[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/15092795/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/15125146/THCA-TP.mergedcluster.txt"

nPatients in clinical file=501, in cluster file=503, common to both=501
[1]  10 501
[1] "CN_CNMF"
[1] 3
  1   2   3 
 56 355  88 
  1   2   3 
 56 355  88 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
276 155  70 
  1   2   3 
276 155  70 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
61 79 82 
 1  2  3 
61 79 82 
[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 
167 156  59 117 
  1   2   3   4 
167 156  59 117 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
105 135  86  96  77 
  1   2   3   4   5 
105 135  86  96  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
182 152 166 
  1   2   3 
182 152 166 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
179 130 191 
  1   2   3 
179 130 191 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
161 164 145 
  1   2   3 
161 164 145 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
165 127 178 
  1   2   3 
165 127 178 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "RADIATION_EXPOSURE"                    
[17] "EXTRATHYROIDAL_EXTENSION"              
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR_SIZE"                            
[22] "RACE"                                  
[23] "ETHNICITY"                             
[24] "BATCH_NUMBER"                          

Input Data has 24 rows and 501 columns.

[1] "Batch" "24"   
[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=14,	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=425,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_SIZE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH_NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 501 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RADIATION_EXPOSURE"                    
[10] "EXTRATHYROIDAL_EXTENSION"              
[11] "COMPLETENESS_OF_RESECTION"             
[12] "NUMBER_OF_LYMPH_NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR_SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
142 167 167  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
142 167 167  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
142 167 167  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
142 167 167  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
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=30, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=70, 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 344  10
  subtype3  87   1
subtype1 subtype2 subtype3 
      55      354       88 
subtype1 subtype2 subtype3 
       3       10        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 
       12.56         8.28        34.36         2.33        14.43         1.41 
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        14.79        12.26 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BV TCGA-ET-A40S TCGA-FE-A231 TCGA-FE-A239 
       84.89        98.56        42.25         5.03        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        10.26        22.29 
TCGA-L6-A4EU 
        9.50 

$subtype2
TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZE TCGA-BJ-A0ZJ 
       13.78        16.34         8.25        18.87        16.73        17.69 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
       20.71         4.83        42.15        21.04        35.54         5.10 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2NA 
       11.31        17.52         1.22        22.88        18.38        18.97 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45G 
       16.01        13.94        15.48        18.64         5.75         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M9 
        0.10         0.10        15.42        36.46         5.98        18.84 
TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O 
       30.12        30.02        14.70        14.27         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X 
      169.32         3.39         8.71        23.38        18.35         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO 
       11.01        30.61        14.96         7.20         1.45        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.99         5.33        35.41        27.45 
TCGA-DJ-A2PT TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q2 
       38.83        34.85         5.52         8.78         8.42         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       40.24         9.44        37.48        36.46         7.10        35.90 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        21.37        18.51        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        21.47        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
        8.32        24.20        17.23        18.21        21.34        19.07 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       54.90        21.53        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        31.23        22.29        11.70        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       14.27        13.81        14.07        14.27         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM 
       14.70         7.69        20.68        13.78        13.58        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D6 TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX 
      108.36        50.24       115.10        65.39        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      139.00       131.15       108.66        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      147.42       130.72       129.57       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47        66.90        82.82        89.56        78.97        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       53.06        52.50        61.22         7.07        59.44        34.72 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG 
       31.04        34.39        30.51        53.36        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       27.06        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.73        14.50        11.74        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        27.65        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       22.16        13.84        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       12.07        17.39        16.18        15.02        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A4FF TCGA-EM-A4FH 
       12.53        13.91         7.82        11.51        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 
       21.34         5.33        26.37        22.45        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N 
       47.47        48.20        29.69        32.35        12.33        14.79 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       19.76        58.22        13.74        71.01        80.02        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
       80.81        69.24        59.87        43.50        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A4KN TCGA-ET-A4KQ 
      132.36        24.72         7.17         4.80         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       73.74        59.70        44.25        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       66.77        39.95        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11         1.05        22.03        48.10       116.09 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 
       20.42        17.82        19.56        13.91        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       18.08         0.30        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       19.04         1.35         1.68        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A41Y TCGA-IM-A420 
        2.99        20.05        18.61        47.41        21.83         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.65        17.23        27.19        11.24        27.85        24.69 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
        2.47         2.60         0.20       143.57        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
        6.02        19.73         6.74        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37        21.83        36.10        32.45        30.21 

$subtype3
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A18Y 
       18.21        14.73        11.57         7.56        15.12        23.34 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45         0.39        20.22 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A13W 
       15.85        18.54         9.96        17.26        56.19        14.60 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q1 TCGA-DJ-A2Q7 
       13.12         7.99        42.58        26.20        37.74        10.09 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       12.43        35.18        15.09        20.45        31.46        16.41 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A434 TCGA-E8-A436 
       27.62        15.42        12.07        14.04        14.10        14.96 
TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO 
       31.66       139.86        98.53        45.40        57.11        64.87 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       50.20        32.48        62.30        60.16        57.47        37.94 
TCGA-EL-A4K6 TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P 
       44.15        26.86        15.75        10.45        14.53        11.15 
TCGA-EM-A2CJ TCGA-EM-A2OX TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3SX TCGA-EM-A3SZ 
       16.44        19.73         8.35        17.49        15.62        12.79 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L 
       26.37        21.53        60.49        27.09         2.66        65.36 
TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB 
        4.18         0.30         3.22         2.14        81.34        85.15 
TCGA-FK-A3SG TCGA-FY-A2QD TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A4B4 TCGA-GE-A2C6 
        0.92         1.25        16.27         0.76        21.60        12.53 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I 
       16.90         9.63        43.17        31.82         5.75        15.98 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        84.72        20.25        12.89 

subtype1 subtype2 subtype3 
    0.99     0.10     0.30 
subtype1 subtype2 subtype3 
  136.01   169.32   139.86 
subtype1 subtype2 subtype3 
   22.29    20.96    16.67 
[1] "1.0 - 136.0 (22.3)" "0.1 - 169.3 (21.0)" "0.3 - 139.9 (16.7)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      14       14        16        1        10         1
  subtype2     215       32        77        0        26         4
  subtype3      53        6        16        1        10         1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         14      215       53
  STAGE II        14       32        6
  STAGE III       16       77       16
  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 103 114 121  15
  subtype3  30  31  24   3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8      103       30
  T2       21      114       31
  T3       22      121       24
  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 157 162
  subtype3  43  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   23
  subtype2  157  162
  subtype3   43   40
   clus
vv  subtype1 subtype2 subtype3
  0       24      157       43
  1       23      162       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1  24   1
  subtype2 204   6
  subtype3  49   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2  204    6
  subtype3   49    2
   clus
vv  subtype1 subtype2 subtype3
  0       24      204       49
  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 265  90
  subtype3  64  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   19
  subtype2  265   90
  subtype3   64   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37      265       64
  MALE         19       90       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            40
  subtype2              8                                           255
  subtype3              1                                            61
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     12
  subtype2                                                                     64
  subtype3                                                                     22
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   4
  subtype2                                                                  28
  subtype3                                                                   4
D1V8, 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                                                                8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               255
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          28
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       22
  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"
D1V9, binary
          cls
clus         0   1
  subtype1   2  54
  subtype2  11 344
  subtype3   1  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   54
  subtype2   11  344
  subtype3    1   87
     clus
vv    subtype1 subtype2 subtype3
  NO         2       11        1
  YES       54      344       87
[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"
D1V10, binary
          cls
clus         0   1
  subtype1  49   3
  subtype2 296  12
  subtype3  76   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    3
  subtype2  296   12
  subtype3   76    2
     clus
vv    subtype1 subtype2 subtype3
  NO        49      296       76
  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          100                      13  231                   0
  subtype3           17                       1   65                   0
D1V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  15      100       17
  MODERATE/ADVANCED (T4A)        4       13        1
  NONE                          34      231       65
  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 279  36   3  15
  subtype3  64   7   1   9
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       38      279       64
  R1        9       36        7
  R2        0        3        1
  RX        6       15        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"
D1V13, continuous
D1V14, binary
          cls
clus         0   1
  subtype1  21  35
  subtype2 155 194
  subtype3  49  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   35
  subtype2  155  194
  subtype3   49   35
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       21      155       49
  UNIFOCAL         35      194       35
[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    40                        17
  subtype3                                0    11                         6
          vv
clus       WHITE
  subtype1    39
  subtype2   232
  subtype3    54
D1V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1       40       11
  BLACK OR AFRICAN AMERICAN               4       17        6
  WHITE                                  39      232       54
[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  27 259
  subtype3   7  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   37
  subtype2   27  259
  subtype3    7   62
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4       27        7
  NOT HISPANIC OR LATINO       37      259       62
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 269   7
  subtype2 150   3
  subtype3  66   4
subtype1 subtype2 subtype3 
     276      153       70 
subtype1 subtype2 subtype3 
       7        3        4 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z 
        4.24        14.73         8.25         4.01        15.12        20.71 
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         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3MD 
        6.18        21.63         4.93        23.47         0.53         0.20 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       10.68         0.10        20.22        15.42        36.46        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        18.35         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         7.99        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         7.99        35.41        27.45 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28        34.85         5.52         8.78         8.42 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2QA TCGA-DJ-A2QC 
        9.44        36.46        10.09         7.10        12.43        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UU 
       15.09        31.04        20.45        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        21.47        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VJ 
       21.27        20.48        24.82        22.92        18.97        24.20 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       18.21        19.07        14.70         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       54.90        21.53        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       30.31        14.04        19.59        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-EL-A3CL 
       14.70        14.96         7.69        20.68        13.78        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CU 
       26.73       155.54       158.83         7.66        45.53       157.15 
TCGA-EL-A3CX TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       80.91       139.86        98.53       108.36         1.41        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39       136.01        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
      139.99        43.36        49.71        83.57       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T1 
      108.66        57.63        17.52        52.50        29.65       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZK TCGA-EL-A3ZL 
      132.07        41.29       107.47        82.82        31.50        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JW 
       36.03        47.38        52.50        61.22        59.44        34.72 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 
       37.94        31.04        34.39        53.36        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX 
       12.36        14.73        11.74        27.65        13.15        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       33.96        17.59        14.60        15.68        33.07        13.38 
TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O7 
       29.72        27.95        23.77        21.01        17.49         7.33 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN 
       29.95        15.62        12.79        84.59         5.33        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       22.45        24.46        47.47        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       12.33        14.79        27.09        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       12.26        16.08         2.66        71.01        80.02        61.02 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       58.72        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         2.37         4.50 
TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T 
       69.24        43.50        24.72         7.17         4.80         2.14 
TCGA-FE-A22Z TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       73.74        31.59        44.25        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       66.77        81.34        39.95       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR 
      116.09        20.42        19.56        15.68        18.08        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 
       15.16         6.58         1.35        21.60         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        47.41        10.26        16.90        21.83         2.96 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       17.23        27.19        11.24        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 
        2.47         2.60         0.20       143.57        15.68         6.02 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP 
        6.74        32.45        87.39        84.72        35.28        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        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        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        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 
        5.10        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         5.75        10.88         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M 
        8.98         0.23         0.39         5.98        18.84        17.26 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        14.60        13.12         7.20         1.45         5.33 
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-A3VL 
       24.23        11.34        21.37        18.51         8.32        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 
       27.62        15.42        12.07        13.61        13.81        14.07 
TCGA-E8-A434 TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       14.10        58.82        45.40        57.11        64.87        50.20 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3TA TCGA-EL-A3ZG 
       49.32        33.50       130.72        32.48        66.90        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 
       78.97        53.06        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 
       16.44        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        10.49        22.16        13.84        32.32        17.29 
TCGA-EM-A3AI TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL TCGA-EM-A3FN 
       22.52        14.14         8.35        37.25        16.80        12.07 
TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       17.39        15.02        15.06        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR 
        7.82        11.51        13.51        29.33        21.34        21.53 
TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 
       60.49        13.68        48.20        18.38        29.19        19.76 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       58.22        13.74        65.36        98.56         0.30       132.36 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I4 
        3.22         1.94        33.63         1.05         1.25        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 
        7.82         0.99        16.14        16.27        16.57         0.76 
TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A76V TCGA-H2-A2K9 TCGA-H2-A3RH 
       17.06        22.49        19.04         1.68        21.67        12.46 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-KS-A41I TCGA-KS-A41L 
        9.63        43.17        31.82        27.85        15.98        86.70 
TCGA-KS-A4I3 TCGA-MK-A84Z TCGA-QD-A8IV 
       19.73        20.25        12.89 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        17.69        35.54        11.31        17.52         1.22 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
       15.48        21.01         0.10        11.38         0.10        18.54 
TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
        9.96        14.07         3.39        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        14.14        17.82         2.33        31.23        22.29 
TCGA-E8-A2JQ TCGA-E8-A414 TCGA-E8-A419 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CT 
       11.70        14.27        25.45        13.58        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        11.15         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        57.11 
TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40S 
       42.25        80.81        59.87        17.98        25.32         5.03 
TCGA-ET-A4KN TCGA-FE-A230 TCGA-FE-A23A TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 
        4.01        59.70        81.83        13.91         0.30        12.53 
TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A4EB TCGA-KS-A4ID 
       17.00        48.92         8.65        33.24 

subtype1 subtype2 subtype3 
    0.10     0.23     0.10 
subtype1 subtype2 subtype3 
  169.32   132.36   147.42 
subtype1 subtype2 subtype3 
  23.295   17.230   17.900 
[1] "0.1 - 169.3 (23.3)" "0.2 - 132.4 (17.2)" "0.1 - 147.4 (17.9)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1     148       20        67        0        36         4
  subtype2      89       31        27        1         4         2
  subtype3      46        2        15        1         6         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        148       89       46
  STAGE II        20       31        2
  STAGE III       67       27       15
  STAGE IV         0        1        1
  STAGE IVA       36        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  64  89 102  20
  subtype2  53  58  43   1
  subtype3  25  20  22   2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       64       53       25
  T2       89       58       20
  T3      102       43       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  96 159
  subtype2 100  29
  subtype3  30  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96  159
  subtype2  100   29
  subtype3   30   37
   clus
vv  subtype1 subtype2 subtype3
  0       96      100       30
  1      159       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 164   6
  subtype2  73   3
  subtype3  41   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  164    6
  subtype2   73    3
  subtype3   41    0
   clus
vv  subtype1 subtype2 subtype3
  0      164       73       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 203  73
  subtype2 112  43
  subtype3  52  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  203   73
  subtype2  112   43
  subtype3   52   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      203      112       52
  MALE         73       43       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"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              5                                           225
  subtype2              2                                            75
  subtype3              2                                            56
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     17
  subtype2                                                                     78
  subtype3                                                                      5
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  29
  subtype2                                                                   0
  subtype3                                                                   7
D2V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               225
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       17
  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)       78
  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"
D2V9, binary
          cls
clus         0   1
  subtype1  11 265
  subtype2   1 154
  subtype3   2  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  265
  subtype2    1  154
  subtype3    2   68
     clus
vv    subtype1 subtype2 subtype3
  NO        11        1        2
  YES      265      154       68
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
          cls
clus         0   1
  subtype1 238   8
  subtype2 125   6
  subtype3  59   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  238    8
  subtype2  125    6
  subtype3   59    3
     clus
vv    subtype1 subtype2 subtype3
  NO       238      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  160                   0
  subtype2           24                       0  122                   0
  subtype3           15                       1   50                   1
D2V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  93       24       15
  MODERATE/ADVANCED (T4A)       17        0        1
  NONE                         160      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 207  36   4  18
  subtype2 123   9   0   8
  subtype3  53   7   0   4
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      207      123       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 125 146
  subtype2  71  81
  subtype3  30  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125  146
  subtype2   71   81
  subtype3   30   38
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL      125       71       30
  UNIFOCAL        146       81       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   188
  subtype2    85
  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                                 188       85       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  24 207
  subtype2   7  99
  subtype3   7  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  207
  subtype2    7   99
  subtype3    7   53
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           24        7        7
  NOT HISPANIC OR LATINO      207       99       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 57  4
  subtype2 75  4
  subtype3 77  5
subtype1 subtype2 subtype3 
      61       79       82 
subtype1 subtype2 subtype3 
       4        4        5 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       24.79        13.78        18.21        16.34        18.87        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       16.73         7.56        17.69        23.34        20.58         7.04 
TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QM 
       15.85        17.26        14.60         8.32        30.61         1.45 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 
       10.09         7.99         8.28         8.42         6.77        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EL-A3CL 
       10.09        35.90        12.43        15.88        12.07        31.66 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CW TCGA-EL-A3CY 
      155.54        97.74       158.83       157.15        57.01         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GV TCGA-EL-A3H1 TCGA-EM-A1CW 
       58.82        45.40        57.11        50.37        49.32        18.05 
TCGA-EM-A1YD TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CQ 
       57.01        10.45        16.44        17.88        13.18        12.30 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AP 
       13.15        22.16        30.94        14.14        33.07         8.35 
TCGA-EM-A3FL TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A3BP TCGA-ET-A3DP TCGA-FY-A2QD 
       16.80        58.22        13.74         4.18        69.24         1.25 
TCGA-J8-A3O0 
       43.17 

$subtype2
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A290 
       14.73         8.25         4.01        44.35        42.15        30.21 
TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-CE-A3ME TCGA-DE-A0Y2 
       18.38        20.48        18.97        16.01         0.23        15.42 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QG 
       14.07         3.39         8.71        11.01       135.91        13.12 
TCGA-DJ-A1QO TCGA-DJ-A2PP TCGA-DJ-A2PY TCGA-DJ-A2Q0 TCGA-DJ-A2Q8 TCGA-DJ-A2QB 
       47.41         5.33         8.78        34.36         7.10        35.18 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA 
       21.53        31.07        40.21        30.31        14.04        22.29 
TCGA-EL-A3CM TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CV TCGA-EL-A3D6 TCGA-EL-A3GS 
       26.73        45.53        60.95        37.94       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-A3N2 TCGA-EL-A3N3 TCGA-EM-A1CT TCGA-EM-A1YA TCGA-EM-A1YB 
       52.50        29.65       147.42        18.18        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A2CO TCGA-EM-A2OY 
       78.61        14.73        14.50        11.74         6.05        32.32 
TCGA-EM-A2P1 TCGA-EM-A3FP TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O 
       17.46        17.39        47.47        14.79        12.33        27.09 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BT TCGA-ET-A3DO 
       22.09        16.08        58.72        59.15        24.72        80.81 
TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A234 
       24.72        73.74        59.70        31.59        44.25        68.22 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FY-A3BL TCGA-IM-A3EB TCGA-J8-A3NZ 
       66.77        81.34        81.83        20.42        48.92        17.23 
TCGA-J8-A3O1 
       27.19 

$subtype3
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       20.71         4.83        21.04        35.54         5.10        11.31 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A3F0 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        1.22        22.88        13.94         0.53         0.10         0.20 
TCGA-DE-A2OL TCGA-DJ-A13V TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A2PQ 
        5.98        18.35        14.96         7.20        42.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 
       27.45        26.20        12.56        34.85        37.74         9.44 
TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 TCGA-E8-A2JQ TCGA-EL-A3CR TCGA-EL-A3CX 
       37.48        54.90        66.38        11.70         7.66        80.91 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
      139.86        98.53        64.87         1.41        50.24       115.10 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H8 
       50.20       147.75       139.99        33.50        43.36       131.15 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1YE TCGA-EM-A22M 
       57.63        17.52        20.91        12.36        54.08        14.53 
TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A3AI 
       14.24        23.51         2.99        13.64        27.65        22.52 
TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3FN TCGA-EM-A3FO TCGA-ET-A2MZ TCGA-ET-A2N1 
       13.38        27.95        12.07        17.49        12.26        29.19 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39R 
        2.66        71.01        65.36        84.89        98.56        57.11 
TCGA-ET-A3BN TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
       28.24         5.56        38.30        42.25         2.37         4.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DV TCGA-FE-A233 TCGA-FE-A235 TCGA-FE-A239 
        0.30        17.98       132.36        24.69       117.40        33.63 
TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-IM-A3ED 
       19.56        12.53        21.67        47.41 

subtype1 subtype2 subtype3 
    1.25     0.23     0.10 
subtype1 subtype2 subtype3 
  158.83   147.42   147.75 
subtype1 subtype2 subtype3 
  16.800   27.190   23.195 
[1] "1.2 - 158.8 (16.8)" "0.2 - 147.4 (27.2)" "0.1 - 147.8 (23.2)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      31       11        14         2         1
  subtype2      31       13        21        14         0
  subtype3      55        9        11         4         3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         31       31       55
  STAGE II        11       13        9
  STAGE III       14       21       11
  STAGE IVA        2       14        4
  STAGE IVC        1        0        3
[1] 5 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 22 23 15  0
  subtype2 12 25 34  8
  subtype3 17 36 26  3
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       12       17
  T2       23       25       36
  T3       15       34       26
  T4        0        8        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"
D3V5, binary
          cls
clus        0  1
  subtype1 34 18
  subtype2 29 41
  subtype3 35 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   18
  subtype2   29   41
  subtype3   35   36
   clus
vv  subtype1 subtype2 subtype3
  0       34       29       35
  1       18       41       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"
D3V6, binary
          cls
clus        0  1
  subtype1 38  1
  subtype2 43  1
  subtype3 37  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    1
  subtype2   43    1
  subtype3   37    3
   clus
vv  subtype1 subtype2 subtype3
  0       38       43       37
  1        1        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 43 18
  subtype2 57 22
  subtype3 54 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   18
  subtype2   57   22
  subtype3   54   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       57       54
  MALE         18       22       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            35
  subtype2              1                                            55
  subtype3              1                                            68
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     25
  subtype2                                                                     14
  subtype3                                                                     13
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                   9
  subtype3                                                                   0
D3V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                35
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                55
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           9
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                68
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           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"
D3V9, binary
          cls
clus        0  1
  subtype1  0 61
  subtype2  9 70
  subtype3  4 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   61
  subtype2    9   70
  subtype3    4   78
     clus
vv    subtype1 subtype2 subtype3
  NO         0        9        4
  YES       61       70       78
[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"
D3V10, binary
          cls
clus        0  1
  subtype1 52  3
  subtype2 67  4
  subtype3 65  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    3
  subtype2   67    4
  subtype3   65    4
     clus
vv    subtype1 subtype2 subtype3
  NO        52       67       65
  YES        3        4        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"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           12                       0   48
  subtype2           28                       8   41
  subtype3           15                       2   60
D3V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  12       28       15
  MODERATE/ADVANCED (T4A)        0        8        2
  NONE                          48       41       60
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 48  6  1  5
  subtype2 58 13  0  4
  subtype3 62  4  1  5
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       48       58       62
  R1        6       13        4
  R2        1        0        1
  RX        5        4        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
D3V14, binary
          cls
clus        0  1
  subtype1 35 23
  subtype2 27 50
  subtype3 39 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   23
  subtype2   27   50
  subtype3   39   41
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       35       27       39
  UNIFOCAL         23       50       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    34
  subtype2     4                         4    59
  subtype3     9                         2    54
D3V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        4        9
  BLACK OR AFRICAN AMERICAN        7        4        2
  WHITE                           34       59       54
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V17, binary
          cls
clus        0  1
  subtype1  1 46
  subtype2  8 59
  subtype3  7 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    8   59
  subtype3    7   63
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        8        7
  NOT HISPANIC OR LATINO       46       59       63
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 43  4
  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 
       4        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        18.21        18.87        11.57         7.56 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A28V TCGA-BJ-A2N9 TCGA-DE-A2OL 
       17.69        23.34        20.58         5.10        20.48         5.98 
TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A1QL TCGA-DJ-A2PO TCGA-DJ-A2Q2 TCGA-E3-A3DZ 
       17.26        14.60         7.20         7.99         6.77        12.07 
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        58.82        45.40 
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        16.44        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        16.80 
TCGA-ET-A39I TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DV TCGA-FY-A2QD 
       13.74         4.18        69.24       132.36         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        14.07         8.32         1.45        10.09 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       35.41        26.20         8.28         8.42        36.46        10.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-EL-A3CL TCGA-EL-A3CV TCGA-EL-A3GQ 
       35.90        12.43        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        12.33        12.26 
TCGA-ET-A39P TCGA-FE-A232 TCGA-FE-A236 TCGA-J8-A3O0 
       58.72        44.25        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         8.25         4.01        30.21        16.01         0.23 
TCGA-DE-A0Y2 TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QO TCGA-DJ-A2PY TCGA-DJ-A2Q8 
       15.42        11.01       135.91        47.41         8.78         7.10 
TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GU 
       21.53        40.21        30.31       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        11.74 
TCGA-EM-A2P1 TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A230 
       17.46        47.47        14.79        80.81        24.72        59.70 
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         1.22        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        29.19        58.22        65.36        98.56        57.11 
TCGA-ET-A3BS TCGA-ET-A3DS TCGA-ET-A3DT TCGA-FE-A239 TCGA-H2-A2K9 
        5.56         0.30        17.98        33.63        21.67 

$subtype5
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28T TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       20.71         4.83        35.54         0.53         0.10         0.20 
TCGA-DJ-A13V TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PR TCGA-DJ-A2PU 
       18.35        30.61        14.96        42.58        27.45        12.56 
TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 
       34.85        37.74         9.44        37.48        54.90        66.38 
TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-EL-A3CX TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR 
       22.29        11.70        80.91        98.53         1.41       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       131.15        57.63        20.91 
TCGA-EM-A1CV TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A3AO TCGA-EM-A3FO TCGA-ET-A2N4 
       12.36        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 
       71.01        84.89        28.24        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-FE-A233 TCGA-FE-A235 TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB 
        4.50        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         3.39         8.71        13.12         5.33 
TCGA-DJ-A2Q0 TCGA-DJ-A2QB TCGA-E3-A3DY TCGA-EL-A3MZ TCGA-EM-A1YA TCGA-EM-A1YB 
       34.36        35.18        31.07        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        27.09 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39T TCGA-ET-A3BT TCGA-FE-A22Z TCGA-FE-A231 
       22.09        16.08        59.15        24.72        73.74        31.59 
TCGA-FE-A237 TCGA-FY-A3BL TCGA-J8-A3O1 
       81.34        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        14.04        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     1.45     0.23     0.30     0.10     3.39    14.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  158.83    66.77   139.00   155.54   147.75    81.34   147.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   17.88    17.26    30.21    21.04    27.65    24.72    42.15 
[1] "1.2 - 158.8 (17.9)"  "1.4 - 66.8 (17.3)"   "0.2 - 139.0 (30.2)" 
[4] "0.3 - 155.5 (21.0)"  "0.1 - 147.8 (27.6)"  "3.4 - 81.3 (24.7)"  
[7] "14.0 - 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 10 10  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       10        0
  T3        9        8       17       12       16       10        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"
          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
D4V8, 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"
D4V9, binary
          cls
clus        0  1
  subtype1  0 47
  subtype2  2 26
  subtype3  4 29
  subtype4  1 28
  subtype5  3 46
  subtype6  3 24
  subtype7  0  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   47
  subtype2    2   26
  subtype3    4   29
  subtype4    1   28
  subtype5    3   46
  subtype6    3   24
  subtype7    0    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        2        4        1        3        3        0
  YES       47       26       29       28       46       24        9
[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"
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 28 16
  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   28   16
  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       28       12       12       12       25       10        2
  UNIFOCAL         16       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    24
  subtype2     2                         1    19
  subtype3     3                         0    28
  subtype4     2                         1    20
  subtype5     7                         2    32
  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                           24       19       28       20       32
                           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 160   7
  subtype2 152   3
  subtype3  57   2
  subtype4 114   2
subtype1 subtype2 subtype3 subtype4 
     167      155       59      116 
subtype1 subtype2 subtype3 subtype4 
       7        3        2        2 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
        4.24         8.25         4.01        15.12        20.71        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         6.18         4.93         0.23 
TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MA TCGA-DE-A4MB 
        0.10         0.10        15.42        36.46        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         7.99        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         9.44        31.04        19.56 
TCGA-DJ-A3UY TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VB 
       21.37        36.99        19.20        23.21        21.27        22.92 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
        7.76        24.20        19.07         3.12        15.81        24.33 
TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A3X7 TCGA-E8-A417 
       21.53        40.21        30.31        31.23        19.59        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
        3.02        25.45        14.70        14.96         7.69        13.78 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3D6 
       26.73       155.54         7.66        45.53        60.95       108.36 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 
      115.10        65.39       136.01       147.75       101.13        49.71 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      139.00       131.15        17.52        52.50        29.65       147.42 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZM 
      129.57       132.07        98.24         5.72        31.50        36.03 
TCGA-EL-A3ZO TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4K1 TCGA-EL-A4K4 
       47.38        59.44        34.72        45.96        34.39        53.36 
TCGA-EL-A4KG TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2OZ 
       24.30        18.18        20.91        14.73        11.74        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3SU 
       17.59        14.60        23.77        21.01        17.49        29.95 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-ET-A25G 
       12.79        84.59         5.33        26.37        22.45        47.47 
TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25R TCGA-ET-A2MX 
       29.69        14.79        12.33        14.79        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BN 
       22.09        16.08        61.02        58.72        59.15        28.24 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW 
       24.72        38.30        42.25         4.50        80.81        24.72 
TCGA-ET-A40Q TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        7.17         4.01        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       24.69        68.22        66.77        81.34        39.95        81.83 
TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA 
       22.03        20.42        17.82        19.56        15.68        18.08 
TCGA-FY-A3YR TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A421 TCGA-H2-A422 
       17.36         6.58         1.35        21.60        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 
       48.92        47.41        10.26        16.90        21.83         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A4HW 
        8.65        17.23        27.19        24.69        22.29         2.60 
TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N6 
       15.68        19.73        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        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        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 
        5.10        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         5.75        10.88         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R 
        8.98         0.39         5.98        18.84        17.26         3.39 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        14.60        13.12         7.20         1.45         5.33 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US 
       34.36         6.77        12.43        35.18        16.41        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM 
       24.23        18.51        21.47         8.32        17.23        27.62 
TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 
       15.42        17.82        12.07        13.81        14.07        14.10 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       80.91        58.82        45.40        57.11        64.87        50.20 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZN 
       49.32        33.50       130.72        32.48        78.97        53.06 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KI 
       60.16        57.47        30.51        44.15        43.59        23.90 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.50        15.75        10.45        10.65        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 
       13.64        10.49        22.16        13.84        32.32        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL 
       22.52        30.94        14.14         8.35        37.25        16.80 
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        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
       13.91         7.82        11.51        13.51        29.33        21.34 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 
       21.53        60.49        13.68        48.20        18.38        19.76 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39S TCGA-ET-A3DQ 
       58.22        13.74        65.36        98.56        55.10        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 
       43.50         0.30       132.36         3.22         1.94        33.63 
TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 
        1.05         1.25         7.82         0.99        16.14        16.27 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A76V 
       16.57         0.76        17.06        22.49        19.04         1.68 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YE 
       21.67        12.46         9.63        43.17        31.82        27.85 
TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L TCGA-MK-A84Z TCGA-QD-A8IV 
        0.20        15.98        86.70        20.25        12.89 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        17.69        35.54        11.31        17.52         1.22 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-CE-A27D TCGA-CE-A481 TCGA-DE-A4M8 TCGA-DJ-A13L 
       15.48        21.01         0.10        11.38        18.54         9.96 
TCGA-DJ-A13O TCGA-DJ-A2PX TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UW 
       14.07         5.52        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        14.14         2.33        22.29 
TCGA-E8-A2JQ TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CU 
       11.70        13.61        14.27        13.58        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         1.41        43.36        83.57 
TCGA-EL-A3TA TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JZ TCGA-EM-A22M TCGA-EM-A22P 
       66.90        52.50         7.07        37.94        14.53        11.15 
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        57.11         5.85 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A3PB TCGA-FY-A3R6 
       17.98        25.32         4.80         5.03        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         7.82        21.63        23.47         0.53 
TCGA-CE-A3MD TCGA-CE-A482 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P 
        0.20        10.68        20.22        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        18.35         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 
        7.99        35.41        27.45        26.20        12.56         8.28 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       37.48        36.46        10.09        15.88        15.09        20.45 
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        18.21        14.70        54.90        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL 
       66.38        63.19        14.04        14.43        20.68        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        12.36        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        15.62 
TCGA-EM-A4FV TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J 
       24.46        32.35        27.09        12.26         2.66        71.01 
TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW 
       80.02        84.89         4.18         2.43         5.56         2.37 
TCGA-ET-A3DP TCGA-ET-A40T TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       69.24         2.14       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         6.02         6.74 
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 
     0.1      0.2      0.1      0.2 
subtype1 subtype2 subtype3 subtype4 
  155.54   132.36   157.15   169.32 
subtype1 subtype2 subtype3 subtype4 
   22.29    17.23    16.34    27.27 
[1] "0.1 - 155.5 (22.3)" "0.2 - 132.4 (17.2)" "0.1 - 157.2 (16.3)"
[4] "0.2 - 169.3 (27.3)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      84        7        45        1        28         2
  subtype2      90       30        27        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       90       41       67
  STAGE II         7       30        1       15
  STAGE III       45       27       13       23
  STAGE IV         1        1        0        0
  STAGE IVA       28        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 27 47 77 15
  subtype2 53 57 44  2
  subtype3 27 14 15  2
  subtype4 34 48 31  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       27       53       27       34
  T2       47       57       14       48
  T3       77       44       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  51 101
  subtype2 101  29
  subtype3  23  36
  subtype4  50  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51  101
  subtype2  101   29
  subtype3   23   36
  subtype4   50   58
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       51      101       23       50
  1      101       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 94  3
  subtype2 70  3
  subtype3 41  0
  subtype4 72  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    3
  subtype2   70    3
  subtype3   41    0
  subtype4   72    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       94       70       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 120  47
  subtype2 113  43
  subtype3  43  16
  subtype4  89  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  120   47
  subtype2  113   43
  subtype3   43   16
  subtype4   89   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      120      113       43       89
  MALE         47       43       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"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              4                                           134
  subtype2              2                                            71
  subtype3              1                                            50
  subtype4              2                                           100
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      3
  subtype2                                                                     82
  subtype3                                                                      3
  subtype4                                                                     12
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   1
  subtype3                                                                   5
  subtype4                                                                   3
D5V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               134
  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)       82
  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                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               100
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       12
  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"
D5V9, binary
          cls
clus         0   1
  subtype1  11 156
  subtype2   1 155
  subtype3   0  59
  subtype4   2 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  156
  subtype2    1  155
  subtype3    0   59
  subtype4    2  115
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11        1        0        2
  YES      156      155       59      115
[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"
D5V10, binary
          cls
clus         0   1
  subtype1 143   5
  subtype2 129   6
  subtype3  49   2
  subtype4  99   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  143    5
  subtype2  129    6
  subtype3   49    2
  subtype4   99    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       143      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   81                   1
  subtype2           23                       1  123                   0
  subtype3           13                       2   41                   0
  subtype4           29                       1   85                   0
D5V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  67       23       13       29
  MODERATE/ADVANCED (T4A)       14        1        2        1
  NONE                          81      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 126  26   2   9
  subtype2 124   9   0   8
  subtype3  41   7   0   5
  subtype4  90  10   2   8
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      126      124       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 66 99
  subtype2 74 79
  subtype3 26 31
  subtype4 59 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   99
  subtype2   74   79
  subtype3   26   31
  subtype4   59   55
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       66       74       26       59
  UNIFOCAL         99       79       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   118
  subtype2    88
  subtype3    45
  subtype4    75
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                                 118       88       45       75
[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  23 120
  subtype2   9  98
  subtype3   3  49
  subtype4   3  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23  120
  subtype2    9   98
  subtype3    3   49
  subtype4    3   90
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           23        9        3        3
  NOT HISPANIC OR LATINO      120       98       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 130   4
  subtype3  85   1
  subtype4  93   2
  subtype5  75   2
subtype1 subtype2 subtype3 subtype4 subtype5 
     105      134       86       95       77 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        4        1        2        2 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A3PU 
        4.24         8.25         4.01        20.71        42.15        18.64 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J 
        6.18         4.93        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         7.99        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        22.29        11.70        19.59 
TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR 
       25.45        14.70        13.78        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         1.41       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 
       47.47        29.69        14.79        12.33        29.49        22.09 
TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A3BO TCGA-ET-A3BT TCGA-ET-A3BV 
       16.08        61.02        58.72         5.85        24.72        42.25 
TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN TCGA-FE-A22Z 
       80.81        25.32        24.72         7.17         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FY-A3R8 
       59.70        68.22        81.34        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 
       10.26        16.90         2.96         8.65        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        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        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 
        5.10        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         5.75        10.88         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S 
        8.98         0.39         5.98        18.84        17.26         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       14.60        13.12         7.20         5.33        34.36         6.77 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.18        16.41        24.23         8.32        17.23        27.62 
TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A416 TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CZ 
       15.42        12.07        14.07        97.74        80.91        58.82 
TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T2 
       57.11        64.87        50.20        49.32        33.50        32.48 
TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI 
       78.97        60.16        57.47        30.51        44.15        23.90 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.50        15.75        10.45        10.65        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2CR 
       17.88        13.18        23.51         6.05        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI 
       10.49        22.16        13.84        32.32        17.29        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP 
       30.94        14.14         8.35        16.80        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        15.06        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU 
       11.51        13.51        29.33        21.34        21.53        60.49 
TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I 
       13.68        48.20        18.38        19.76        58.22        13.74 
TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       65.36        98.56         0.30       132.36         3.22         1.94 
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-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V TCGA-H2-A2K9 
       16.57         0.76        17.06        22.49         1.68        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L 
       12.46         9.63        43.17         0.20        15.98        86.70 
TCGA-MK-A84Z TCGA-QD-A8IV 
       20.25        12.89 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        17.69        35.54        11.31        17.52         1.22 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-BJ-A45H TCGA-CE-A27D TCGA-CE-A485 TCGA-DE-A0XZ 
       15.48        21.01         7.82         0.10         0.10        20.22 
TCGA-DE-A4M8 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A1QM TCGA-DJ-A2PR TCGA-DJ-A2PS 
       18.54        14.07         3.39         1.45        27.45        26.20 
TCGA-DJ-A2PX TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3US 
        5.52        40.24        37.48        35.90        12.43        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        21.37        18.51        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3VD TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       30.61        21.47        21.01        21.34        19.07        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E3-A3E2 
       14.70        17.82        15.81        24.33         2.33        63.19 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       13.61        14.27        13.81        14.10        14.96         7.69 
TCGA-E8-A44M TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D4 TCGA-EL-A3H3 TCGA-EL-A3T0 
       13.58        57.01         4.18        45.40        43.36       130.72 
TCGA-EL-A3TA TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EM-A22M 
       66.90        53.06        52.50        61.22         7.07        14.53 
TCGA-EM-A22P TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A4FO 
       11.15         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        57.11        55.10         5.56        59.87 
TCGA-ET-A3DT TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-FE-A232 TCGA-FY-A3R6 
       17.98         4.80         5.03         2.14        44.25        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         0.53         0.20        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        18.35 
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        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
        8.28        34.85        10.09        15.88        15.09        20.45 
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        18.21        54.90 
TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP 
       66.38        14.04        14.43        20.68        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        12.36 
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        15.62        32.35 
TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A3BP 
       27.09        12.26         2.66        71.01        80.02         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PD 
        2.43         2.37        69.24       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         6.02         6.74        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         0.23         0.10 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QO 
       15.42        36.46        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         7.99         9.44        31.04        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3VA TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY 
       21.27        24.82        24.20         3.12        21.53        31.07 
TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CS TCGA-EL-A3CT 
       40.21        30.31        14.27         3.02        45.53        60.95 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 
      115.10        65.39       147.75       101.13        49.71       131.15 
TCGA-EL-A3T3 TCGA-EL-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EM-A1CT 
      132.07        89.56        31.50        59.44        34.72        18.18 
TCGA-EM-A1CU TCGA-EM-A22O TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3FK TCGA-EM-A4FN 
       20.91        11.74        33.96        17.59        23.77        26.37 
TCGA-ET-A25N TCGA-ET-A2MX TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BX 
       14.79        54.05        59.15        28.24        38.30         4.50 
TCGA-ET-A3DR TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A3PC 
       43.50        31.59        24.69        66.77        39.95        85.68 
TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A4B3 
       22.03        20.42        17.82        19.56        18.08         1.35 
TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A41Y TCGA-J8-A3O1 TCGA-J8-A3YE 
       21.60         2.99        18.61        21.83        27.19        27.85 
TCGA-J8-A3YG TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4IC 
       22.29         2.60        15.68        19.73        35.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.41     0.20     0.10     0.20     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  157.15   132.36   130.72   169.32   147.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.920   16.650   17.755   27.950   23.470 
[1] "1.4 - 157.2 (22.9)" "0.2 - 132.4 (16.6)" "0.1 - 130.7 (17.8)"
[4] "0.2 - 169.3 (27.9)" "0.1 - 147.8 (23.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      46        2        39        1        16         1
  subtype2      76       30        21        1         4         2
  subtype3      57        3        18        0         8         0
  subtype4      54       12        19        0         8         2
  subtype5      49        6        11        0        10         1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         46       76       57       54       49
  STAGE II         2       30        3       12        6
  STAGE III       39       21       18       19       11
  STAGE IV         1        1        0        0        0
  STAGE IVA       16        4        8        8       10
  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 22 56 10
  subtype2 43 55 35  2
  subtype3 38 22 23  1
  subtype4 26 41 25  4
  subtype5 17 26 28  6
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       17       43       38       26       17
  T2       22       55       22       41       26
  T3       56       35       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 90 19
  subtype3 38 45
  subtype4 43 45
  subtype5 25 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   68
  subtype2   90   19
  subtype3   38   45
  subtype4   43   45
  subtype5   25   47
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       29       90       38       43       25
  1       68       19       45       45       47
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 56  1
  subtype2 56  3
  subtype3 60  0
  subtype4 58  3
  subtype5 47  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    1
  subtype2   56    3
  subtype3   60    0
  subtype4   58    3
  subtype5   47    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       56       56       60       58       47
  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 39
  subtype3 61 25
  subtype4 74 22
  subtype5 50 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84   21
  subtype2   96   39
  subtype3   61   25
  subtype4   74   22
  subtype5   50   27
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       84       96       61       74       50
  MALE         21       39       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"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              1                                            79
  subtype2              2                                            57
  subtype3              2                                            68
  subtype4              0                                            83
  subtype5              4                                            68
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      2
  subtype2                                                                     76
  subtype3                                                                     10
  subtype4                                                                     11
  subtype5                                                                      1
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  23
  subtype2                                                                   0
  subtype3                                                                   6
  subtype4                                                                   2
  subtype5                                                                   4
D6V8, 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)       76
  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                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                68
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        1
  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"
D6V9, binary
          cls
clus         0   1
  subtype1   5 100
  subtype2   1 134
  subtype3   1  85
  subtype4   2  94
  subtype5   5  72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  100
  subtype2    1  134
  subtype3    1   85
  subtype4    2   94
  subtype5    5   72
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         5        1        1        2        5
  YES      100      134       85       94       72
[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"
D6V10, binary
          cls
clus         0   1
  subtype1  95   3
  subtype2 111   5
  subtype3  66   6
  subtype4  85   1
  subtype5  63   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    3
  subtype2  111    5
  subtype3   66    6
  subtype4   85    1
  subtype5   63    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        95      111       66       85       63
  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           15                       1  110                   0
  subtype3           20                       1   62                   0
  subtype4           22                       1   71                   0
  subtype5           22                       5   49                   0
D6V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  MINIMAL (T3)                  53       15       20       22       22
  MODERATE/ADVANCED (T4A)       10        1        1        1        5
  NONE                          38      110       62       71       49
  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 103  10   0   8
  subtype3  70   4   0   6
  subtype4  76   8   2   6
  subtype5  62   7   0   4
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       70      103       70       76       62
  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 68
  subtype3 43 41
  subtype4 47 46
  subtype5 32 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   66
  subtype2   64   68
  subtype3   43   41
  subtype4   47   46
  subtype5   32   43
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  MULTIFOCAL       39       64       43       47       32
  UNIFOCAL         66       68       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    74
  subtype3    60
  subtype4    59
  subtype5    56
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       74       60       59       56
[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 81
  subtype3  3 71
  subtype4  3 71
  subtype5  8 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   77
  subtype2    9   81
  subtype3    3   71
  subtype4    3   71
  subtype5    8   57
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           15        9        3        3        8
  NOT HISPANIC OR LATINO       77       81       71       71       57
[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 148   3
  subtype3 164   1
subtype1 subtype2 subtype3 
     182      151      165 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28X 
        4.24         8.25         4.01        20.71        35.54        17.52 
TCGA-BJ-A291 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I 
       22.88        15.48        23.31        21.01         7.82         6.18 
TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
        4.93         0.10         0.20        11.38         0.10        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        14.07        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ 
      135.91        30.61         7.99         1.45        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         8.28         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         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       12.43        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 
       21.37        18.51        36.99        21.47        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        24.20        19.07        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA 
       14.70        15.81         2.33        40.21        31.23        22.29 
TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       11.70        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
       14.43        14.70        14.10        14.96         7.69        13.78 
TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       13.58        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        45.40         1.41        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       130.72         5.72        66.90        31.50 
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        52.50         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        11.15        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 
       47.47        14.79        12.33        16.08        71.01        84.89 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       58.72        55.10        28.24        24.72        38.30        42.25 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T 
       59.87        43.50        17.98        25.32         7.17         2.14 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PB TCGA-FK-A3SE 
        4.01        73.74        81.34        39.95        85.15        22.03 
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        10.26         2.96         8.65        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        19.73        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        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
        7.56        17.69        23.34        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         5.10        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         5.75        10.88         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DE-A4MD 
        8.98         0.23         0.39         5.98        18.84        25.12 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG 
       17.26         3.39         8.71        14.60         8.32        13.12 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        7.20         5.33        34.36         6.77        35.18        16.41 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UP 
       32.81        24.23         8.32        17.23        27.62        21.34 
TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E5 
       15.42        17.82        54.90        12.07        66.38        14.04 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GS TCGA-EL-A3GW 
       80.91        58.82        57.11        64.87        65.39        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        16.44        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        10.49        22.16        13.84 
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 
       16.80        12.07        17.39        15.02        15.06        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH 
        9.24        13.91         7.82        11.51        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        48.20        18.38 
TCGA-ET-A2MX TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N 
       54.05        19.76        58.22        13.74        65.36        98.56 
TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
        2.43         2.37        69.24         0.30       132.36         3.22 
TCGA-ET-A40R TCGA-ET-A4KQ TCGA-FE-A236 TCGA-FE-A239 TCGA-FE-A3PD TCGA-FK-A3S3 
        4.80         1.94        66.77        33.63        78.77        71.08 
TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 
        1.05         1.25         7.82         0.99        16.14        16.57 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
        0.76        17.06        21.67        12.46         9.63        43.17 
TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB TCGA-KS-A4ID TCGA-MK-A84Z 
       27.19        15.98        86.70        84.72        33.24        20.25 
TCGA-QD-A8IV 
       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         1.22        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         0.53 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       10.68         0.10        20.22        15.42        36.46        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         7.99        35.41        27.45        12.56 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
       34.85         5.52         9.44        10.09        15.88        15.09 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 
       20.45        31.46        36.33        20.22        30.61        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       24.82        22.92        18.97        18.21         3.12        24.33 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 
       21.53        31.07        63.19        30.31        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3D6 TCGA-EL-A3GV TCGA-EL-A3GX 
       25.45        20.68        31.66       108.36        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 
      101.13        43.36        49.71       131.15       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-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 
       89.56        61.22        59.44        45.96        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CV 
       43.59        24.30        27.06        26.86        18.18        12.36 
TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK 
       14.73        14.53        11.74        27.65        33.96        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       33.07        13.38        29.72        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       17.49         7.33        29.95        15.62        12.79        84.59 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N 
       26.37        22.45        24.46        29.69        32.35        14.79 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 
       27.09        29.49        22.09        12.26        29.19         2.66 
TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP 
       80.02        61.02        57.11        59.15         5.85         4.18 
TCGA-ET-A3BS TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A230 
        5.56         4.50        80.81        24.72         5.03        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A23A 
       31.59        44.25        24.69        68.22       117.40        81.83 
TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL 
      106.36        85.68         4.11         0.92       116.09        20.42 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A40N TCGA-FY-A4B4 TCGA-FY-A76V 
       19.56        15.68        18.08        19.04        21.60         1.68 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3U3 TCGA-IM-A41Y 
        2.99        20.05        18.61        48.92        16.90        21.83 
TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       17.23        27.85         5.75         0.20       143.57        15.68 
TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-L6-A4EP TCGA-L6-A4EQ 
        6.02         6.74        32.45        87.39        33.40        40.37 
TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83        32.45        30.21 

subtype1 subtype2 subtype3 
    0.10     0.23     0.10 
subtype1 subtype2 subtype3 
  158.83   132.36   169.32 
subtype1 subtype2 subtype3 
  20.105   17.060   24.330 
[1] "0.1 - 158.8 (20.1)" "0.2 - 132.4 (17.1)" "0.1 - 169.3 (24.3)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      90        6        56        1        26         2
  subtype2      93       29        21        1         5         2
  subtype3      99       18        32        0        15         2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         90       93       99
  STAGE II         6       29       18
  STAGE III       56       21       32
  STAGE IV         1        1        0
  STAGE IVA       26        5       15
  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 39 70 15
  subtype2 43 68 39  2
  subtype3 43 60 57  6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       56       43       43
  T2       39       68       60
  T3       70       39       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  96  28
  subtype3  65  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65  108
  subtype2   96   28
  subtype3   65   88
   clus
vv  subtype1 subtype2 subtype3
  0       65       96       65
  1      108       28       88
[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  65   3
  subtype3  90   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  122    2
  subtype2   65    3
  subtype3   90    4
   clus
vv  subtype1 subtype2 subtype3
  0      122       65       90
  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  43
  subtype3 122  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135   47
  subtype2  109   43
  subtype3  122   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      135      109      122
  MALE         47       43       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"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              4                                           144
  subtype2              2                                            67
  subtype3              3                                           144
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      8
  subtype2                                                                     83
  subtype3                                                                      9
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   0
  subtype3                                                                  10
D7V8, 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)       83
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               144
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  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"
D7V9, binary
          cls
clus         0   1
  subtype1   3 179
  subtype2   3 149
  subtype3   8 158
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  179
  subtype2    3  149
  subtype3    8  158
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        8
  YES      179      149      158
[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"
D7V10, binary
          cls
clus         0   1
  subtype1 154   7
  subtype2 127   5
  subtype3 140   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  154    7
  subtype2  127    5
  subtype3  140    5
     clus
vv    subtype1 subtype2 subtype3
  NO       154      127      140
  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           16                       0  128                   0
  subtype3           51                       4  107                   0
D7V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  64       16       51
  MODERATE/ADVANCED (T4A)       14        0        4
  NONE                          97      128      107
  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 119  10   0  10
  subtype3 131  16   1   8
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      132      119      131
  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 81
  subtype3 77 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   99
  subtype2   66   81
  subtype3   77   85
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       82       66       77
  UNIFOCAL         99       81       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    86
  subtype3   108
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       86      108
[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  95
  subtype3  15 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  144
  subtype2   10   95
  subtype3   15  119
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13       10       15
  NOT HISPANIC OR LATINO      144       95      119
[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 126   3
  subtype3 189   1
subtype1 subtype2 subtype3 
     179      129      190 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W 
        4.24         4.01         7.56        20.71        35.54        11.31 
TCGA-BJ-A28X TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H 
       17.52        18.97        15.48        23.31        21.01         7.82 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
        6.18         4.93         0.10        11.38         0.10        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        14.07        11.01       135.91 
TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS 
        7.99         1.45        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         8.28         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         7.10        35.90        12.43        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        21.37        18.51        36.99 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       21.47        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 
       24.20        21.34        19.07        14.14        14.70        17.82 
TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       15.81         2.33        40.21        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 
       19.59        13.61        14.27        13.81        14.07        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
       14.70        14.10        14.96         7.69        13.78        13.58 
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         1.41        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 
      130.72       129.57         5.72        66.90        31.50        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        52.50         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        11.15        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 
       47.47        14.79        12.33        29.49        16.08        71.01 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BV TCGA-ET-A3DQ 
       58.72        55.10        28.24        24.72        42.25        59.87 
TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 
       43.50         7.17         2.14         4.01        73.74        81.34 
TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 
       85.15         4.11        22.03        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        10.26         2.96         8.65 
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 
       19.73         6.74        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        18.21        18.87        11.57        16.73 
TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V 
       23.34        20.58         4.83        44.35        21.04         5.10 
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 
        5.75        10.88         3.45         6.35         8.98         0.39 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W 
        5.98        18.84        17.26         3.39         8.71        14.60 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB 
       13.12         7.20         5.33        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        24.23         8.32        17.23        27.62        15.42 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       12.07        58.82        45.40        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        16.44        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        10.49        22.16        13.84 
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 
       16.80        12.07        17.39        15.02        15.06        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH 
        9.24        13.91         7.82        11.51        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        48.20        18.38 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       19.76        58.22        13.74        98.56         0.30       132.36 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 
        3.22         1.94        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         9.63        43.17        27.19        15.98        86.70 
TCGA-KS-A4ID TCGA-MK-A84Z TCGA-QD-A8IV 
       33.24        20.25        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         8.25        15.12        17.69        42.15 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 
        1.22        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 
        0.53         0.20         0.23        10.68         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       15.42        36.46        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         7.99        35.41        27.45 
TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 
       12.56        34.85         5.52         9.44        37.48        10.09 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3US 
       15.88        15.09        20.45        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-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
       18.21         3.12        24.33        54.90        21.53        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A417 TCGA-E8-A418 
       66.38        63.19        30.31        14.04        14.27         3.02 
TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CX TCGA-EL-A3D6 TCGA-EL-A3GS 
       25.45        20.68        31.66        80.91       108.36        65.39 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 
       50.37       147.75       101.13        43.36        49.71       131.15 
TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      108.66        29.65       132.07        98.24        41.29       107.47 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 
       82.82        89.56        61.22        45.96        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       43.59        27.06        26.86        18.18        20.91        12.36 
TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK 
       14.73        14.53        11.74        27.65        33.96        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       33.07        13.38        29.72        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       17.49        16.18         7.33        29.95        15.62        12.79 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N 
       26.37        22.45        24.46        29.69        32.35        14.79 
TCGA-ET-A25O TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 
       27.09        54.05        22.09        12.26        29.19         2.66 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T 
       80.02        65.36        84.89        61.02        57.11        59.15 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW 
        5.85         4.18         2.43         5.56        38.30         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DW 
        4.50        80.81        69.24        17.98        25.32        24.72 
TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.80         5.03        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
       68.22       117.40        66.77        39.95        81.83       106.36 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL 
       85.68        78.77        71.08         0.92       116.09        20.42 
TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B4 TCGA-FY-A76V 
       19.56        18.08        22.49        19.04        21.60         1.68 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 
        2.99        20.05        18.61        48.92        47.41        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-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP 
       15.68         6.02        32.45        87.39        84.72        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 
     0.1      0.3      0.1 
subtype1 subtype2 subtype3 
  158.83   132.36   169.32 
subtype1 subtype2 subtype3 
   19.20    16.57    24.97 
[1] "0.1 - 158.8 (19.2)" "0.3 - 132.4 (16.6)" "0.1 - 169.3 (25.0)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      88        5        57        1        25         2
  subtype2      74       28        20        1         4         2
  subtype3     120       20        32        0        17         2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         88       74      120
  STAGE II         5       28       20
  STAGE III       57       20       32
  STAGE IV         1        1        0
  STAGE IVA       25        4       17
  STAGE IVC        2        2        2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 55 37 70 15
  subtype2 41 53 35  1
  subtype3 46 77 61  7
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55       41       46
  T2       37       53       77
  T3       70       35       61
  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  74 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66  103
  subtype2   86   19
  subtype3   74  102
   clus
vv  subtype1 subtype2 subtype3
  0       66       86       74
  1      103       19      102
[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  98   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  124    2
  subtype2   55    3
  subtype3   98    4
   clus
vv  subtype1 subtype2 subtype3
  0      124       55       98
  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 139  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135   44
  subtype2   92   38
  subtype3  139   52
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      135       92      139
  MALE         44       38       52
[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              4                                           163
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      9
  subtype2                                                                     77
  subtype3                                                                     14
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   0
  subtype3                                                                  10
D8V8, 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                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               163
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  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"
D8V9, binary
          cls
clus         0   1
  subtype1   2 177
  subtype2   1 129
  subtype3  11 180
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  177
  subtype2    1  129
  subtype3   11  180
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1       11
  YES      177      129      180
[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"
D8V10, binary
          cls
clus         0   1
  subtype1 153   6
  subtype2 107   5
  subtype3 161   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  153    6
  subtype2  107    5
  subtype3  161    6
     clus
vv    subtype1 subtype2 subtype3
  NO       153      107      161
  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           49                       4  134                   0
D8V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  67       15       49
  MODERATE/ADVANCED (T4A)       14        0        4
  NONE                          91      107      134
  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 152  17   1  10
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      129      101      152
  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  62  66
  subtype3  87  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76  101
  subtype2   62   66
  subtype3   87   98
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       76       62       87
  UNIFOCAL        101       66       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   125
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      125
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V17, binary
          cls
clus         0   1
  subtype1  13 142
  subtype2   8  76
  subtype3  17 140
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  142
  subtype2    8   76
  subtype3   17  140
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        8       17
  NOT HISPANIC OR LATINO      142       76      140
[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 162   2
  subtype3 141   2
subtype1 subtype2 subtype3 
     161      164      143 
subtype1 subtype2 subtype3 
      10        2        2 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
        4.24         4.01        20.71        35.54        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E 
        1.22        22.88        18.97        15.48        23.31        21.01 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB 
        7.82         6.18         4.93         0.10        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        14.07        11.01       135.91         7.99 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PW 
        1.45        47.41        17.56        38.83         8.28        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         7.10 
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 
       21.37        36.99        21.47        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        24.20        14.14        14.70        17.82 
TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       15.81         2.33        31.23        22.29        11.70        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A419 TCGA-E8-A432 
       13.61        14.27        13.81        14.07        25.45        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN 
       14.70        14.10        14.96        13.78        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         1.41        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       130.72       129.57         5.72        66.90 
TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW 
       31.50        36.03        47.38        52.50         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        11.15        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        47.47 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A3BU TCGA-ET-A3BV 
       14.79        12.33        84.89        61.02        38.30        42.25 
TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T 
       80.81        59.87        17.98        25.32         7.17         2.14 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE 
        4.01        73.74        81.34        85.15         4.11        22.03 
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        10.26         2.96         8.65        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        18.21        16.34        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
        7.56        15.12        23.34        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         5.10        16.01        13.94        18.64 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
        0.10         0.20         0.23        15.42        36.46        15.85 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF 
      169.32         3.39         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 
       13.12        14.96         7.20        42.58        10.09         5.33 
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-A3VL TCGA-DJ-A3VM TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
       18.97        17.23        27.62        54.90        21.53        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3D5 TCGA-EL-A3GO 
       14.27         3.02       158.83        98.53        57.11        64.87 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T6 TCGA-EL-A3T8 TCGA-EL-A3TB 
       49.71       108.66        29.65        98.24       107.47        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EM-A1CS 
       78.97        62.30        53.06        61.22        59.44        26.86 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2CO 
       12.36        18.05        19.79        19.46        54.08         6.05 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P2 
       22.16        13.84        19.73        33.96        17.59        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FN 
        8.35        29.72        37.25        27.95        23.77        12.07 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        15.06         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
        7.82        29.69        32.35        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A39K TCGA-ET-A39P TCGA-ET-A39R 
       29.49        54.05        12.26        80.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW 
       55.10        59.15        28.24         2.43         5.56         2.37 
TCGA-ET-A3BX TCGA-ET-A3DR TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R TCGA-FE-A230 
        4.50        43.50       132.36         3.22         4.80        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       117.40        66.77 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FY-A3BL TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON 
       71.08         1.05        20.42         0.99        16.14        19.56 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3WA TCGA-FY-A40N TCGA-H2-A3RH TCGA-H2-A3RI 
       16.57        18.08        17.06        19.04        12.46         2.99 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 
       18.61        48.92        47.41         9.63        43.17        27.19 
TCGA-KS-A41F TCGA-KS-A41J 
      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         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O9 
       10.88         3.45         6.35        21.63         8.98        23.47 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A2OL 
       11.38        10.68         0.10         0.39        20.22         5.98 
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         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       35.41        26.20        12.56         5.52         9.44        37.48 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       10.09        12.43        35.18        15.88        15.09        20.45 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       31.46        16.41        24.23        18.51        20.22        30.61 
TCGA-DJ-A3VG TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4V2 
        8.32        18.21        21.34        19.07        15.42         3.12 
TCGA-DJ-A4V5 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3GV 
       24.33         7.69        20.68        13.58        31.66        50.37 
TCGA-EL-A3H1 TCGA-EL-A3H8 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3ZG 
       49.32       131.15        32.48       132.07        41.29        89.56 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       60.16        57.47        30.51        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       43.59        27.06        23.90        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        10.65        11.74        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3ST TCGA-EM-A3SU 
       10.49        13.15        17.49        17.39        11.51        29.95 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FR 
       12.79        84.59        29.33        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       60.49        24.46        13.68        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39N TCGA-ET-A3BO 
       19.76        58.22        13.74        71.01        98.56         5.85 
TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A40S TCGA-ET-A4KQ TCGA-FK-A3SG 
        4.18        69.24         0.30         5.03         1.94         0.92 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3W9 TCGA-FY-A40M TCGA-FY-A4B4 TCGA-FY-A76V 
      116.09         1.25         0.76        22.49        21.60         1.68 
TCGA-H2-A2K9 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YD TCGA-J8-A3YE 
       21.67        16.90        21.83        17.23        31.82        27.85 
TCGA-J8-A3YH TCGA-J8-A4HW TCGA-KS-A41I TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
        5.75         2.60        15.98         6.02        19.73         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       32.45        87.39        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       21.83        32.45        30.21        20.25        12.89 

subtype1 subtype2 subtype3 
     0.1      0.1      0.1 
subtype1 subtype2 subtype3 
  157.15   169.32   132.07 
subtype1 subtype2 subtype3 
   19.20    23.13    19.07 
[1] "0.1 - 157.2 (19.2)" "0.1 - 169.3 (23.1)" "0.1 - 132.1 (19.1)"
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       28        20        0         8         2
  subtype3      83       17        30        1        11         2
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         78      105       83
  STAGE II         6       28       17
  STAGE III       52       20       30
  STAGE IV         1        0        1
  STAGE IVA       22        8       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 35 68 15
  subtype2 47 67 45  5
  subtype3 46 55 41  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       47       46
  T2       35       67       55
  T3       68       45       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 87 58
  subtype3 66 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   95
  subtype2   87   58
  subtype3   66   58
   clus
vv  subtype1 subtype2 subtype3
  0       59       87       66
  1       95       58       58
[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  71   4
  subtype3  82   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108    2
  subtype2   71    4
  subtype3   82    3
   clus
vv  subtype1 subtype2 subtype3
  0      108       71       82
  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  45
  subtype3 106  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119   42
  subtype2  119   45
  subtype3  106   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      119      119      106
  MALE         42       45       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              3                                           126
  subtype2              2                                           113
  subtype3              4                                           100
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     46
  subtype3                                                                     37
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   3
  subtype3                                                                   4
D9V8, 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)       46
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               100
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       37
  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"
D9V9, binary
          cls
clus         0   1
  subtype1   2 159
  subtype2  12 152
  subtype3   0 145
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  159
  subtype2   12  152
  subtype3    0  145
     clus
vv    subtype1 subtype2 subtype3
  NO         2       12        0
  YES      159      152      145
[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"
D9V10, binary
          cls
clus         0   1
  subtype1 135   5
  subtype2 136   8
  subtype3 125   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135    5
  subtype2  136    8
  subtype3  125    3
     clus
vv    subtype1 subtype2 subtype3
  NO       135      136      125
  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           30                       2  127                   0
  subtype3           34                       1  105                   0
D9V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  60       30       34
  MODERATE/ADVANCED (T4A)       14        2        1
  NONE                          79      127      105
  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 137   9   1  11
  subtype3 109  15   0   9
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      112      137      109
  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 87
  subtype3 68 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   86
  subtype2   71   87
  subtype3   68   75
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       75       71       68
  UNIFOCAL         86       87       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   107
  subtype3    79
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      107       79
[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  12 117
  subtype3   9  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  130
  subtype2   12  117
  subtype3    9   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14       12        9
  NOT HISPANIC OR LATINO      130      117       93
[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 123   3
  subtype3 176   1
subtype1 subtype2 subtype3 
     165      126      177 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
        4.24         4.01        20.71        35.54        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E 
        1.22        22.88        18.97        15.48        23.31        21.01 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 
        7.82         6.18         4.93         0.10        11.38         0.10 
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        14.07        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PS 
      135.91         7.99         1.45        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         8.28         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         7.10        35.90        12.43        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        21.37        18.51        36.99 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       21.47        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 
       24.20        21.34        19.07        14.14        14.70        17.82 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       15.81        24.33         2.33        31.23        22.29        11.70 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 
       19.59        13.61        14.27        13.81        14.07        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
       14.70        14.10        14.96         7.69        13.78        13.58 
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         1.41 
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       130.72         5.72        66.90        31.50 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW 
       36.03        53.06        47.38        52.50         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        11.15 
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        47.47        14.79        12.33        29.49        16.08 
TCGA-ET-A39M TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BV TCGA-ET-A3DQ 
       84.89        58.72        55.10        28.24        42.25        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN 
       43.50        17.98        25.32         7.17         2.14         4.01 
TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
       73.74        81.34        85.15        22.03        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        10.26 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A4HW 
        8.65        11.24        31.82        24.69        22.29         2.60 
TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU 
       19.73        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        18.21        16.34        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        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 
        5.10        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 
        5.75        10.88         3.45         6.35         8.98         0.39 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A1QL 
        5.98        18.84         3.39         8.71        13.12         7.20 
TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2Q4 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        5.33        34.36         6.77         9.44        35.18        16.41 
TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DO-A1JZ 
       24.23         8.32        17.23        27.62        15.42        54.90 
TCGA-E3-A3DZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 
       12.07        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-A4K7 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       41.13        43.59        23.90        18.05        19.79        19.46 
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 
       16.44        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-A2P2 
       12.30        13.64        10.49        22.16        13.84        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FN TCGA-EM-A3FP 
       22.52        30.94        14.14         8.35        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        15.06         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A4FH TCGA-EM-A4FR TCGA-EM-A4FU 
        7.82        11.51        29.95        29.33        21.53        60.49 
TCGA-EM-A4G1 TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I 
       13.68        18.38        29.19        19.76        58.22        13.74 
TCGA-ET-A39N TCGA-ET-A39T TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       98.56        59.15         0.30       132.36         3.22         1.94 
TCGA-FE-A236 TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3NM TCGA-FY-A3NP 
       66.77        33.63         1.05         1.25         0.99        16.14 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V TCGA-H2-A2K9 
       16.57         0.76        17.06        22.49         1.68        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-KS-A41I TCGA-MK-A84Z TCGA-QD-A8IV 
       12.46         9.63        43.17        15.98        20.25        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         0.20         0.23        10.68         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J 
       15.42        36.46        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         7.99        35.41        27.45        12.56 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
       34.85         5.52        37.48        10.09        15.88        15.09 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3VA 
       20.45        31.46        36.33        20.22        30.61        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY 
       22.92        18.97        18.21         3.12        21.53        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A417 
       66.38        40.21        63.19        30.31        14.04        14.27 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CN TCGA-EL-A3CP 
        3.02        25.45        20.68        31.66       155.54       158.83 
TCGA-EL-A3D6 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      108.36        50.24        50.37       147.75       101.13       139.99 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T1 
       43.36        49.71       131.15       108.66        29.65       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG 
      132.07        98.24        41.29       107.47        82.82        89.56 
TCGA-EL-A3ZL TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K9 TCGA-EL-A4KG 
       62.30        61.22        59.44        45.96        47.84        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M 
       27.06        26.86        20.91        12.36        14.73        14.53 
TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3AK 
       11.74        27.65        19.73        33.96        17.59        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       33.07        13.38        29.72        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FN TCGA-EM-A4FQ 
       17.49        16.18        12.79        84.59        26.37        22.45 
TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MX 
       24.46        29.69        32.35        14.79        27.09        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39R 
       22.09        12.26        71.01        80.02        61.02        57.11 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW 
        5.85         4.18         2.43         5.56        38.30         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 
        4.50        80.81        69.24         4.80         5.03        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A238 
       31.59        44.25        24.69        68.22       117.40        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-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA 
        0.92       116.09        20.42        19.56        15.68        18.08 
TCGA-FY-A40N TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       19.04         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE 
       16.90        21.83         2.96        17.23        27.19        27.85 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 
        5.75         2.47       143.57        15.68         6.02         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       32.45        87.39        33.24        33.40        40.37        21.83 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       36.10        32.45        30.21 

subtype1 subtype2 subtype3 
     0.1      0.3      0.1 
subtype1 subtype2 subtype3 
  157.15   132.36   169.32 
subtype1 subtype2 subtype3 
  18.970   16.375   27.090 
[1] "0.1 - 157.2 (19.0)" "0.3 - 132.4 (16.4)" "0.1 - 169.3 (27.1)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      77        4        58        1        23         2
  subtype2      70       27        23        1         3         2
  subtype3     119       20        21        0        15         2
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         77       70      119
  STAGE II         4       27       20
  STAGE III       58       23       21
  STAGE IV         1        1        0
  STAGE IVA       23        3       15
  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 34 67 15
  subtype2 38 54 34  1
  subtype3 50 69 53  6
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       47       38       50
  T2       34       54       69
  T3       67       34       53
  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 22
  subtype3 73 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   98
  subtype2   80   22
  subtype3   73   91
   clus
vv  subtype1 subtype2 subtype3
  0       59       80       73
  1       98       22       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  51   3
  subtype3  96   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    2
  subtype2   51    3
  subtype3   96    4
   clus
vv  subtype1 subtype2 subtype3
  0      114       51       96
  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  85  42
  subtype3 134  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125   40
  subtype2   85   42
  subtype3  134   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      125       85      134
  MALE         40       42       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"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           130
  subtype2              2                                            56
  subtype3              4                                           153
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     69
  subtype3                                                                     14
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   0
  subtype3                                                                   7
D10V8, 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                                56
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       69
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               153
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  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"
D10V9, binary
          cls
clus         0   1
  subtype1   2 163
  subtype2   3 124
  subtype3   9 169
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  163
  subtype2    3  124
  subtype3    9  169
     clus
vv    subtype1 subtype2 subtype3
  NO         2        3        9
  YES      163      124      169
[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"
D10V10, binary
          cls
clus         0   1
  subtype1 139   6
  subtype2 106   5
  subtype3 151   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139    6
  subtype2  106    5
  subtype3  151    5
     clus
vv    subtype1 subtype2 subtype3
  NO       139      106      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  103                   0
  subtype3           44                       3  127                   0
D10V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  63       17       44
  MODERATE/ADVANCED (T4A)       14        0        3
  NONE                          81      103      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  97   9   0   9
  subtype3 146  13   2   9
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      115       97      146
  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 62
  subtype3 80 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   92
  subtype2   62   62
  subtype3   80   94
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       72       62       80
  UNIFOCAL         92       62       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    69
  subtype3   117
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       69      117
[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  79
  subtype3  18 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  136
  subtype2    7   79
  subtype3   18  125
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10        7       18
  NOT HISPANIC OR LATINO      136       79      125
[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"
