  subtype3   41    0
   clus
vv  subtype1 subtype2 subtype3
  0      165       74       41
  1        6        3        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus         0   1
  subtype1 204  73
  subtype2 112  44
  subtype3  52  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  204   73
  subtype2  112   44
  subtype3   52   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      204      112       52
  MALE         73       44       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus         0   1
  subtype1 102 168
  subtype2  57  86
  subtype3  27  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102  168
  subtype2   57   86
  subtype3   27   39
     clus
vv    subtype1 subtype2 subtype3
  NO       102       57       27
  YES      168       86       39
[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                                           226
  subtype2              2                                            75
  subtype3              2                                            56
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     18
  subtype2                                                                     79
  subtype3                                                                      5
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  29
  subtype2                                                                   0
  subtype3                                                                   7
D2V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               226
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       18
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          29
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                75
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       79
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                56
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        5
  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"
D2V10, binary
          cls
clus         0   1
  subtype1 239   8
  subtype2 125   6
  subtype3  59   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  239    8
  subtype2  125    6
  subtype3   59    3
     clus
vv    subtype1 subtype2 subtype3
  NO       239      125       59
  YES        8        6        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           93                      17  161                   0
  subtype2           25                       0  122                   0
  subtype3           15                       1   50                   1
D2V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  93       25       15
  MODERATE/ADVANCED (T4A)       17        0        1
  NONE                         161      122       50
  VERY ADVANCED (T4B)            0        0        1
[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 208  36   4  18
  subtype2 124   9   0   8
  subtype3  53   7   0   4
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      208      124       53
  R1       36        9        7
  R2        4        0        0
  RX       18        8        4
[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"
D2V13, continuous
D2V14, binary
          cls
clus         0   1
  subtype1 126 146
  subtype2  71  82
  subtype3  30  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  126  146
  subtype2   71   82
  subtype3   30   38
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL      126       71       30
  UNIFOCAL        146       82       38
[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"
D2V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    30                        17
  subtype2                                0    14                         9
  subtype3                                0     8                         1
          vv
clus       WHITE
  subtype1   191
  subtype2    86
  subtype3    53
D2V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  30       14        8
  BLACK OR AFRICAN AMERICAN              17        9        1
  WHITE                                 191       86       53
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
          cls
clus         0   1
  subtype1  24 208
  subtype2   7 100
  subtype3   7  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  208
  subtype2    7  100
  subtype3    7   53
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           24        7        7
  NOT HISPANIC OR LATINO      208      100       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"

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-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZG 
       24.79        13.78        49.78        16.34        11.57        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13W 
       42.08        51.39        20.58        15.85        48.79        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QM TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PV 
        8.32        30.61         6.02        10.09         7.82        31.99 
TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        8.42         6.77        36.46        35.11        35.90        33.53 
TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EL-A3CL TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       15.88        47.21        31.66       155.54        97.74       158.83 
TCGA-EL-A3CS TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3CZ 
       45.53       157.15        37.94        57.01         4.18        79.50 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EM-A1CW 
       69.57        57.11        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-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A192 TCGA-BJ-A28R 
       14.73        41.33         4.01        16.73        44.35        42.15 
TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-DE-A0Y2 TCGA-DJ-A13O 
       18.38        20.48        18.97        16.01        21.63        38.17 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QG TCGA-DJ-A2PP 
       18.58         8.71        11.01       135.91        44.98        30.58 
TCGA-DJ-A2PY TCGA-DJ-A2Q0 TCGA-DJ-A2Q8 TCGA-DJ-A2QB TCGA-DO-A1K0 TCGA-E3-A3E1 
        8.78        34.36        39.09        35.18        21.53        80.52 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA TCGA-EL-A3CM TCGA-EL-A3D6 TCGA-EL-A3GS 
       52.44        39.95        35.67        26.73       108.36        65.39 
TCGA-EL-A3GU TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
      136.01       101.13        49.71        83.57       139.00       108.66 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EM-A1CT TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       52.50       147.42        18.18        19.79        19.46        78.61 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A2CO TCGA-EM-A2OY TCGA-ET-A25G 
       14.73        14.50        44.19         6.05        32.32        81.93 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39T 
       56.58        60.20        65.29        58.75        52.60        98.20 
TCGA-ET-A3BT TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A231 TCGA-FE-A236 
       87.62       116.78        24.72        73.74        31.59        66.77 
TCGA-FE-A237 TCGA-FE-A23A TCGA-FY-A3BL TCGA-J8-A3NZ 
      112.80        81.83        20.42        17.23 

$subtype3
TCGA-BJ-A0ZA TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
       18.87        41.52         4.83        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A291 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-CE-A13K TCGA-CE-A27D 
       11.31        22.88         7.04        13.94        12.66        12.30 
TCGA-CE-A3MD TCGA-DE-A2OL TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DO-A1JZ 
       12.79        37.64        14.96        17.59        42.58        54.90 
TCGA-EL-A3CX TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 
      106.62        64.87       115.10       139.99        33.50        43.36 
TCGA-EL-A3H8 TCGA-EM-A1CV TCGA-EM-A22Q TCGA-EM-A2CL TCGA-EM-A2CP TCGA-EM-A2CR 
      150.48        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        13.38        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-A28Z TCGA-BJ-A290 TCGA-CE-A3ME TCGA-DJ-A13V TCGA-DJ-A1QO TCGA-DJ-A2PQ 
       11.08        30.21        12.46        43.17        47.41        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 
       27.45        26.20        33.96        34.85        37.74        33.93 
TCGA-DJ-A2Q5 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E8-A2JQ TCGA-EL-A3CR TCGA-EL-A3CT 
       37.48        92.55        66.38        11.70         7.66        60.95 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GX TCGA-EL-A3MX 
      139.86        98.53        49.51        50.24       147.75        57.63 
TCGA-EL-A3MY TCGA-EL-A3N2 TCGA-EM-A1CU TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A2P1 
       17.52        29.65        20.91        14.53        27.65        17.46 
TCGA-EM-A3FJ TCGA-EM-A3FO TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39P TCGA-ET-A3BN 
       27.95        17.49         2.66       106.09        95.34        28.24 
TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DS 
        5.79        77.82        75.42        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   147.42   166.62   147.75 
subtype1 subtype2 subtype3 subtype4 
  33.385   40.640   32.450   37.480 
[1] "1.2 - 158.8 (33.4)" "4.0 - 147.4 (40.6)" "3.0 - 166.6 (32.5)"
[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 32 30
  subtype2 25 39
  subtype3 20 21
  subtype4 15 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   30
  subtype2   25   39
  subtype3   20   21
  subtype4   15   35
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        32       25       20       15
  YES       30       39       21       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-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZG 
       24.79        13.78        49.78        18.87        11.57        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A28V TCGA-BJ-A2N9 TCGA-DE-A2OL 
       42.08        51.39        20.58        32.45        20.48        37.64 
TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A1QL TCGA-DJ-A2PO TCGA-DJ-A2Q2 TCGA-E3-A3DZ 
       48.79        52.37        17.59         7.82         6.77        47.21 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CW TCGA-EL-A3CZ TCGA-EL-A3D4 
       97.74       158.83       157.15        57.01        79.50        69.57 
TCGA-EL-A3D5 TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EM-A1CW TCGA-EM-A1YD 
       57.11        50.20        49.32        33.50        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-BJ-A0Z3 TCGA-DE-A3KN TCGA-DJ-A13O TCGA-DJ-A13X TCGA-DJ-A1QM TCGA-DJ-A2PN 
       16.34        15.85        38.17         8.32         6.02        10.09 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       35.41        26.20        31.99         8.42        36.46        35.11 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-EL-A3CL TCGA-EL-A3CV TCGA-EL-A3GQ 
       35.90        33.53        15.88        31.66        37.94        50.24 
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-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-CE-A3ME 
       14.73        41.33         4.01        30.21        16.01        12.46 
TCGA-DE-A0Y2 TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QO TCGA-DJ-A2PY TCGA-DJ-A2Q8 
       21.63        11.01       135.91        47.41         8.78        39.09 
TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GU 
       21.53        80.52        52.44       108.36        65.39       136.01 
TCGA-EL-A3GY TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EM-A22O 
      101.13        83.57       139.00       108.66        29.65        44.19 
TCGA-EM-A2P1 TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A230 
       17.46        81.93        56.58       116.78        24.72        71.44 
TCGA-FE-A234 TCGA-FE-A23A TCGA-J8-A3NZ 
       68.22        81.83        17.23 

$subtype4
TCGA-BJ-A0ZE TCGA-BJ-A28S TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2P4 
       16.73        21.04        11.31        11.08        22.88         7.04 
TCGA-BJ-A3F0 TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GO 
       13.94       155.54         7.66         4.18       139.86        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-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28T TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       41.52         4.83        35.54        12.66        12.30        12.79 
TCGA-DJ-A13V TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PR TCGA-DJ-A2PU 
       43.17        30.61        14.96        42.58        27.45        33.96 
TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 
       34.85        37.74        33.93        37.48        54.90        66.38 
TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-EL-A3CX TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR 
       35.67        11.70       106.62        98.53        49.51       115.10 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GZ TCGA-EL-A3H8 TCGA-EL-A3MX TCGA-EM-A1CU 
       50.37       147.75       139.99       150.48        57.63        20.91 
TCGA-EM-A1CV TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A3AO TCGA-EM-A3FO TCGA-ET-A2N4 
       48.49        14.53        27.65        13.38        17.49         2.66 
TCGA-ET-A39J TCGA-ET-A39M TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
      106.09        84.89        28.24        77.82        75.42        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-BJ-A28R TCGA-BJ-A2NA TCGA-E3-A3E5 TCGA-EL-A3CM TCGA-EL-A3CS TCGA-EL-A3CT 
       42.15        18.97        39.95        26.73        45.53        60.95 
TCGA-EL-A3H4 TCGA-EL-A3MY TCGA-EL-A3N3 
       49.71        17.52       147.42 

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   147.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   33.50    33.30    47.41    22.52    37.74    34.36    42.15 
[1] "1.2 - 166.6 (33.5)"  "6.0 - 95.3 (33.3)"   "4.0 - 139.0 (47.4)" 
[4] "3.0 - 155.5 (22.5)"  "2.7 - 150.5 (37.7)"  "6.0 - 112.8 (34.4)" 
[7] "17.5 - 147.4 (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 22 23
  subtype2 14 14
  subtype3 14 19
  subtype4 11 16
  subtype5 20 28
  subtype6  8 19
  subtype7  3  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   23
  subtype2   14   14
  subtype3   14   19
  subtype4   11   16
  subtype5   20   28
  subtype6    8   19
  subtype7    3    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        22       14       14       11       20        8        3
  YES       23       14       19       16       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 161   7
  subtype2 151   5
  subtype3  57   2
  subtype4 114   2
subtype1 subtype2 subtype3 subtype4 
     168      156       59      116 
subtype1 subtype2 subtype3 subtype4 
       7        5        2        2 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
        4.24        41.33         4.01        15.12        41.52        42.15 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A3ME 
       18.97        16.01        18.64        15.45        19.43        12.46 
TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MA TCGA-DE-A4MB 
       15.02        12.66        21.63        50.17        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A7U5 TCGA-DJ-A13U TCGA-DJ-A1QD 
       30.02        25.12        14.70         2.76        23.38        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PT 
      135.91        42.51        47.41        17.56        10.09        38.83 
TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3UQ 
       34.85         8.78         8.42        33.93        31.04        19.56 
TCGA-DJ-A3UY TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VB 
       35.87        36.99        19.20        23.21        21.27        22.92 
TCGA-DJ-A3VF TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4V2 TCGA-DJ-A4V4 
        7.76         3.12        36.43        33.04         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A3X7 
       35.38        21.53        80.52        52.44        31.23        31.27 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
        0.26         3.02        25.45         0.16        14.96         7.69 
TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
        0.39        26.73       155.54         7.66        45.53        60.95 
TCGA-EL-A3D6 TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3GY 
      108.36       115.10        65.39       136.01       147.75       101.13 
TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
       49.71       139.00       150.48        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZK 
      147.42       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        47.38        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-A2P0 TCGA-EM-A2P3 TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO 
       33.96        17.59        14.60        23.77        21.01        17.49 
TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ 
       29.95        12.79        84.59         5.33        26.37        22.45 
TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25R 
       81.93        77.56        56.58        60.20        63.39        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39T 
       88.41        58.75        52.60       100.57        95.34        98.20 
TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BX TCGA-ET-A3DO 
       28.24        87.62        77.82        75.42        52.47       116.78 
TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       24.72        46.26        33.17        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       79.69        24.69        68.22        66.77       112.80        39.95 
TCGA-FE-A23A TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R8 
       81.83        13.28        20.42        17.82        19.56        15.68 
TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A421 
       18.08        17.36         6.58         1.35        21.60        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YF TCGA-J8-A3YG 
        8.22        25.64        17.23        27.19        24.69        22.29 
TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N6 
        2.60        15.68        43.69        87.39         9.50        36.10 

$subtype2
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-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-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
       32.45        22.88        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         7.99        10.88         3.45        23.84 
TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R 
       23.18        12.43        37.64        18.84        48.79        18.58 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        52.37        44.98        17.59         6.02        30.58 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US 
       34.36         6.77        33.53        35.18        16.41        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VK TCGA-DJ-A3VL 
       36.33        40.96        42.54        35.67        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 
       27.62        34.78        35.54        47.21        31.04         0.72 
TCGA-E8-A434 TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO 
        0.23       106.62        79.50        69.57        57.11        64.87 
TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3ZH 
       50.20        49.32        33.50       142.52        32.48        78.97 
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-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR 
       17.29        22.52        30.94        14.14         8.35        37.25 
TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 
       47.38        12.07        17.39        15.02        15.06         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH 
        9.24        13.91        38.66        38.86        13.51        29.33 
TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P 
       21.34        21.53        60.49        13.68        81.70        18.38 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39S 
       83.34        80.88        33.24       108.46       123.32        55.10 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       84.85        80.58        66.84       166.62        43.99        31.40 
TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP 
       33.63         1.05         1.25         7.82         0.99        16.14 
TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N 
       16.27        16.57         0.76        17.06        22.49        19.04 
TCGA-FY-A76V TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
        1.68        21.67        12.46        31.10        43.17        31.82 
TCGA-J8-A3YE TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L TCGA-MK-A84Z TCGA-QD-A8IV 
       27.85         0.20        15.98       113.85        23.93        12.89 

$subtype3
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-CE-A27D TCGA-CE-A481 TCGA-DE-A4M8 TCGA-DJ-A13L 
       36.39        21.01        12.30        11.38        18.54         9.96 
TCGA-DJ-A13O TCGA-DJ-A2PX TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UW 
       38.17        28.96        37.74        40.24        35.90        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3VD TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DO-A2HM TCGA-E8-A2EA 
       11.34        21.01        21.34        27.06         2.33        35.67 
TCGA-E8-A2JQ TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CU 
       11.70        29.98        31.50         0.39        97.74       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3GP TCGA-EL-A3H3 TCGA-EL-A3H5 
       37.94        57.01         4.18        49.51        43.36        83.57 
TCGA-EL-A3TA TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JZ TCGA-EM-A22M TCGA-EM-A22P 
       66.90        65.49         7.07        37.94        14.53        41.29 
TCGA-EM-A2P1 TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FO TCGA-ET-A39R TCGA-ET-A3BO 
       17.46        16.18        14.50        26.37        94.13        50.40 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A3PB TCGA-FY-A3R6 
       43.73        62.83        44.38        40.21        85.15        13.91 
TCGA-FY-A3TY TCGA-GE-A2C6 TCGA-H2-A26U TCGA-J8-A3O2 TCGA-KS-A4ID 
        0.30        12.53        17.00        11.24        33.24 

$subtype4
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45H TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K 
       14.73        30.21        28.44        21.63        23.47        12.66 
TCGA-CE-A3MD TCGA-CE-A482 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P 
       12.79        10.68        35.84        15.85        14.27       169.32 
TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN 
       56.19        43.17         8.32        30.61        14.96        42.58 
TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV 
        7.82        35.41        27.45        26.20        33.96        31.99 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       37.48        36.46        35.11        15.88        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V9 
       31.46        36.33        17.69        20.22        30.61        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4UW TCGA-DO-A1JZ TCGA-E3-A3DY 
       24.82        18.97        30.87        26.93        54.90        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL 
       66.38        63.19        39.95        30.61        33.50        31.66 
TCGA-EL-A3CP TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GZ 
      158.83       139.86        98.53        50.24        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-A3AQ TCGA-EM-A3FJ TCGA-EM-A3O7 TCGA-EM-A3SX 
       33.07        13.38        29.72        27.95         7.33        29.85 
TCGA-EM-A4FV TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J 
       24.46        70.42        65.29        37.25         2.66       106.09 
TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW 
      107.41        84.89        79.10        76.64         5.79        46.65 
TCGA-ET-A3DP TCGA-ET-A40T TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       94.59        37.48       117.40       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K 
       71.08         4.11         0.92        48.10       116.09        15.16 
TCGA-H2-A3RI TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 
        2.99         5.75         2.47       143.57        26.70        18.64 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       32.45        84.72        35.28        33.40        40.37        21.83 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45        30.21 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.20     0.30     0.92 
subtype1 subtype2 subtype3 subtype4 
  155.54   166.62   157.15   169.32 
subtype1 subtype2 subtype3 subtype4 
  29.800   23.675   30.970   33.235 
[1] "0.2 - 155.5 (29.8)" "0.2 - 166.6 (23.7)" "0.3 - 157.2 (31.0)"
[4] "0.9 - 169.3 (33.2)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      84        6        46        1        29         2
  subtype2      91       29        28        1         5         2
  subtype3      41        1        13        0         4         0
  subtype4      67       15        23        0         9         2
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         84       91       41       67
  STAGE II         6       29        1       15
  STAGE III       46       28       13       23
  STAGE IV         1        1        0        0
  STAGE IVA       29        5        4        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 28 46 78 15
  subtype2 53 57 45  2
  subtype3 27 14 15  2
  subtype4 34 48 31  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       28       53       27       34
  T2       46       57       14       48
  T3       78       45       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  51 102
  subtype2 102  29
  subtype3  23  36
  subtype4  50  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51  102
  subtype2  102   29
  subtype3   23   36
  subtype4   50   58
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       51      102       23       50
  1      102       29       36       58
[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 95  3
  subtype2 71  3
  subtype3 41  0
  subtype4 72  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    3
  subtype2   71    3
  subtype3   41    0
  subtype4   72    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       95       71       41       72
  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 121  47
  subtype2 113  44
  subtype3  43  16
  subtype4  89  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  121   47
  subtype2  113   44
  subtype3   43   16
  subtype4   89   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      121      113       43       89
  MALE         47       44       16       28
[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  56 107
  subtype2  58  85
  subtype3  26  31
  subtype4  45  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  107
  subtype2   58   85
  subtype3   26   31
  subtype4   45   69
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        56       58       26       45
  YES      107       85       31       69
[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              4                                           135
  subtype2              2                                            71
  subtype3              1                                            50
  subtype4              1                                           100
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      3
  subtype2                                                                     83
  subtype3                                                                      3
  subtype4                                                                     13
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   1
  subtype3                                                                   5
  subtype4                                                                   3
D5V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               135
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          26
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                71
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       83
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                50
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           5
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               100
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           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"
D5V10, binary
          cls
clus         0   1
  subtype1 144   5
  subtype2 129   6
  subtype3  49   2
  subtype4  99   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144    5
  subtype2  129    6
  subtype3   49    2
  subtype4   99    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       144      129       49       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           67                      14   82                   1
  subtype2           24                       1  123                   0
  subtype3           13                       2   41                   0
  subtype4           29                       1   85                   0
D5V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  67       24       13       29
  MODERATE/ADVANCED (T4A)       14        1        2        1
  NONE                          82      123       41       85
  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 127  26   2   9
  subtype2 125   9   0   8
  subtype3  41   7   0   5
  subtype4  90  10   2   8
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      127      125       41       90
  R1       26        9        7       10
  R2        2        0        0        2
  RX        9        8        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 67 99
  subtype2 74 80
  subtype3 26 31
  subtype4 59 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   99
  subtype2   74   80
  subtype3   26   31
  subtype4   59   55
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       67       74       26       59
  UNIFOCAL         99       80       31       55
[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    17                        11
  subtype2                                0    11                         9
  subtype3                                0     7                         1
  subtype4                                0    16                         6
          vv
clus       WHITE
  subtype1   120
  subtype2    89
  subtype3    45
  subtype4    76
D5V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                  17       11        7       16
  BLACK OR AFRICAN AMERICAN              11        9        1        6
  WHITE                                 120       89       45       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  23 121
  subtype2   9  99
  subtype3   3  49
  subtype4   3  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23  121
  subtype2    9   99
  subtype3    3   49
  subtype4    3   90
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           23        9        3        3
  NOT HISPANIC OR LATINO      121       99       49       90
[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 129   6
  subtype3  85   1
  subtype4  93   2
  subtype5  76   2
subtype1 subtype2 subtype3 subtype4 subtype5 
     105      135       86       95       78 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        6        1        2        2 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A3PU 
        4.24        41.33         4.01        41.52        42.15        18.64 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J 
       15.45        19.43        30.12        11.57        30.02        14.70 
TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A2PT TCGA-DJ-A2PY 
        2.76         9.96       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         7.76        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-A3CR 
       25.45         0.16         0.39        26.73       155.54         7.66 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 
      157.15        37.94       108.36        49.51       136.01        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T1 
      139.00        17.52        52.50        29.65       147.42       129.57 
TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EL-A4JZ 
       98.24         5.72        36.03        47.38        45.96        37.94 
TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A22I TCGA-EM-A2P3 TCGA-EM-A3FM 
       34.39        53.36        24.30        14.73        14.60        21.01 
TCGA-EM-A3O3 TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FQ 
       14.50        29.95        12.79        84.59         5.33        22.45 
TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R TCGA-ET-A2MY 
       81.93        77.56        56.58        60.20        63.45        58.75 
TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A3BO TCGA-ET-A3BT TCGA-ET-A3BV 
       52.60       100.57        95.34        50.40        87.62        75.42 
TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN TCGA-FE-A22Z 
      116.78        62.83        24.72        46.26        33.17        73.74 
TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FY-A3R8 
       71.44        68.22       112.80        81.83        85.15        15.68 
TCGA-FY-A3YR TCGA-FY-A40L TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 TCGA-IM-A3EB 
       17.36         6.58        12.53        17.00        20.05        48.92 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3YF 
       18.51        16.90         8.22        25.64        17.23        24.69 
TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39         9.50        36.10 

$subtype2
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-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-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
       32.45        22.88        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         7.99        10.88         3.45        23.84 
TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S 
       23.18        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         6.77 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VK TCGA-DJ-A3VL 
       35.18        16.41        36.33        35.67        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A416 TCGA-EL-A3CO TCGA-EL-A3CX 
       27.62        34.78        47.21         0.72        97.74       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 
       79.50        57.11        64.87        50.20        49.32        33.50 
TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 
       32.48        78.97        60.16        57.47        30.51        44.15 
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-A2CQ 
       47.57        17.88        13.18        23.51         6.05        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 
       13.64        48.46        22.16        40.34        32.32        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN 
       22.52        30.94        14.14         8.35        47.38        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         0.49         9.24        13.91 
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-A2N3 TCGA-ET-A2N5 
       60.49        13.68        81.70        18.38        83.34        80.88 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       33.24       108.46       123.32        66.84       166.62        43.99 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
       31.40        33.63         1.05         1.25         7.82         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V 
       16.14        16.57         0.76        17.06        22.49         1.68 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A4HY TCGA-KS-A41I 
       21.67        12.46        31.10        43.17         0.20        15.98 
TCGA-KS-A41L TCGA-MK-A84Z TCGA-QD-A8IV 
      113.85        23.93        12.89 

$subtype3
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-A0XZ 
       36.39        21.01        28.44        12.30        12.66        35.84 
TCGA-DE-A4M8 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A1QM TCGA-DJ-A2PR TCGA-DJ-A2PS 
       18.54        38.17        18.58         6.02        27.45        26.20 
TCGA-DJ-A2PX TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3US 
       28.96        40.24        37.48        35.90        33.53        32.81 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V2 
       17.69        59.57        11.34        35.87        40.96        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3VD TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       30.61        42.54        21.01        21.34        33.04        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E3-A3E2 
       26.93        35.54        15.81        35.38         2.33        63.19 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       29.98        31.50        31.04         0.23        14.96         7.69 
TCGA-E8-A44M TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D4 TCGA-EL-A3H3 TCGA-EL-A3T0 
        0.39        57.01         4.18        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         0.30        19.04        47.41        11.24        31.82 
TCGA-J8-A42S TCGA-KS-A4ID 
        2.47        33.24 

$subtype4
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45J TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A481 
       14.73        30.21        21.63        12.66        12.79        11.38 
TCGA-CE-A482 TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13V 
       10.68        15.85        14.27       169.32        56.19        43.17 
TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PQ TCGA-DJ-A2PU 
        8.32        30.61        14.96        42.58        35.41        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       31.99        34.85        35.11        15.88        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V9 TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DO-A1JZ 
       31.46        36.33        20.48        18.97        30.87        54.90 
TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP 
       66.38        39.95        30.61        33.50        31.66       158.83 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GZ TCGA-EL-A3MW 
      139.86        98.53        50.24        50.37       139.99       108.66 
TCGA-EL-A3MX TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZL TCGA-EL-A4K0 
       57.63        41.29       107.47        82.82        62.30        31.04 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CV 
       41.13        47.84        43.59        27.06        26.86        48.49 
TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       27.65        13.15        19.73        15.68        33.07        13.38 
TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-ET-A25K 
       29.72        27.95        17.49         7.33        29.85        70.42 
TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A3BP 
       65.29        37.25         2.66       106.09       107.41        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PD 
       76.64        46.65        94.59       117.40       106.36        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K 
       71.08         4.11         0.92        48.10       116.09        15.16 
TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB 
        5.75       143.57        26.70        18.64        32.45        84.72 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37        21.83        32.45        30.21 

$subtype5
TCGA-BJ-A0ZH TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A4O9 TCGA-CE-A3ME TCGA-CE-A483 
       15.12        18.97        16.01        23.47        12.46        15.02 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QO 
       21.63        50.17        25.12        23.38        11.01        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3V7 
       17.56        10.09         7.82        33.93        31.04        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3VA TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DO-A1K0 
       21.27        24.82         3.12        36.43         3.12        21.53 
TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CS 
       92.55        80.52        52.44         0.26         3.02        45.53 
TCGA-EL-A3CT TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 
       60.95       115.10        65.39       147.75       101.13        49.71 
TCGA-EL-A3H8 TCGA-EL-A3T3 TCGA-EL-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZT TCGA-EL-A4JW 
      150.48       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        13.28        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 
        1.35        21.60         2.99        18.61        21.83        27.19 
TCGA-J8-A3YE TCGA-J8-A3YG TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4IC 
       27.85        22.29         2.60        15.68        43.69        35.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.16     0.20     0.23     0.92     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  157.15   166.62   142.52   169.32   150.48 
subtype1 subtype2 subtype3 subtype4 subtype5 
  34.390   22.520   30.790   33.500   25.745 
[1] "0.2 - 157.2 (34.4)" "0.2 - 166.6 (22.5)" "0.2 - 142.5 (30.8)"
[4] "0.9 - 169.3 (33.5)" "0.3 - 150.5 (25.7)"
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 32 72
  subtype2 48 78
  subtype3 38 41
  subtype4 38 56
  subtype5 29 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   72
  subtype2   48   78
  subtype3   38   41
  subtype4   38   56
  subtype5   29   45
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        32       48       38       38       29
  YES       72       78       41       56       45
[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              2                                            68
  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                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                68
  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    60
  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       60       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 71
  subtype4  3 71
  subtype5  8 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   77
  subtype2    9   82
  subtype3    3   71
  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       71       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 172  10
  subtype2 147   5
  subtype3 165   1
subtype1 subtype2 subtype3 
     182      152      166 
subtype1 subtype2 subtype3 
      10        5        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28X 
        4.24        41.33         4.01        41.52        35.54        30.97 
TCGA-BJ-A291 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I 
       22.88        36.39        23.31        21.01        28.44        15.45 
TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
       19.43        12.30        12.79        11.38        12.66        18.54 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A1QD 
       30.12        11.57         2.76         9.96        38.17        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ 
      135.91        30.61        42.51         6.02        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       10.09        26.20        38.83        31.99         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       37.74        40.24        37.48        36.46        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       33.53        31.04        19.56        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       35.87        40.96        36.99        42.54        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       20.48        21.01         7.76        36.43        33.04        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA 
       26.93        15.81         2.33        80.52        31.23        35.67 
TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       11.70        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
       30.61         0.16         0.23        14.96         7.69         0.39 
TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
        0.39        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY 
       45.53        60.95       157.15        37.94        57.01         4.18 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
      139.86        98.53        69.57        49.51        50.24       115.10 
TCGA-EL-A3GU TCGA-EL-A3GZ TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY 
      136.01       139.99        83.57       139.00        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK 
       52.50       147.42       142.52         5.72        66.90        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
       62.30        36.03        53.06        47.38        65.49         7.07 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EM-A1CU 
       34.72        37.94        31.04        34.39        53.36        20.91 
TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P0 TCGA-EM-A2P1 
       57.01        41.29        13.15        19.73        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO 
       14.60        37.25        16.18        14.50         5.33        26.37 
TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A2N0 TCGA-ET-A39J TCGA-ET-A39M 
       81.93        56.58        60.20        52.60       106.09        84.89 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       95.34        55.10        28.24        87.62        77.82        75.42 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T 
       84.85        80.58        43.73        62.83        46.26        37.48 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PB TCGA-FK-A3SE 
       33.17        73.74       112.80        39.95        85.15        13.28 
TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A3YR 
       48.10        17.82        13.91        16.27         0.30        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U 
       15.16         6.58        22.49         1.35        12.53        17.00 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD 
       47.41        18.51         8.22        25.64        11.24        31.82 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-KS-A4I3 TCGA-KS-A4IC 
       24.69        22.29         2.47         2.60        43.69        35.28 
TCGA-L6-A4EU TCGA-MK-A4N6 
        9.50        36.10 

$subtype2
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-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       25.48        42.08        51.39        20.58         4.83        44.35 
TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       21.04        32.45        11.31        18.38        16.57        20.48 
TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
        7.04        13.94         7.99        10.88         3.45        23.84 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DE-A4MD 
       23.18        12.46        12.43        37.64        18.84        25.12 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG 
       48.79        18.58         8.71        52.37         8.32        44.98 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
       17.59        30.58        34.36         6.77        35.18        16.41 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       32.81        36.33        35.67        24.76        17.23        27.62 
TCGA-DJ-A4UP TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 
       21.34        34.78        35.54        54.90        47.21        66.38 
TCGA-E3-A3E5 TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GS 
       39.95       106.62        79.50        57.11        64.87        65.39 
TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR 
       50.20        49.32        33.50        32.48        78.97        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-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-A2OV 
        6.05         2.99        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 
        0.49         9.24        13.91        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-A2MX TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L 
       18.38        88.41        83.34        80.88        33.24       108.46 
TCGA-ET-A39N TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV 
      123.32        76.64        46.65        94.59        66.84       166.62 
TCGA-ET-A40P TCGA-ET-A40R TCGA-ET-A4KQ TCGA-FE-A236 TCGA-FE-A239 TCGA-FE-A3PD 
       43.99        44.38        31.40        66.77        33.63        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP 
       71.08         1.05         1.25         7.82         0.99        16.14 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z 
       16.57         0.76        17.06        21.67        12.46        31.10 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB TCGA-KS-A4ID 
       43.17        27.19        15.98       113.85        84.72        33.24 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A28Z TCGA-BJ-A290 
       16.34        14.73        15.12        42.15        11.08        30.21 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K 
       18.97        16.01        18.64        21.63        23.47        12.66 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       10.68        15.02        35.84        21.63        50.17        15.85 
TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U 
       30.02        14.70        14.27       169.32        56.19        23.38 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
       14.96        42.58         7.82        35.41        27.45        33.96 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
       34.85        28.96        33.93        35.11        15.88        36.92 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 
       32.42        31.46        36.33        20.22        30.61        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VI TCGA-DJ-A4UL TCGA-DJ-A4V2 
       24.82        22.92        18.97         3.12        30.87         3.12 
TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 
       35.38        21.53        92.55        63.19        52.44         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3D6 TCGA-EL-A3GV 
        3.02        25.45        33.50        31.66       108.36        50.37 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW 
      147.75       101.13        43.36        49.71       150.48       108.66 
TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
       29.65       129.57       132.07        98.24        41.29       107.47 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 
       82.82        89.56        61.22        59.44        45.96        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ 
       48.49        14.73        14.53        44.19        27.65        33.96 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK 
       15.68        33.07        13.38        29.72        27.95        23.77 
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-A25J TCGA-ET-A25K 
       84.59        26.37        22.45        24.46        77.56        70.42 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 
       63.39        65.29        63.45        58.75        37.25        54.35 
TCGA-ET-A2N4 TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO 
        2.66       107.41       100.57        94.13        98.20        50.40 
TCGA-ET-A3BP TCGA-ET-A3BS TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-ET-A40S 
       79.10         5.79        52.47       116.78        24.72        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-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A4UB 
       81.83       106.36        85.68         4.11         0.92       116.09 
TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A40N TCGA-FY-A4B4 
       20.42        19.56        15.68        18.08        19.04        21.60 
TCGA-FY-A76V TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3U3 
        1.68         2.99        20.05        18.61        48.92        16.90 
TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY TCGA-KS-A41F 
       21.83        17.23        27.85         5.75         0.20       143.57 
TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-L6-A4EP 
       15.68        26.70        18.64        32.45        87.39        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83        32.45        30.21 

subtype1 subtype2 subtype3 
    0.16     0.49     0.20 
subtype1 subtype2 subtype3 
  158.83   166.62   169.32 
subtype1 subtype2 subtype3 
  31.385   24.775   30.210 
[1] "0.2 - 158.8 (31.4)" "0.5 - 166.6 (24.8)" "0.2 - 169.3 (30.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      90        6        56        1        26         2
  subtype2      94       28        22        1         5         2
  subtype3      99       17        33        0        16         2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         90       94       99
  STAGE II         6       28       17
  STAGE III       56       22       33
  STAGE IV         1        1        0
  STAGE IVA       26        5       16
  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 56 38 71 15
  subtype2 43 68 40  2
  subtype3 44 60 57  6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       56       43       44
  T2       38       68       60
  T3       71       40       57
  T4       15        2        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"
D7V5, binary
          cls
clus         0   1
  subtype1  65 108
  subtype2  97  28
  subtype3  65  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65  108
  subtype2   97   28
  subtype3   65   89
   clus
vv  subtype1 subtype2 subtype3
  0       65       97       65
  1      108       28       89
[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"
D7V6, binary
          cls
clus         0   1
  subtype1 122   2
  subtype2  66   3
  subtype3  91   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  122    2
  subtype2   66    3
  subtype3   91    4
   clus
vv  subtype1 subtype2 subtype3
  0      122       66       91
  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"
D7V7, binary
          cls
clus         0   1
  subtype1 135  47
  subtype2 109  44
  subtype3 123  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135   47
  subtype2  109   44
  subtype3  123   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      135      109      123
  MALE         47       44       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1  67 105
  subtype2  56  88
  subtype3  63  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67  105
  subtype2   56   88
  subtype3   63   99
     clus
vv    subtype1 subtype2 subtype3
  NO        67       56       63
  YES      105       88       99
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              4                                           144
  subtype2              2                                            67
  subtype3              2                                           145
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      8
  subtype2                                                                     84
  subtype3                                                                     10
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   0
  subtype3                                                                  10
D7V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               144
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          26
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                67
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               145
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  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"
D7V10, binary
          cls
clus         0   1
  subtype1 154   7
  subtype2 127   5
  subtype3 141   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  154    7
  subtype2  127    5
  subtype3  141    5
     clus
vv    subtype1 subtype2 subtype3
  NO       154      127      141
  YES        7        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           64                      14   97                   1
  subtype2           17                       0  128                   0
  subtype3           51                       4  108                   0
D7V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  64       17       51
  MODERATE/ADVANCED (T4A)       14        0        4
  NONE                          97      128      108
  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 132  26   3  12
  subtype2 120  10   0  10
  subtype3 132  16   1   8
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      132      120      132
  R1       26       10       16
  R2        3        0        1
  RX       12       10        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
D7V14, binary
          cls
clus        0  1
  subtype1 82 99
  subtype2 66 82
  subtype3 78 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   99
  subtype2   66   82
  subtype3   78   85
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       82       66       78
  UNIFOCAL         99       82       85
[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"
D7V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    25                         8
  subtype2                                0     9                        10
  subtype3                                1    18                         9
          vv
clus       WHITE
  subtype1   132
  subtype2    87
  subtype3   111
D7V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  25        9       18
  BLACK OR AFRICAN AMERICAN               8       10        9
  WHITE                                 132       87      111
[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"
D7V17, binary
          cls
clus         0   1
  subtype1  13 144
  subtype2  10  96
  subtype3  15 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  144
  subtype2   10   96
  subtype3   15  120
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13       10       15
  NOT HISPANIC OR LATINO      144       96      120
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 169  10
  subtype2 124   5
  subtype3 191   1
subtype1 subtype2 subtype3 
     179      129      192 
subtype1 subtype2 subtype3 
      10        5        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W 
        4.24         4.01        25.48        41.52        35.54        11.31 
TCGA-BJ-A28X TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H 
       30.97        18.97        36.39        23.31        21.01        28.44 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
       15.45        19.43        12.30        11.38        12.66        18.54 
TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE 
       11.57         2.76         9.96        38.17        11.01       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-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       42.54        19.20        21.27        20.48        21.01         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       36.43        21.34        33.04        27.06        26.93        35.54 
TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       15.81         2.33        80.52        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         0.72        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        0.16         0.23        14.96         7.69         0.39         0.39 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 
       60.95       157.15        37.94        57.01         4.18       139.86 
TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GZ 
       98.53        49.51        50.24       115.10       136.01       139.99 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 
       83.57       139.00        57.63        17.52        52.50       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL 
      142.52       129.57         5.72        66.90        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A3ZT 
       36.03        53.06        47.38        65.49         7.07        59.44 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG 
       34.72        37.94        31.04        34.39        53.36        24.30 
TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P0 TCGA-EM-A2P1 
       57.01        41.29        13.15        19.73        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FO 
       14.60        37.25        14.50        84.59         5.33        26.37 
TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R TCGA-ET-A2N0 TCGA-ET-A39J 
       81.93        56.58        60.20        63.45        52.60       106.09 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BV TCGA-ET-A3DQ 
       95.34        55.10        28.24        87.62        75.42        84.85 
TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 
       80.58        46.26        37.48        33.17        73.74       112.80 
TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 
       85.15         4.11        13.28        48.10        17.82        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       16.27        15.68         0.30        17.36        15.16         6.58 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB 
        1.35        12.53        17.00        18.51         8.22        25.64 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW 
       11.24        31.82        24.69        22.29         2.47         2.60 
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-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-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 
       22.88        18.38        16.57        20.48         7.04        13.94 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 
        7.99        10.88         3.45        23.84        23.18        12.43 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W 
       37.64        18.84        48.79        18.58         8.71        52.37 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB 
       44.98        17.59        30.58        34.36         6.77        35.18 
TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR 
       16.41        36.33        35.67        17.23        27.62        34.78 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       47.21        79.50        69.57        57.11        64.87        50.20 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV 
       49.32        33.50        32.48        78.97        60.16        57.47 
TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       30.51        44.15        23.90        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       78.61        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-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP 
       32.32        17.29        22.52        30.94        14.14         8.35 
TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 
       47.38        12.07        17.39        15.02        15.06         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH 
        9.24        13.91        38.66        38.86        13.51        29.33 
TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P 
       21.34        21.53        60.49        13.68        81.70        18.38 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       83.34        80.88        33.24       123.32        66.84       166.62 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 
       43.99        31.40        33.63         1.05         1.25         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 
        0.99        16.14        16.57         0.76        17.06        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L 
       12.46        31.10        43.17        27.19        15.98       113.85 
TCGA-KS-A4ID TCGA-MK-A84Z TCGA-QD-A8IV 
       33.24        23.93        12.89 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A28R 
       16.34        14.73        41.33        15.12        42.08        42.15 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 
       11.08        30.21        16.01        18.64        21.63        23.47 
TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ 
       12.66        12.79        12.46        10.68        15.02        35.84 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       21.63        50.17        15.85        30.12        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X 
       14.70        14.27       169.32        56.19        23.38         8.32 
TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       30.61        14.96        42.58         7.82        35.41        27.45 
TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 
       33.96        34.85        28.96        33.93        37.48        35.11 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3US 
       15.88        36.92        32.42        31.46        36.33        32.81 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       20.22        30.61        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
        3.12        24.76        30.87         3.12        35.38        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       21.53        92.55        66.38        63.19        52.44        39.95 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CX 
        0.26         3.02        25.45        33.50        31.66       106.62 
TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 
      108.36        65.39        50.37       147.75       101.13        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       49.71       150.48       108.66        29.65       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A4JX 
       41.29       107.47        82.82        89.56        61.22        45.96 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       41.13        47.84        43.59        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS 
       20.91        48.49        14.73        14.53        44.19        27.65 
TCGA-EM-A2OZ TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ 
       33.96        15.68        33.07        13.38        29.72        27.95 
TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU 
       23.77        21.01        17.49        16.18         7.33        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J 
       29.85        12.79        26.37        22.45        24.46        77.56 
TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       70.42        63.39        65.29        88.41        58.75        37.25 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       54.35         2.66       107.41       108.46        84.89       100.57 
TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       94.13        98.20        50.40        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DT 
       77.82        46.65        52.47       116.78        94.59        43.73 
TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 
       62.83        24.72        44.38        40.21        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 
       79.69        24.69        68.22       117.40        66.77        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SG 
       81.83       106.36        85.68        78.77        71.08         0.92 
TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A40M TCGA-FY-A40N 
      116.09        20.42        19.56        18.08        22.49        19.04 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.60         1.68         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH 
       47.41        16.90        21.83        17.23        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-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       84.72        33.40        40.37        21.83        32.45        30.21 

subtype1 subtype2 subtype3 
    0.16     0.49     0.20 
subtype1 subtype2 subtype3 
  158.83   166.62   169.32 
subtype1 subtype2 subtype3 
   31.04    22.16    32.45 
[1] "0.2 - 158.8 (31.0)" "0.5 - 166.6 (22.2)" "0.2 - 169.3 (32.5)"
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  70  99
  subtype2  45  76
  subtype3  71 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70   99
  subtype2   45   76
  subtype3   71  117
     clus
vv    subtype1 subtype2 subtype3
  NO        70       45       71
  YES       99       76      117
[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              3                                           164
          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                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               164
  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   130
  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                                 130       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  13 142
  subtype2   8  76
  subtype3  17 142
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  142
  subtype2    8   76
  subtype3   17  142
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        8       17
  NOT HISPANIC OR LATINO      142       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 151  10
  subtype2 163   2
  subtype3 140   4
subtype1 subtype2 subtype3 
     161      165      144 
subtype1 subtype2 subtype3 
      10        2        4 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
        4.24         4.01        41.52        35.54        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E 
       11.08        22.88        18.97        36.39        23.31        21.01 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB 
       28.44        15.45        19.43        12.66        18.54        11.57 
TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH 
        2.76         9.96        38.17        11.01       135.91        42.51 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PW 
        6.02        47.41        17.56        38.83        31.99        34.85 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        8.78         8.42        37.74        40.24        36.46        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       35.90        31.04        19.56        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       35.87        36.99        42.54        19.20        21.27        20.48 
TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.01         7.76        36.43        27.06        26.93        35.54 
TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       15.81         2.33        31.23        35.67        11.70        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A419 TCGA-E8-A432 
       29.98        31.50        31.04         0.72        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN 
        0.16         0.23        14.96         0.39        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
       97.74         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       57.01         4.18       139.86       108.36        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY 
      115.10       136.01        83.57       139.00        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T9 TCGA-EL-A3TA 
       52.50       147.42       142.52       129.57         5.72        66.90 
TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW 
       51.78        36.03        47.38        65.49         7.07        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG 
       45.96        37.94        31.04        34.39        53.36        24.30 
TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CR TCGA-EM-A2P1 TCGA-EM-A2P3 
       20.91        57.01        41.29        13.64        17.46        14.60 
TCGA-EM-A3FM TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G 
       21.01        16.18        14.50         5.33        26.37        81.93 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A3BU TCGA-ET-A3BV 
       56.58        60.20        84.89       100.57        77.82        75.42 
TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T 
      116.78        84.85        43.73        62.83        46.26        37.48 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE 
       33.17        73.74       112.80        85.15         4.11        13.28 
TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       48.10        17.82         7.82        13.91        16.27        15.68 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 TCGA-GE-A2C6 
        0.30        17.36        15.16         6.58         1.35        12.53 
TCGA-H2-A26U TCGA-H2-A421 TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O2 
       17.00        20.05        18.51         8.22        25.64        11.24 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-L6-A4EU TCGA-MK-A4N6 
       24.69        22.29         2.47         9.50        36.10 

$subtype2
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        49.78        16.34        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       25.48        15.12        51.39        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PU 
       42.15        21.04        32.45        16.01        13.94        18.64 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       12.30        12.79        12.46        21.63        50.17        15.85 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF 
      169.32        18.58         8.71        56.19         8.32        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PP 
       44.98        14.96        17.59        42.58        10.09        30.58 
TCGA-DJ-A2PR TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A3UR TCGA-DJ-A3VA TCGA-DJ-A3VB 
       27.45        34.36         6.77        36.33        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DO-A1JZ TCGA-DO-A1K0 
       18.97        24.76        17.23        27.62        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3D5 
       39.95         0.26         3.02       158.83        98.53        57.11 
TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H2 
       64.87        50.20       147.75       101.13       139.99        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T6 TCGA-EL-A3T8 
       43.36        49.71       108.66        29.65        98.24       107.47 
TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZT 
       82.82        78.97        62.30        53.06        61.22        59.44 
TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       26.86        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A2CO TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
        6.05        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FN TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       12.07        15.02        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O 
       13.91        38.66        77.56        70.42        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A39K TCGA-ET-A39P 
       18.38        63.45        88.41        37.25       107.41        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ TCGA-ET-A3BS 
       94.13        55.10        98.20        28.24        76.64         5.79 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DR TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R 
       46.65        52.47        80.58       166.62        43.99        44.38 
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-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC 
       66.77        39.95        33.63        81.83       106.36        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FY-A3BL TCGA-FY-A3NM TCGA-FY-A3NP 
       78.77        71.08         1.05        20.42         0.99        16.14 
TCGA-FY-A3ON TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3WA TCGA-FY-A40N TCGA-H2-A3RH 
       19.56        16.57        18.08        17.06        19.04        12.46 
TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A41Z TCGA-J8-A3O0 
        2.99        18.61        48.92        47.41        31.10        43.17 
TCGA-J8-A3O1 TCGA-KS-A41F TCGA-KS-A41J 
       27.19       143.57        15.68 

$subtype3
TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A45C 
       30.21        18.38        16.57        20.48         7.04         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O9 
       10.88         3.45        23.84        21.63        23.18        23.47 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A2OL 
       11.38        10.68        15.02        12.43        35.84        37.64 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A2PO 
       18.84        30.12        30.02        14.70        14.27         7.82 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       35.41        26.20        33.96        28.96        33.93        37.48 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       35.11        33.53        35.18        15.88        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       31.46        16.41        36.33        40.96        20.22        30.61 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       35.67         3.12        30.87        21.34        33.04        34.78 
TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44M TCGA-EL-A3CL 
        3.12        35.38         7.69        33.50         0.39        31.66 
TCGA-EL-A3GV TCGA-EL-A3H1 TCGA-EL-A3H8 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T7 
       50.37        49.32       150.48        32.48       132.07        41.29 
TCGA-EL-A3ZG TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4K7 
       89.56        60.16        57.47        30.51        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A22I TCGA-EM-A22J 
       47.84        43.59        27.06        23.90        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q 
       15.75        10.45        14.53        10.65        44.19        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3ST 
       27.65        48.46        13.15        17.49        17.39        38.86 
TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FN TCGA-EM-A4FQ 
       29.95        12.79        84.59        29.33        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A2MY TCGA-ET-A2N0 
       21.53        60.49        24.46        13.68        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39N 
       54.35        83.34        80.88        33.24       106.09       123.32 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A40S TCGA-ET-A4KQ 
       50.40        79.10        94.59        66.84        40.21        31.40 
TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3W9 TCGA-FY-A40M TCGA-FY-A4B4 
        0.92       116.09         1.25         0.76        22.49        21.60 
TCGA-FY-A76V TCGA-H2-A2K9 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YD 
        1.68        21.67        16.90        21.83        17.23        31.82 
TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HW TCGA-KS-A41I TCGA-KS-A4I1 TCGA-KS-A4I3 
       27.85         5.75         2.60        15.98        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       18.64        32.45        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       40.37        21.83        32.45        30.21        23.93        12.89 

subtype1 subtype2 subtype3 
    0.16     0.26     0.39 
subtype1 subtype2 subtype3 
  157.15   169.32   150.48 
subtype1 subtype2 subtype3 
  30.610   31.590   29.145 
[1] "0.2 - 157.2 (30.6)" "0.3 - 169.3 (31.6)" "0.4 - 150.5 (29.1)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      78        6        52        1        22         2
  subtype2     105       27        21        0         9         2
  subtype3      84       16        31        1        11         2
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         78      105       84
  STAGE II         6       27       16
  STAGE III       52       21       31
  STAGE IV         1        0        1
  STAGE IVA       22        9       11
  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 42 34 69 15
  subtype2 47 67 46  5
  subtype3 47 55 41  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       47       47
  T2       34       67       55
  T3       69       46       41
  T4       15        5        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 59 95
  subtype2 88 58
  subtype3 66 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   95
  subtype2   88   58
  subtype3   66   59
   clus
vv  subtype1 subtype2 subtype3
  0       59       88       66
  1       95       58       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 108   2
  subtype2  72   4
  subtype3  83   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108    2
  subtype2   72    4
  subtype3   83    3
   clus
vv  subtype1 subtype2 subtype3
  0      108       72       83
  1        2        4        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"
D9V7, binary
          cls
clus         0   1
  subtype1 119  42
  subtype2 119  46
  subtype3 107  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119   42
  subtype2  119   46
  subtype3  107   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      119      119      107
  MALE         42       46       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1 61 92
  subtype2 68 91
  subtype3 46 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   92
  subtype2   68   91
  subtype3   46   90
     clus
vv    subtype1 subtype2 subtype3
  NO        61       68       46
  YES       92       91       90
[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                                           126
  subtype2              2                                           113
  subtype3              3                                           101
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     47
  subtype3                                                                     38
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   3
  subtype3                                                                   4
D9V9, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               126
  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                               113
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       47
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               101
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       38
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
[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"
D9V10, binary
          cls
clus         0   1
  subtype1 135   5
  subtype2 136   8
  subtype3 126   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135    5
  subtype2  136    8
  subtype3  126    3
     clus
vv    subtype1 subtype2 subtype3
  NO       135      136      126
  YES        5        8        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           60                      14   79                   1
  subtype2           31                       2  127                   0
  subtype3           34                       1  106                   0
D9V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  60       31       34
  MODERATE/ADVANCED (T4A)       14        2        1
  NONE                          79      127      106
  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 112  25   3   9
  subtype2 138   9   1  11
  subtype3 110  15   0   9
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      112      138      110
  R1       25        9       15
  R2        3        1        0
  RX        9       11        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
D9V14, binary
          cls
clus        0  1
  subtype1 75 86
  subtype2 71 88
  subtype3 69 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   86
  subtype2   71   88
  subtype3   69   75
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       75       71       69
  UNIFOCAL         86       88       75
[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"
D9V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    18                         6
  subtype2                                0    12                         7
  subtype3                                1    19                        13
          vv
clus       WHITE
  subtype1   122
  subtype2   109
  subtype3    81
D9V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  18       12       19
  BLACK OR AFRICAN AMERICAN               6        7       13
  WHITE                                 122      109       81
[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"
D9V17, binary
          cls
clus         0   1
  subtype1  14 130
  subtype2  12 118
  subtype3   9  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  130
  subtype2   12  118
  subtype3    9   94
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14       12        9
  NOT HISPANIC OR LATINO      130      118       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 155  10
  subtype2 122   5
  subtype3 177   1
subtype1 subtype2 subtype3 
     165      127      178 
subtype1 subtype2 subtype3 
      10        5        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
        4.24         4.01        41.52        35.54        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E 
       11.08        22.88        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-A13L TCGA-DJ-A13O TCGA-DJ-A1QD 
       18.54        11.57         2.76         9.96        38.17        11.01 
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-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       42.54        19.20        21.27        20.48        21.01         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       36.43        21.34        33.04        27.06        26.93        35.54 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       15.81        35.38         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         0.72        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        0.16         0.23        14.96         7.69         0.39         0.39 
TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73        97.74         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GP 
       37.94        57.01         4.18       139.86        98.53        49.51 
TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY 
      115.10       136.01        83.57       139.00        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK 
       52.50       147.42       142.52         5.72        66.90        51.78 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW 
       36.03        53.06        47.38        65.49         7.07        34.72 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EM-A1YD TCGA-EM-A22P 
       37.94        31.04        34.39        53.36        57.01        41.29 
TCGA-EM-A2CU TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 TCGA-EM-A4FM 
       13.15        17.46        14.60        37.25        14.50         5.33 
TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R TCGA-ET-A2N0 
       26.37        81.93        56.58        60.20        63.45        52.60 
TCGA-ET-A39M TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BV TCGA-ET-A3DQ 
       84.89        95.34        55.10        28.24        75.42        84.85 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN 
       80.58        43.73        62.83        46.26        37.48        33.17 
TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
       73.74       112.80        85.15        13.28        48.10        17.82 
TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
        7.82        13.91        16.27         0.30        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 
        6.58         1.35        21.60        12.53        17.00        18.51 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A4HW 
       25.64        11.24        31.82        24.69        22.29         2.60 
TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU 
       43.69        35.28         9.50 

$subtype2
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        49.78        16.34        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         7.04        13.94 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 
        7.99        10.88         3.45        23.84        23.18        12.43 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A1QL 
       37.64        18.84        18.58         8.71        44.98        17.59 
TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2Q4 TCGA-DJ-A2QB TCGA-DJ-A3UP 
       30.58        34.36         6.77        33.93        35.18        16.41 
TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR 
       36.33        35.67         3.12        17.23        27.62        34.78 
TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 
       54.90        47.21        57.11        64.87        50.20        49.32 
TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       33.50        32.48        78.97        60.16        57.47        30.51 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA 
       44.15        41.13        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-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       17.39        15.02        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A4FH TCGA-EM-A4FR 
       13.91        38.66        38.86        29.95        29.33        21.53 
TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 
       60.49        13.68        18.38        54.35        83.34        80.88 
TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A39T TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       33.24       123.32        98.20        66.84       166.62        43.99 
TCGA-ET-A4KQ TCGA-FE-A236 TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3NM 
       31.40        66.77        33.63         1.05         1.25         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V 
       16.14        16.57         0.76        17.06        22.49         1.68 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-KS-A41I TCGA-MK-A84Z 
       21.67        12.46        31.10        43.17        15.98        23.93 
TCGA-QD-A8IV 
       12.89 

$subtype3
TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J 
       15.12        42.15        30.21        16.01        18.64        21.63 
TCGA-BJ-A4O9 TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ 
       23.47        12.79        12.46        10.68        15.02        35.84 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J 
       21.63        50.17        15.85        30.12        30.02        14.70 
TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI 
       14.27       169.32        56.19         8.32        30.61        14.96 
TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
       42.58        10.09         7.82        35.41        27.45        33.96 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
       34.85        28.96        37.48        35.11        15.88        36.92 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3VA 
       32.42        31.46        36.33        20.22        30.61        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VK TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DO-A1K0 
       22.92        18.97        24.76        30.87         3.12        21.53 
TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       92.55        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CN 
        0.26         3.02        25.45        33.50        31.66       155.54 
TCGA-EL-A3CP TCGA-EL-A3D6 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      158.83       108.36        50.24        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 
      139.99        43.36        49.71       150.48       108.66        29.65 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB 
      129.57       132.07        98.24        41.29       107.47        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZL TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K9 
       89.56        62.30        61.22        59.44        45.96        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-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK 
       15.68        33.07        13.38        29.72        27.95        23.77 
TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FN 
       21.01        17.49        16.18        12.79        84.59        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-A39J TCGA-ET-A39K TCGA-ET-A39O 
       88.41        58.75        37.25       106.09       107.41       100.57 
TCGA-ET-A39R TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU 
       94.13        50.40        79.10        76.64         5.79        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A40R TCGA-ET-A40S 
       46.65        52.47       116.78        94.59        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-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-A3R8 
        4.11         0.92       116.09        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         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3O1 
       47.41        16.90        21.83         8.22        17.23        27.19 
TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 
       27.85         5.75         2.47       143.57        15.68        26.70 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       18.64        32.45        87.39        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83        36.10        32.45        30.21 

subtype1 subtype2 subtype3 
    0.16     0.49     0.26 
subtype1 subtype2 subtype3 
  157.15   166.62   169.32 
subtype1 subtype2 subtype3 
   31.04    21.67    32.76 
[1] "0.2 - 157.2 (31.0)" "0.5 - 166.6 (21.7)" "0.3 - 169.3 (32.8)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      77        4        58        1        23         2
  subtype2      71       26        24        1         3         2
  subtype3     119       19        22        0        16         2
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         77       71      119
  STAGE II         4       26       19
  STAGE III       58       24       22
  STAGE IV         1        1        0
  STAGE IVA       23        3       16
  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 68 15
  subtype2 39 54 34  1
  subtype3 50 69 54  6
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       47       39       50
  T2       33       54       69
  T3       68       34       54
  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 59 98
  subtype2 80 23
  subtype3 74 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   98
  subtype2   80   23
  subtype3   74   91
   clus
vv  subtype1 subtype2 subtype3
  0       59       80       74
  1       98       23       91
[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 114   2
  subtype2  52   3
  subtype3  97   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    2
  subtype2   52    3
  subtype3   97    4
   clus
vv  subtype1 subtype2 subtype3
  0      114       52       97
  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 125  40
  subtype2  86  42
  subtype3 134  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125   40
  subtype2   86   42
  subtype3  134   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      125       86      134
  MALE         40       42       45
[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  94
  subtype2  45  74
  subtype3  70 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   94
  subtype2   45   74
  subtype3   70  105
     clus
vv    subtype1 subtype2 subtype3
  NO        60       45       70
  YES       94       74      105
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           130
  subtype2              2                                            57
  subtype3              3                                           153
          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                               130
  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                                57
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       69
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               153
  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 139   6
  subtype2 107   5
  subtype3 151   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139    6
  subtype2  107    5
  subtype3  151    5
     clus
vv    subtype1 subtype2 subtype3
  NO       139      107      151
  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   81                   1
  subtype2           17                       0  104                   0
  subtype3           45                       3  127                   0
D10V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  63       17       45
  MODERATE/ADVANCED (T4A)       14        0        3
  NONE                          81      104      127
  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 115  27   2  11
  subtype2  98   9   0   9
  subtype3 147  13   2   9
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      115       98      147
  R1       27        9       13
  R2        2        0        2
  RX       11        9        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
          cls
clus        0  1
  subtype1 72 92
  subtype2 62 63
  subtype3 81 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   92
  subtype2   62   63
  subtype3   81   94
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       72       62       81
  UNIFOCAL         92       63       94
[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    25                         5
  subtype2                                0     7                         9
  subtype3                                1    17                        12
          vv
clus       WHITE
  subtype1   122
  subtype2    70
  subtype3   120
D10V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  25        7       17
  BLACK OR AFRICAN AMERICAN               5        9       12
  WHITE                                 122       70      120
[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  10 136
  subtype2   7  80
  subtype3  18 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  136
  subtype2    7   80
  subtype3   18  126
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10        7       18
  NOT HISPANIC OR LATINO      136       80      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"
