[1] "ofn"        "-oTLIHC-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/LIHC-TP/15082975/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/15111045/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=363, in cluster file=377, common to both=363
[1]   8 363
[1] "CN_CNMF"
[1] 3
  1   2   3 
106 119 132 
  1   2   3 
106 119 132 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 82 166 115 
  1   2   3 
 82 166 115 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
59 97 70 65 66 
 1  2  3  4  5 
59 97 70 65 66 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 52  55 113  82  55 
  1   2   3   4   5 
 52  55 113  82  55 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
 62 127  49 120 
  1   2   3   4 
 62 127  49 120 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 41  96  56 118  47 
  1   2   3   4   5 
 41  96  56 118  47 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 91  84 118  41 
  1   2   3   4 
 91  84 118  41 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
63 87 98 34 52 
 1  2  3  4  5 
63 87 98 34 52 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 363 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=106,	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=227,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	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=2,	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:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'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 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=22,	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 363 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "NEOPLASM_DISEASESTAGE"    
 [3] "PATHOLOGY_T_STAGE"         "PATHOLOGY_N_STAGE"        
 [5] "PATHOLOGY_M_STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL_TYPE"         "COMPLETENESS_OF_RESECTION"
 [9] "RACE"                      "ETHNICITY"                
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 179  91  77  13 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  180    91    77    13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 179  91  77  13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  180    91    77    13 
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=3, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
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 69 35
  subtype2 68 38
  subtype3 88 36
subtype1 subtype2 subtype3 
     104      106      124 
subtype1 subtype2 subtype3 
      35       38       36 
$subtype1
TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       41.79        40.41        18.25         1.18         8.55        13.02 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 
       10.59        11.97        48.99        46.78         2.99        44.42 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EE 
        0.13        79.73        53.33         7.33        90.71        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       12.95        45.11         6.02        21.14         5.62        19.76 
TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NR TCGA-DD-A73D 
       17.59         0.36        30.97        39.78         0.30        22.78 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM 
      114.35        76.41        12.53        53.19        69.11        58.16 
TCGA-DD-AACQ TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       14.20        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM 
       44.22        40.54        39.52        35.67        34.49         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE9 
       29.52        15.06        14.33        18.21        18.15        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVQ 
       15.72        25.08        23.64        25.78        50.33        89.69 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       59.93        76.18        64.77        62.47        66.25        49.48 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A2KC 
       53.69        13.35         9.73         1.84        18.74         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A4ZP 
        9.96        22.85        14.40        23.97         8.12        81.73 
TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ 
        0.39        22.13        19.53        20.42         5.98        11.24 
TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        9.70         8.75         2.99        16.83         3.72        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I 
       13.38        13.97        12.03         9.57        12.85        20.71 
TCGA-O8-A75V TCGA-RC-A7SF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 
       17.69        19.04        12.99        13.55        35.77        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57        11.21 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H8 
       23.80        24.89        27.88       120.82        56.91        20.81 
TCGA-2Y-A9H9 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       14.99        10.13        27.52        27.52        23.34         1.12 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        13.84         0.26        22.36        17.98        14.60 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.66         0.07         3.19         4.24         0.07         0.10 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00         2.60        21.76        49.15        33.04        13.64 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       13.78        30.61        30.51        29.56        73.81         9.30 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       13.48         0.53        75.65        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
        6.41        42.81        13.64        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       50.33        42.58        22.09        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV 
       40.47         3.78        20.91        14.89        66.67        18.87 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
       19.30        18.25        18.25        18.61         4.64        21.83 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PY 
       16.37        35.08        79.07        72.39        13.41        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B 
        0.20        13.15        13.35        20.61        19.59        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25X 
       19.10        27.88         6.38         0.03        13.68        58.49 
TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 
       14.86        25.25        12.03        11.80         2.14         3.02 
TCGA-LG-A6GG TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       12.72        19.92        21.01        15.39        15.52        24.13 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
        0.76        17.59        16.44        15.98         7.04        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       11.34         0.99        24.43        40.80 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       53.39        63.75        83.24        80.28        41.33        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D 
       11.74        37.25         8.61        10.78         0.66        11.08 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A69I 
        1.51        27.91        37.32        25.32        69.57        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        13.45        36.66         2.86         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D 
        3.32         0.10        37.78        83.57         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EK TCGA-DD-A39W 
       79.40        66.31        19.79        75.65        18.35        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69        25.81         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI 
      107.11        33.14        32.52        90.28        30.15        26.83 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       56.25       108.76        12.26        80.75        78.84        23.93 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACK 
       23.05         1.45        35.67        11.41        55.40         0.30 
TCGA-DD-AACL TCGA-DD-AACO TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AADG TCGA-DD-AADJ 
        3.52        61.68        46.82         5.59        37.64        35.05 
TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAVR 
       15.58        20.98        19.99        21.17        18.90        82.62 
TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       56.48        65.39        12.69        15.85        13.91         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A3RK TCGA-FV-A3R3 
       14.04        13.41         0.20        19.99        11.93        12.03 
TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        0.33        51.06        53.79        28.27        30.74        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC 
       25.64         5.92        19.23        22.95        17.10         7.76 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        1.84         8.55         9.17         0.89         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-MI-A75E 
       37.91        20.75        17.06         2.14        24.36        16.67 
TCGA-MI-A75G TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A7S9 
       18.38         0.62        10.85        58.88         3.09        21.04 
TCGA-RC-A7SB TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WX-AA46 TCGA-ZP-A9CY 
       19.33        19.76         1.71        10.32        24.85        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CF 
       23.21        23.57         0.69        79.30 

subtype1 subtype2 subtype3 
    0.13     0.03     0.10 
subtype1 subtype2 subtype3 
  114.35   120.82   108.76 
subtype1 subtype2 subtype3 
  18.395   18.115   21.010 
[1] "0.1 - 114.3 (18.4)" "0.0 - 120.8 (18.1)" "0.1 - 108.8 (21.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      58       25         0         14          1          0        1
  subtype2      47       33         1         22          3          2        2
  subtype3      63       26         2         23          4          5        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          58       47       63
  STAGE II         25       33       26
  STAGE III         0        1        2
  STAGE IIIA       14       22       23
  STAGE IIIB        1        3        4
  STAGE IIIC        0        2        5
  STAGE IV          1        2        0
  STAGE IVA         1        0        0
  STAGE IVB         0        1        1
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    61 26 17  1
  subtype2    50 36 27  6
  subtype3    68 29 29  5
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       61       50       68
  T2          26       36       29
  T3          17       27       29
  T4           1        6        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"
D1V5, binary
          cls
clus        0  1
  subtype1 73  1
  subtype2 86  1
  subtype3 90  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    1
  subtype2   86    1
  subtype3   90    1
   clus
vv  subtype1 subtype2 subtype3
  0       73       86       90
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 77  1
  subtype2 91  2
  subtype3 92  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77    1
  subtype2   91    2
  subtype3   92    1
   clus
vv  subtype1 subtype2 subtype3
  0       77       91       92
  1        1        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 23 83
  subtype2 43 76
  subtype3 47 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   83
  subtype2   43   76
  subtype3   47   85
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       43       47
  MALE         83       76       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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                      104
  subtype2                       0                      116
  subtype3                       2                      128
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                3
  subtype3                                2
D1V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        0        2
  HEPATOCELLULAR CARCINOMA              104      116      128
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        3        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  95   6   1   3
  subtype2 103   6   0   9
  subtype3 117   3   0   7
D1V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       95      103      117
  R1        6        6        3
  R2        1        0        0
  RX        3        9        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    49                         5
  subtype2                                0    63                         4
  subtype3                                0    44                         8
          vv
clus       WHITE
  subtype1    46
  subtype2    51
  subtype3    76
D1V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  49       63       44
  BLACK OR AFRICAN AMERICAN               5        4        8
  WHITE                                  46       51       76
[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"
D1V11, binary
          cls
clus         0   1
  subtype1   5  96
  subtype2   4 112
  subtype3   2 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   96
  subtype2    4  112
  subtype3    2  121
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        4        2
  NOT HISPANIC OR LATINO       96      112      121
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1  51  24
  subtype2 104  53
  subtype3  72  34
subtype1 subtype2 subtype3 
      75      157      106 
subtype1 subtype2 subtype3 
      24       53       34 
$subtype1
TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-5R-AA1D 
       83.24        41.79        80.28        24.89        56.91        11.08 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3EP TCGA-CC-5260 
       48.99        27.91        25.32        69.57        13.45         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A1E9 TCGA-DD-A1EC 
        3.39         3.32         0.10        37.78        90.71        19.79 
TCGA-DD-A1ED TCGA-DD-A1EL TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       75.65        13.64       107.11        33.14        32.52        90.28 
TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       30.15        56.25       108.76        12.26         0.30        80.75 
TCGA-DD-A73C TCGA-DD-AACC TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACZ TCGA-DD-AAD2 
       23.05        55.40         3.52        58.16         5.62        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADK TCGA-DD-AAE8 TCGA-DD-AAEK TCGA-ED-A4XI 
       42.58        44.22        34.49        21.83        35.08        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K 
       15.85        13.91         0.20        14.04        13.41         0.20 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI 
       11.93        14.40        51.06        28.27        30.74         5.92 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-HP-A5MZ TCGA-HP-A5N0 
       22.95        12.03         1.84         9.17         2.99        37.91 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       20.75        17.06        16.83         3.72        24.36        13.97 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-RG-A7D4 TCGA-T1-A6J8 
       16.67        20.71         0.62        10.85        24.13         0.76 
TCGA-UB-AA0V TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        24.85        13.55 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       23.80        53.39        27.88       120.82        40.41        47.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       37.25        14.99         1.18         8.55        13.02         8.61 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        0.66        11.97         1.51        46.78        27.52        27.52 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5263 
       17.98        12.72        18.48        44.81         0.66         4.24 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
        0.10        83.57         2.60        21.76        51.29        79.40 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       11.47        45.11        33.04        18.35        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 
        5.62        19.76        25.81         7.66        70.06       102.74 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        30.97        26.37        26.83        30.51        39.78 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 
       78.84        23.93        22.78         1.45        35.67         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ 
       75.65        76.41        63.48        12.00         6.41        69.11 
TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACX 
        0.30        13.64        14.20        51.52        50.33         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADF 
       47.67         4.50        22.09        40.08        40.47         3.78 
TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       37.64        20.91         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE1 TCGA-DD-AAE2 
       66.67        15.58        18.21        18.87        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
       18.61        19.99         4.64        21.17        23.74        18.90 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAW1 
       15.72        16.37        25.78        50.33        72.39        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       49.48        53.69         0.20        18.74        19.99        20.61 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
        0.62         9.96        22.85        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG 
        6.38         0.03        13.68        53.79        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        24.46        20.42        17.10         7.76 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 
       11.24         8.55        11.80         9.70         0.89         8.75 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        1.02         2.20         2.14        11.84        13.38        12.72 
TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
       18.38        12.85        58.88        21.01         3.09        19.33 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L 
       19.04        15.52        16.44         1.71        10.75        11.34 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       12.99        35.77        25.71         0.69        12.99        40.80 
TCGA-ZS-A9CF 
       79.30 

$subtype3
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H8 TCGA-5C-A9VG 
       63.75        41.33        18.25        11.74        20.81        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H 
       10.59        37.32        10.13         2.99         5.03        14.60 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC 
       36.66         0.07         0.16         3.19         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EB 
       79.73        53.33       113.00         7.33         0.46        66.31 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A3 TCGA-DD-A3A4 
       12.95        49.15         6.02        55.69        17.59        20.12 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       13.78        30.61        21.70        29.56        73.81         9.30 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACI 
      114.35        13.48        11.41        12.53        15.42        53.19 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AAD1 
       42.81        61.68        59.31        51.35        46.82        18.54 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADI TCGA-DD-AADJ 
       40.54        40.83        13.97        39.52        35.67        35.05 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAED TCGA-DD-AAEG 
       14.89        19.30        18.25        18.25        25.08        23.64 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        89.69        82.62        59.93        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y 
       64.77        62.47        66.25        13.41        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B 
       12.82        13.15        13.35         1.84        19.59        60.89 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25X 
       27.88        12.03         0.33        81.73         0.39        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M7 TCGA-G3-AAV6 TCGA-G3-AAV7 
       14.86        25.64        25.25         5.98         2.14         3.02 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH 
       12.03         9.57        19.92        17.69        21.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-ZP-A9CZ 
       17.59        19.76        15.98         7.04         0.99        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.57        24.43        45.57        11.21 

subtype1 subtype2 subtype3 
    0.10     0.03     0.07 
subtype1 subtype2 subtype3 
  108.76   120.82   114.35 
subtype1 subtype2 subtype3 
  20.750   19.040   19.445 
[1] "0.1 - 108.8 (20.8)" "0.0 - 120.8 (19.0)" "0.1 - 114.3 (19.4)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      38       16         0         17          3          4        0
  subtype2      79       40         2         25          4          3        1
  subtype3      52       28         1         20          1          2        2
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          38       79       52
  STAGE II         16       40       28
  STAGE III         0        2        1
  STAGE IIIA       17       25       20
  STAGE IIIB        3        4        1
  STAGE IIIC        4        3        2
  STAGE IV          0        1        2
  STAGE IVA         0        1        0
  STAGE IVB         0        1        1
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    40 18 20  3
  subtype2    85 43 30  7
  subtype3    55 30 27  3
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       40       85       55
  T2          18       43       30
  T3          20       30       27
  T4           3        7        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"
D2V5, binary
          cls
clus         0   1
  subtype1  56   1
  subtype2 112   2
  subtype3  84   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    1
  subtype2  112    2
  subtype3   84    1
   clus
vv  subtype1 subtype2 subtype3
  0       56      112       84
  1        1        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1  58   0
  subtype2 120   1
  subtype3  88   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    0
  subtype2  120    1
  subtype3   88    3
   clus
vv  subtype1 subtype2 subtype3
  0       58      120       88
  1        0        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"
D2V7, binary
          cls
clus         0   1
  subtype1  29  53
  subtype2  42 124
  subtype3  45  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   53
  subtype2   42  124
  subtype3   45   70
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       42       45
  MALE         53      124       70
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       2                       78
  subtype2                       0                      164
  subtype3                       0                      112
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                2
  subtype3                                3
D2V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 2        0        0
  HEPATOCELLULAR CARCINOMA               78      164      112
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        2        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  68   3   0   7
  subtype2 149   6   0   8
  subtype3 103   6   1   5
D2V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       68      149      103
  R1        3        6        6
  R2        0        0        1
  RX        7        8        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    26                         8
  subtype2                                1    68                         8
  subtype3                                0    65                         1
          vv
clus       WHITE
  subtype1    45
  subtype2    85
  subtype3    46
D2V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  26       68       65
  BLACK OR AFRICAN AMERICAN               8        8        1
  WHITE                                  45       85       46
[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"
D2V11, binary
          cls
clus         0   1
  subtype1   2  76
  subtype2   4 151
  subtype3   6 107
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   76
  subtype2    4  151
  subtype3    6  107
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        4        6
  NOT HISPANIC OR LATINO       76      151      107
[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 = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 28 25
  subtype2 64 31
  subtype3 40 18
  subtype4 45 19
  subtype5 46 16
subtype1 subtype2 subtype3 subtype4 subtype5 
      53       95       58       64       62 
subtype1 subtype2 subtype3 subtype4 subtype5 
      25       31       18       19       16 
$subtype1
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10U 
       23.80        24.89       120.82         0.66        27.91        27.52 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
        2.99         5.03        44.42        13.84        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       18.48        13.45         0.16         4.24         3.32         0.10 
TCGA-DD-A114 TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 
       37.78        45.11        13.64         5.62         7.66        13.78 
TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       33.14        12.26         0.30        15.42         6.41        53.19 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN TCGA-DD-AADQ 
        0.30         3.52         5.62        44.22        29.52        14.33 
TCGA-ED-A459 TCGA-ED-A7PZ TCGA-EP-A2KA TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25S 
       13.41         0.20        20.61         8.12        81.73        13.68 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG 
       22.95        12.03         1.84         3.02         1.02        17.06 
TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-MI-A75I TCGA-RG-A7D4 TCGA-WJ-A86L 
        3.72        13.38        20.71        24.13        11.34 

$subtype2
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       53.39        83.24        27.88        47.74        14.99         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5R-AAAM TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y 
       13.02         8.61         1.51        46.78        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-A3MB 
        1.12         0.26        17.98        44.81         0.66         0.10 
TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
       83.57         2.60         0.46        21.76        51.29        66.31 
TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NJ 
       18.35        70.06       102.74        21.70        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       39.78        56.25        73.81        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACO TCGA-DD-AACQ 
       23.05        35.67        63.48        12.00        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF 
       59.31        50.33        47.67        42.58        40.08         3.78 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AAE2 
       20.91         0.39        66.67        15.58        18.87        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEH TCGA-DD-AAEI 
       18.61        19.99        21.17        18.90        25.78        50.33 
TCGA-ED-A7XO TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A496 
       14.04        22.85        23.97        19.10         6.38         0.33 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI 
       53.79        21.53        22.13        25.64         5.92        25.25 
TCGA-G3-A5SK TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-KR-A7K8 
       24.46        11.24         8.55         2.20        37.91        24.36 
TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF 
       12.72        12.03        18.38         0.62        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MB 
        3.09        19.33        19.04        15.52         0.76        19.76 
TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.85        25.71        23.21        40.80        79.30 

$subtype3
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-5C-A9VG 
       63.75        41.33        18.25        37.25        20.81        10.78 
TCGA-5C-A9VH TCGA-CC-5258 TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EF 
       10.59         0.07         3.19        79.73       113.00        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A9 TCGA-DD-A4NH 
       49.15        33.04        19.76        17.59        30.61        30.15 
TCGA-DD-A4NN TCGA-DD-A73G TCGA-DD-AACC TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACW 
       29.56       114.35        55.40        42.81        13.64        46.82 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO 
       40.54        40.83        13.97        35.67        35.05        14.89 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED 
       19.30        18.25        18.25        18.15         4.64        25.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-ED-A5KG 
       89.69        59.93        72.39        76.18        62.47        15.85 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         9.73        12.82        13.35         1.84        19.59 
TCGA-FV-A23B TCGA-G3-A25Y TCGA-G3-AAV6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA 
       60.89        14.86         2.14        21.04        15.39        17.59 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-ZP-A9D0 
       15.98         7.04         0.99        23.57 

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H6 TCGA-5R-AA1D TCGA-BC-4072 
       41.79        80.28        56.91        11.74        11.08        48.99 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3ER TCGA-CC-5260 
       37.32        10.13        25.32        69.57        36.66         2.86 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EI 
        3.39         0.07         0.13         7.33        19.79         6.02 
TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NS TCGA-DD-AA3A 
       55.69       107.11        32.52        90.28        80.75        13.48 
TCGA-DD-AAC9 TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADK 
       11.41        51.35        51.52        18.54        21.63        34.49 
TCGA-DD-AADP TCGA-DD-AAEG TCGA-DD-AAVR TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 
       15.06        23.64        82.62        66.25        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I0 
        0.20        13.41         0.20         9.96        14.40        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A5SM 
       12.03         0.03        51.06        28.27        58.49        17.10 
TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-MI-A75E 
        5.98         2.99        20.75        16.83        11.84        16.67 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-YA-A8S7 
       10.85        17.69        10.75        10.32        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       35.77         0.69        24.43        45.57 

$subtype5
TCGA-2Y-A9H1 TCGA-2Y-A9HA TCGA-5R-AA1C TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA 
       40.41         1.18        11.97        12.72        53.33        79.40 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A4 TCGA-DD-A3A8 
       75.65        11.47        21.14        27.19        20.12         0.36 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       30.97        26.37       108.76        22.78         1.45         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 
       75.65        76.41        12.53        69.11         5.59         4.50 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADU TCGA-DD-AAE9 TCGA-DD-AAEB 
       22.09        40.47        37.64        18.21        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 
       16.37        35.08        79.07        56.48        64.77        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       49.48        53.69        13.15        18.74        19.99         0.62 
TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       11.93         0.39        19.53        19.23        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-UB-A7MD 
       13.97         9.57        12.85        19.92        16.44         1.71 
TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.10     0.07     0.03     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  120.82   102.74   114.35   107.11   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.640   21.760   19.675   16.965   18.475 
[1] "0.1 - 120.8 (13.6)" "0.1 - 102.7 (21.8)" "0.1 - 114.3 (19.7)"
[4] "0.0 - 107.1 (17.0)" "0.4 - 108.8 (18.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      15       21         0         12          3          3        1
  subtype2      56       16         1         12          2          0        0
  subtype3      31       17         1         14          1          2        1
  subtype4      33       12         0         10          0          3        1
  subtype5      30       17         1         14          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
  subtype4         0         0
  subtype5         0         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          15       56       31       33       30
  STAGE II         21       16       17       12       17
  STAGE III         0        1        1        0        1
  STAGE IIIA       12       12       14       10       14
  STAGE IIIB        3        2        1        0        1
  STAGE IIIC        3        0        2        3        1
  STAGE IV          1        0        1        1        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        1        1        0        0
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    15 25 15  4
  subtype2    60 17 15  4
  subtype3    34 17 18  1
  subtype4    36 14 12  3
  subtype5    31 17 16  1
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       15       60       34       36       31
  T2          25       17       17       14       17
  T3          15       15       18       12       16
  T4           4        4        1        3        1
[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"
D3V5, binary
          cls
clus        0  1
  subtype1 35  1
  subtype2 64  1
  subtype3 58  2
  subtype4 39  0
  subtype5 51  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    1
  subtype2   64    1
  subtype3   58    2
  subtype4   39    0
  subtype5   51    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       35       64       58       39       51
  1        1        1        2        0        0
[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"
D3V6, binary
          cls
clus        0  1
  subtype1 42  0
  subtype2 67  1
  subtype3 59  2
  subtype4 39  1
  subtype5 53  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    0
  subtype2   67    1
  subtype3   59    2
  subtype4   39    1
  subtype5   53    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       42       67       59       39       53
  1        0        1        2        1        0
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 17 42
  subtype2 26 71
  subtype3 37 33
  subtype4 27 38
  subtype5  8 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   42
  subtype2   26   71
  subtype3   37   33
  subtype4   27   38
  subtype5    8   58
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17       26       37       27        8
  MALE         42       71       33       38       58
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       57
  subtype2                       0                       97
  subtype3                       0                       69
  subtype4                       2                       59
  subtype5                       0                       66
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                0
  subtype3                                1
  subtype4                                4
  subtype5                                0
D3V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        2        0
  HEPATOCELLULAR CARCINOMA               57       97       69       59       66
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        0        1        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 48  5  0  5
  subtype2 84  3  0  8
  subtype3 65  1  0  4
  subtype4 53  6  1  3
  subtype5 64  0  0  0
D3V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       48       84       65       53       64
  R1        5        3        1        6        0
  R2        0        0        0        1        0
  RX        5        8        4        3        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    24                         6
  subtype2                                0    35                         5
  subtype3                                0    45                         1
  subtype4                                0    22                         2
  subtype5                                1    30                         3
          vv
clus       WHITE
  subtype1    27
  subtype2    52
  subtype3    23
  subtype4    39
  subtype5    32
D3V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  24       35       45       22       30
  BLACK OR AFRICAN AMERICAN               6        5        1        2        3
  WHITE                                  27       52       23       39       32
[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"
D3V11, binary
          cls
clus        0  1
  subtype1  3 51
  subtype2  5 86
  subtype3  2 67
  subtype4  2 60
  subtype5  0 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    5   86
  subtype3    2   67
  subtype4    2   60
  subtype5    0   64
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        5        2        2        0
  NOT HISPANIC OR LATINO       51       86       67       60       64
[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(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 23 22
  subtype2 39 16
  subtype3 70 37
  subtype4 52 21
  subtype5 39 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      45       55      107       73       52 
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       16       37       21       13 
$subtype1
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W 
       24.89        56.91        48.99        27.91        37.32         2.99 
TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
        5.03        14.60         0.16         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A3A7 
        0.10         0.07        37.78         5.62       107.11        13.78 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-AA3A TCGA-DD-AACH 
       33.14        30.15        12.26         0.30        13.48         6.41 
TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN TCGA-ED-A7PX TCGA-ED-A82E 
        3.52         5.62        44.22        29.52         0.20        13.41 
TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
        0.20        20.61        27.88        81.73        51.06        58.49 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-K7-AAU7 TCGA-UB-A7MA 
       22.95        12.03         1.84         3.02         3.72        17.59 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D2 
        0.99        13.55        24.43 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5R-AAAM 
       23.80        41.79        80.28         8.55        13.02         1.51 
TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5262 
       46.78        25.32        69.57        13.45        36.66         3.39 
TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A4ND TCGA-DD-A4NJ TCGA-DD-A4NL 
        0.10        45.11         6.02        90.28        30.51        56.25 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACT TCGA-DD-AACU 
       73.81        80.75        11.41        55.40        51.35        51.52 
TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AAE7 TCGA-ED-A627 
       47.67        42.58         0.39        15.06        21.17        13.91 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25V 
        9.96        14.40        23.97         8.12         0.03        28.27 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-K7-A5RF 
       21.53        22.13        17.10         5.98         2.99        20.75 
TCGA-K7-A6G5 TCGA-LG-A9QD TCGA-MI-A75E TCGA-O8-A75V TCGA-RC-A7SK TCGA-T1-A6J8 
       16.83        12.03        16.67        17.69        15.52         0.76 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 
       10.75        10.32        12.99        35.77        25.71         0.69 
TCGA-ZS-A9CD 
       45.57 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       53.39        83.24        27.88       120.82        40.41        47.74 
TCGA-2Y-A9H9 TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       14.99         8.61         0.66        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        44.42        13.84         0.26        22.36        17.98 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
       18.48        44.81         0.66        79.73        83.57         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A39Z 
        0.46        21.76        51.29        66.31        18.35        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI 
        7.66        70.06        17.59       102.74        21.70        26.83 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
       39.78        78.84        23.93         9.30        23.05        35.67 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO 
       12.53        63.48        12.00        69.11         0.30        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AAD8 TCGA-DD-AADF 
       14.20        59.31        50.33         5.59        40.08         3.78 
TCGA-DD-AADL TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADY 
       20.91        14.33        66.67        15.58        18.87        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEA TCGA-DD-AAED 
       20.98        18.61        19.99         4.64        18.90        25.08 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7XO TCGA-ES-A2HS 
       25.78        50.33        72.39        13.41        14.04        22.85 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CH 
       19.10         6.38         0.33        13.68        53.79        25.64 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 
        5.92        25.25        24.46        11.24         8.55         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
        2.20        37.91        17.06        11.84        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF 
        9.57        18.38        20.71         0.62        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MF 
        3.09        21.04        19.33        19.04        19.76         7.04 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-ZP-A9CZ TCGA-ZS-A9CE TCGA-ZS-A9CF 
       11.34        24.85        23.21        40.80        79.30 

$subtype4
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-2Y-A9H8 
       63.75        41.33        18.25        11.74        37.25        20.81 
TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-BC-A10R TCGA-CC-5258 
        1.18        10.78        10.59        11.08        10.13         0.07 
TCGA-CC-5261 TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EF 
        3.19         0.13       113.00         7.33        19.79        12.95 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NB 
       49.15        33.04        55.69        20.12        30.61        32.52 
TCGA-DD-A4NN TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN 
       29.56       114.35        76.41        15.42        53.19        42.81 
TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADA 
       13.64        46.82        18.54        21.63        22.09        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.83        13.97        40.47        35.67        35.05        34.49 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAEG TCGA-DD-AAVQ 
       14.89        19.30        18.25        18.15        23.64        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI 
       82.62        59.93        76.18        62.47        66.25        12.69 
TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 
       15.85        13.35         9.73        12.82         0.20        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25Y 
        1.84        19.59        60.89        12.03         0.39        14.86 
TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7ME 
        2.14        13.38        10.85        15.39        24.13        15.98 
TCGA-ZP-A9D0 
       23.57 

$subtype5
TCGA-5R-AA1C TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE 
       11.97        12.72        53.33        79.40        75.65        11.47 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG 
       13.64        21.14        27.19         0.36        30.97        26.37 
TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AAD0 
      108.76        22.78         1.45         0.53        75.65         4.50 
TCGA-DD-AADG TCGA-DD-AADU TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEK 
       37.64        18.21        23.74        15.72        16.37        35.08 
TCGA-DD-AAVP TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       79.07        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-G3-A3CJ 
       13.15        18.74        19.99         0.62        11.93        19.53 
TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       19.23        20.42         7.76        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF 
        0.89         8.75         2.14        13.97        12.85        19.92 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       16.44         1.71        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.03     0.26     0.07     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11    90.28   120.82   114.35   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.480   17.690   20.710   19.590   17.325 
[1] "0.1 - 107.1 (13.5)" "0.0 - 90.3 (17.7)"  "0.3 - 120.8 (20.7)"
[4] "0.1 - 114.3 (19.6)" "0.4 - 108.8 (17.3)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      10       15         0         15          4          3        0
  subtype2      31       10         0          3          1          2        1
  subtype3      60       25         1         17          1          1        0
  subtype4      40       18         1         16          0          2        2
  subtype5      24       15         1         11          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
  subtype4         0         1
  subtype5         0         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          10       31       60       40       24
  STAGE II         15       10       25       18       15
  STAGE III         0        0        1        1        1
  STAGE IIIA       15        3       17       16       11
  STAGE IIIB        4        1        1        0        1
  STAGE IIIC        3        2        1        2        1
  STAGE IV          0        1        0        2        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    10 18 20  4
  subtype2    37 11  5  2
  subtype3    61 28 18  5
  subtype4    43 18 20  1
  subtype5    25 15 13  1
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       10       37       61       43       25
  T2          18       11       28       18       15
  T3          20        5       18       20       13
  T4           4        2        5        1        1
[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"
D4V5, binary
          cls
clus        0  1
  subtype1 33  1
  subtype2 30  1
  subtype3 76  0
  subtype4 65  2
  subtype5 43  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    1
  subtype2   30    1
  subtype3   76    0
  subtype4   65    2
  subtype5   43    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       33       30       76       65       43
  1        1        1        0        2        0
[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"
D4V6, binary
          cls
clus        0  1
  subtype1 38  0
  subtype2 32  0
  subtype3 81  1
  subtype4 65  3
  subtype5 44  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    0
  subtype2   32    0
  subtype3   81    1
  subtype4   65    3
  subtype5   44    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       38       32       81       65       44
  1        0        0        1        3        0
[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"
D4V7, binary
          cls
clus        0  1
  subtype1 22 30
  subtype2 13 42
  subtype3 34 79
  subtype4 39 43
  subtype5  7 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   30
  subtype2   13   42
  subtype3   34   79
  subtype4   39   43
  subtype5    7   48
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       13       34       39        7
  MALE         30       42       79       43       48
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       47
  subtype2                       0                       55
  subtype3                       0                      111
  subtype4                       2                       80
  subtype5                       0                       55
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                5
  subtype2                                0
  subtype3                                2
  subtype4                                0
  subtype5                                0
D4V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        2        0
  HEPATOCELLULAR CARCINOMA               47       55      111       80       55
  HEPATOCHOLANGIOCARCINOMA (MIXED)        5        0        2        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 42  6  0  3
  subtype2 46  4  0  3
  subtype3 99  4  0  8
  subtype4 74  1  1  6
  subtype5 53  0  0  0
D4V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       42       46       99       74       53
  R1        6        4        4        1        0
  R2        0        0        0        1        0
  RX        3        3        8        6        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    25                         1
  subtype2                                0    14                         4
  subtype3                                0    45                         6
  subtype4                                0    49                         2
  subtype5                                1    23                         4
          vv
clus       WHITE
  subtype1    25
  subtype2    34
  subtype3    56
  subtype4    31
  subtype5    27
D4V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  25       14       45       49       23
  BLACK OR AFRICAN AMERICAN               1        4        6        2        4
  WHITE                                  25       34       56       31       27
[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"
D4V11, binary
          cls
clus        0  1
  subtype1  2 49
  subtype2  4 50
  subtype3  4 98
  subtype4  2 78
  subtype5  0 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   49
  subtype2    4   50
  subtype3    4   98
  subtype4    2   78
  subtype5    0   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        4        4        2        0
  NOT HISPANIC OR LATINO       49       50       98       78       53
[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(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 37 23
  subtype2 78 39
  subtype3 29 13
  subtype4 82 32
subtype1 subtype2 subtype3 subtype4 
      60      117       42      114 
subtype1 subtype2 subtype3 subtype4 
      23       39       13       32 
$subtype1
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       23.80        53.39        24.89       120.82        14.99         1.18 
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       27.91        23.34         1.12        44.81        13.45         0.66 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11D TCGA-DD-A1EG TCGA-DD-A1EK 
        3.39         3.32        83.57        51.29        45.11        18.35 
TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACQ 
        5.62       102.74        13.78        35.67        75.65        14.20 
TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADV TCGA-DD-AAE2 
       40.08         3.78        37.64        20.91        18.87        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A3JL 
       19.99        21.83        16.37        14.04        13.35         9.96 
TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25S 
       11.93        23.97        19.10         8.12         0.03        13.68 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A7M6 TCGA-G3-A7M9 
       30.74        21.53        22.13         5.92        12.03         1.84 
TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75I TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 
        2.20        24.36        20.71        19.04        15.52         0.76 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZS-A9CE TCGA-ZS-A9CF 
       17.59         1.71        11.34        25.71        40.80        79.30 

$subtype2
TCGA-2Y-A9GU TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H7 TCGA-3K-AAZ8 
       63.75        27.88        40.41        47.74        37.25        13.02 
TCGA-4R-AA8I TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 
        8.61        11.97        27.52         2.99        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-CC-5263 TCGA-DD-A113 
        0.26        22.36        17.98        18.48         4.24        79.73 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         2.60         0.46        21.76        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 
       19.79        11.47        13.64        21.14        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NF 
       70.06        17.59        20.12       107.11         0.36        30.97 
TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B 
       26.37       108.76        12.26         0.30        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE 
       23.05        22.78         1.45         0.53        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACV 
       12.00        69.11         0.30        13.64        59.31        50.33 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB 
        5.59         5.62         4.50        44.22        22.09        40.83 
TCGA-DD-AADE TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       39.52        35.05        29.52        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
       15.58        18.21        18.61        23.74        18.90        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVY 
       25.08        25.78        50.33        79.07        72.39        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A8O6 TCGA-EP-A12J 
       65.39        49.48        13.41         9.73         1.84        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U 
       19.99        19.59        22.85         0.33        81.73        53.79 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        25.25        22.95        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80         9.70         9.17         0.89         8.75         2.14 
TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H 
        1.02        12.72        13.97         9.57        18.38        12.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-UB-A7MB TCGA-UB-A7MC 
       58.88        19.92         3.09        19.33        19.76        16.44 
TCGA-UB-A7MF TCGA-ZP-A9D4 TCGA-ZS-A9CG 
        7.04        12.99        11.21 

$subtype3
TCGA-2Y-A9GV TCGA-2Y-A9H8 TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 
       83.24        20.81        48.99        27.52        25.32        69.57 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 TCGA-CC-A3MB 
       14.60        12.72         0.07         0.16         0.10         0.10 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-AA3A TCGA-DD-AACB 
       75.65        49.15        33.04        27.19        13.48        76.41 
TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADD 
       55.40        15.42         3.52        51.35        46.82        40.47 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVZ 
       18.15         4.64        35.08        59.93        56.48        62.47 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B TCGA-FV-A4ZQ TCGA-G3-A5SK 
       53.69        13.35         0.20        60.89         0.39        24.46 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-WX-AA46 
       17.06         3.72        13.38        21.04        24.13        24.85 

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       41.79        80.28        56.91        41.33        18.25        11.74 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        10.78        10.59         0.66        11.08         1.51 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A112 TCGA-BD-A3ER TCGA-CC-5260 
       37.32        10.13        46.78         5.03        36.66         2.86 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        3.19         0.07         0.13        37.78       113.00         7.33 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA 
       12.95         6.02        55.69        25.81        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL 
       32.52        90.28        21.70        30.15        26.83        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC9 
       29.56        73.81        80.75        78.84       114.35        11.41 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACU 
        6.41        53.19        58.16        42.81        61.68        51.52 
TCGA-DD-AACY TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADC 
       47.67        18.54        21.63        42.58        40.54        13.97 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AADY 
       35.67        34.49         0.39        15.06        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW 
       18.25        21.17        23.64        89.69        82.62        76.18 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       66.25        12.69        15.85        13.91         0.20        12.82 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT 
       13.15        13.41         0.20        20.61         0.62        14.40 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       27.88        51.06        28.27        58.49        14.86        25.64 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-HP-A5MZ 
       17.10         5.98        11.24         8.55         3.02         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A9QD 
       37.91        20.75        16.83         2.14        11.84        12.03 
TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SH 
       16.67         0.62        10.85        17.69        21.01        15.39 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
       15.98        10.75        10.32         0.99        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       35.77        23.21        23.57         0.69        24.43        45.57 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.26     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  120.82   108.76    83.24   114.35 
subtype1 subtype2 subtype3 subtype4 
  18.955   19.230   24.655   18.395 
[1] "0.0 - 120.8 (19.0)" "0.3 - 108.8 (19.2)" "0.1 - 83.2 (24.7)" 
[4] "0.1 - 114.3 (18.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      32        8         1          9          3          1        1
  subtype2      59       32         0         26          3          3        0
  subtype3      19       13         2         10          0          2        1
  subtype4      56       30         0         16          2          3        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         0
  subtype3         0         0
  subtype4         0         1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          32       59       19       56
  STAGE II          8       32       13       30
  STAGE III         1        0        2        0
  STAGE IIIA        9       26       10       16
  STAGE IIIB        3        3        0        2
  STAGE IIIC        1        3        2        3
  STAGE IV          1        0        1        1
  STAGE IVA         1        0        0        0
  STAGE IVB         1        0        0        1
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    35 11 13  3
  subtype2    60 33 29  4
  subtype3    22 13 12  2
  subtype4    60 33 22  4
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       35       60       22       60
  T2          11       33       13       33
  T3          13       29       12       22
  T4           3        4        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 40  1
  subtype2 91  1
  subtype3 37  1
  subtype4 81  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    1
  subtype2   91    1
  subtype3   37    1
  subtype4   81    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       40       91       37       81
  1        1        1        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus         0   1
  subtype1  36   1
  subtype2 101   0
  subtype3  39   1
  subtype4  87   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    1
  subtype2  101    0
  subtype3   39    1
  subtype4   87    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36      101       39       87
  1        1        0        1        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 19 43
  subtype2 33 94
  subtype3 19 30
  subtype4 42 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   43
  subtype2   33   94
  subtype3   19   30
  subtype4   42   78
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       33       19       42
  MALE         43       94       30       78
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       61
  subtype2                       0                      127
  subtype3                       0                       47
  subtype4                       2                      114
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                2
  subtype4                                4
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        0        0        2
  HEPATOCELLULAR CARCINOMA               61      127       47      114
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        0        2        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  49   4   0   5
  subtype2 115   4   0   7
  subtype3  43   2   0   4
  subtype4 108   5   1   4
D5V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       49      115       43      108
  R1        4        4        2        5
  R2        0        0        0        1
  RX        5        7        4        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    20                         4
  subtype2                                1    58                         6
  subtype3                                0    27                         3
  subtype4                                0    54                         4
          vv
clus       WHITE
  subtype1    36
  subtype2    59
  subtype3    19
  subtype4    57
D5V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                  20       58       27       54
  BLACK OR AFRICAN AMERICAN               4        6        3        4
  WHITE                                  36       59       19       57
[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"
D5V11, binary
          cls
clus         0   1
  subtype1   2  56
  subtype2   2 119
  subtype3   1  46
  subtype4   7 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   56
  subtype2    2  119
  subtype3    1   46
  subtype4    7  108
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        1        7
  NOT HISPANIC OR LATINO       56      119       46      108
[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 = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 22 16
  subtype2 61 29
  subtype3 27 22
  subtype4 80 31
  subtype5 36  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      38       90       49      111       45 
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       29       22       31        9 
$subtype1
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 TCGA-BC-4073 
       24.89       120.82        14.99         1.18        48.99        27.91 
TCGA-BC-A10Z TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        1.12        13.45         0.66         3.39         4.24         3.32 
TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACA 
       83.57        45.11        18.35        13.64        35.67        75.65 
TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL 
       76.41        40.47         3.78        37.64        35.05        20.91 
TCGA-DD-AADU TCGA-DD-AADV TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-FV-A495 
       18.21        18.87         0.20        13.35         9.96         0.03 
TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB TCGA-MI-A75I TCGA-RC-A7SK 
       13.68        12.03         1.84         2.20        20.71        15.52 
TCGA-UB-A7MD TCGA-WJ-A86L 
        1.71        11.34 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9HB 
       23.80        53.39        83.24        27.88        47.74         8.55 
TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
        8.61        10.13        46.78        27.52        27.52        23.34 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 
        5.03        13.84        22.36        17.98        18.48        44.81 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
        0.10        79.73         2.60        21.76        51.29        66.31 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ 
        7.66        70.06       102.74        13.78        26.37        12.26 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACQ 
       78.84        23.93        23.05        53.19         0.30        14.20 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD8 TCGA-DD-AADM 
       59.31        50.33        47.67         5.62        40.08         0.39 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 
       66.67        18.25        20.98        18.61        19.99        21.83 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEI TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
       16.37        23.64        50.33        20.61         0.62        11.93 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V 
       23.97        19.10         8.12         0.33        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SJ 
       30.74        58.49        21.53        22.13         5.92        22.95 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       24.46        17.10        11.24         8.55         3.02         1.02 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MR-A520 TCGA-NI-A4U2 
       17.06        11.84        24.36        12.72         0.62        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-T1-A6J8 TCGA-UB-A7MA 
       21.01         3.09        19.33        19.04         0.76        17.59 
TCGA-UB-A7MB TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       19.76        25.71        23.21         0.69        40.80        79.30 

$subtype3
TCGA-2Y-A9GU TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-3K-AAZ8 
       63.75        40.41        41.33        37.25        20.81        13.02 
TCGA-5C-AAPD TCGA-BC-A216 TCGA-CC-5261 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A1EF 
        0.66        44.42         3.19       113.00         0.46        12.95 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A6 TCGA-DD-A4NR TCGA-DD-A73B 
        5.62        19.76        17.59       107.11         0.30         9.30 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AADB 
       12.00         6.41        13.64        51.52        44.22        40.83 
TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AAE7 TCGA-DD-AAEA 
       13.97        29.52        14.89        15.58        21.17        18.90 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVX TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY 
       25.08        25.78        56.48        15.85         9.73        12.82 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A5SI TCGA-G3-AAV6 TCGA-K7-A6G5 
        1.84        19.59        81.73        25.25         2.14        16.83 
TCGA-MI-A75C TCGA-MI-A75G TCGA-UB-A7ME TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9D0 
        9.57        18.38        15.98         7.04        13.55        23.57 
TCGA-ZP-A9D2 
       24.43 

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-5C-A9VG 
       41.79        80.28        56.91        18.25        11.74        10.78 
TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X 
       10.59        11.08         1.51        37.32         2.99        25.32 
TCGA-BC-A110 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       69.57        14.60        36.66         0.07         0.16         2.86 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EC 
        0.10         0.07         0.13        37.78         7.33        19.79 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-A39X 
       75.65        49.15         6.02        33.04        27.19        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       25.81        20.12        30.61        33.14        32.52        90.28 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       21.70        30.15        26.83        56.25        29.56        73.81 
TCGA-DD-A4NS TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG 
       80.75       114.35        13.48        11.41        55.40        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACT TCGA-DD-AACW 
        3.52        58.16        42.81        61.68        51.35        46.82 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK 
       18.54        21.63        42.58        40.54        35.67        34.49 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       15.06        14.33        19.30        18.25        18.15         4.64 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X 
       62.47        66.25        13.41        12.69        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HS 
        0.20        14.04        13.15        13.41         0.20        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y 
       14.40        60.89        27.88         0.39        51.06        14.86 
TCGA-G3-A3CH TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-AAU7 
       25.64         5.98         2.99        37.91        20.75         3.72 
TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7S9 
       13.38        12.03        16.67        10.85        17.69        21.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        24.13        10.75        10.32         0.99        12.99 
TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZS-A9CD 
       24.85        35.77        45.57 

$subtype5
TCGA-5R-AA1C TCGA-BC-A3KF TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE 
       11.97         0.26        12.72        53.33        79.40        11.47 
TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E 
       21.14         0.36        30.97       108.76        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 
        0.53        12.53        63.48        69.11         5.59         4.50 
TCGA-DD-AAD6 TCGA-DD-AADE TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAVP TCGA-DD-AAVY 
       22.09        39.52        23.74        15.72        79.07        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A3CJ 
       65.39        49.48        53.69        18.74        19.99        19.53 
TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       19.23        20.42         7.76        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF 
        0.89         8.75         2.14        13.97        12.85        19.92 
TCGA-UB-A7MC TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       16.44        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.30     0.07     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  120.82   102.74   113.00   114.35   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.335   21.270   17.590   21.040   16.440 
[1] "0.0 - 120.8 (14.3)" "0.1 - 102.7 (21.3)" "0.3 - 113.0 (17.6)"
[4] "0.1 - 114.3 (21.0)" "0.3 - 108.8 (16.4)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      20        6         0         11          1          1        0
  subtype2      44       22         1         11          4          1        1
  subtype3      26       14         0         12          1          1        0
  subtype4      53       29         2         19          1          5        2
  subtype5      23       12         0          8          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         0
  subtype4         0         1
  subtype5         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          20       44       26       53       23
  STAGE II          6       22       14       29       12
  STAGE III         0        1        0        2        0
  STAGE IIIA       11       11       12       19        8
  STAGE IIIB        1        4        1        1        1
  STAGE IIIC        1        1        1        5        1
  STAGE IV          0        1        0        2        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         1        0        0        1        0
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    20  7 12  2
  subtype2    49 25 17  5
  subtype3    28 14 14  0
  subtype4    56 32 24  5
  subtype5    24 12  9  1
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       20       49       28       56       24
  T2           7       25       14       32       12
  T3          12       17       14       24        9
  T4           2        5        0        5        1
[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 30  0
  subtype2 57  1
  subtype3 39  1
  subtype4 86  2
  subtype5 37  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2   57    1
  subtype3   39    1
  subtype4   86    2
  subtype5   37    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       30       57       39       86       37
  1        0        1        1        2        0
[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 26  1
  subtype2 64  0
  subtype3 42  0
  subtype4 92  3
  subtype5 39  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   64    0
  subtype3   42    0
  subtype4   92    3
  subtype5   39    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       26       64       42       92       39
  1        1        0        0        3        0
[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 13 28
  subtype2 29 67
  subtype3 19 37
  subtype4 46 72
  subtype5  6 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   28
  subtype2   29   67
  subtype3   19   37
  subtype4   46   72
  subtype5    6   41
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       29       19       46        6
  MALE         28       67       37       72       41
[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       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       41
  subtype2                       0                       94
  subtype3                       0                       55
  subtype4                       2                      112
  subtype5                       0                       47
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                2
  subtype3                                1
  subtype4                                4
  subtype5                                0
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        2        0
  HEPATOCELLULAR CARCINOMA               41       94       55      112       47
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        2        1        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  32   3   0   3
  subtype2  82   5   0   6
  subtype3  50   1   0   5
  subtype4 105   6   1   6
  subtype5  46   0   0   0
D6V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       32       82       50      105       46
  R1        3        5        1        6        0
  R2        0        0        0        1        0
  RX        3        6        5        6        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    17                         5
  subtype2                                0    33                         5
  subtype3                                0    32                         2
  subtype4                                0    56                         4
  subtype5                                1    21                         1
          vv
clus       WHITE
  subtype1    19
  subtype2    52
  subtype3    21
  subtype4    55
  subtype5    24
D6V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  17       33       32       56       21
  BLACK OR AFRICAN AMERICAN               5        5        2        4        1
  WHITE                                  19       52       21       55       24
[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"
D6V11, binary
          cls
clus         0   1
  subtype1   1  39
  subtype2   4  85
  subtype3   3  51
  subtype4   4 110
  subtype5   0  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   39
  subtype2    4   85
  subtype3    3   51
  subtype4    4  110
  subtype5    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        4        3        4        0
  NOT HISPANIC OR LATINO       39       85       51      110       44
[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_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 49 31
  subtype2 55 27
  subtype3 81 34
  subtype4 26  9
subtype1 subtype2 subtype3 subtype4 
      80       82      115       35 
subtype1 subtype2 subtype3 subtype4 
      31       27       34        9 
$subtype1
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-5C-AAPD 
       63.75        24.89       120.82        41.33        37.25         0.66 
TCGA-BC-4073 TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO 
       27.91         2.99        44.42        13.84        22.36        18.48 
TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A118 
        0.66         0.16         4.24         3.32        79.73       113.00 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A3 
       19.79        12.95        33.04        13.64         5.62        17.59 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NN 
       13.78        33.14        21.70        26.37        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACH 
       73.81        12.26       114.35         0.53        12.53         6.41 
TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC 
       13.64         5.62        44.22        22.09        40.83        13.97 
TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAEA 
       35.05        29.52        14.89        19.30        18.25        18.90 
TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y 
       25.08        50.33        89.69        13.41        15.85         9.73 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK 
       12.82        13.35         1.84        20.61        19.59        11.93 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 
       81.73        13.68        30.74        25.25        22.95        12.03 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
        2.14         3.02         1.02        17.06        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-UB-A7MA TCGA-UB-A7ME 
       12.72         9.57        21.01         3.09        17.59        15.98 
TCGA-UB-A7MF TCGA-YA-A8S7 
        7.04        13.55 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       23.80        41.79        80.28        56.91        18.25        11.74 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10R 
        8.55        10.78        11.08         1.51        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3EP TCGA-BD-A3ER 
       27.52        25.32        69.57         5.03        13.45        36.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
        2.86         3.19         3.39         0.07         0.13        37.78 
TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A3A9 
        7.33        45.11         6.02        55.69       107.11        30.61 
TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACU 
       80.75        11.41        53.19        58.16        42.81        51.52 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP 
       18.54        21.63        42.58        35.67        34.49        15.06 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVR TCGA-DD-AAW0 TCGA-ED-A7PX 
       18.25        21.17        23.64        82.62        66.25         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ 
       14.04        13.41         0.20         9.96        14.40        23.97 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         8.12        51.06        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAV3 TCGA-GJ-A9DB 
       22.13        25.64        17.10         5.98         9.17         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MR-A8JO 
        2.99        20.75         3.72        24.36        16.67        10.85 
TCGA-O8-A75V TCGA-RC-A7SH TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-ZP-A9CV 
       17.69        15.39        10.75        10.32        12.99        35.77 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       23.21         0.69        24.43        45.57 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       53.39        83.24        27.88        40.41        47.74        14.99 
TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-5R-AA1C TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10Y 
        1.18         8.61        11.97        46.78        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A2L6 TCGA-DD-A115 TCGA-DD-A116 
        1.12         0.26        17.98        44.81        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
       75.65        11.47        18.35        21.14        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NP TCGA-DD-A73A 
        7.66       102.74        30.97        26.83       108.76        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACE 
        9.30        23.05        22.78        35.67        75.65        63.48 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
       12.00        69.11         0.30        61.68        14.20        59.31 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD8 TCGA-DD-AADE 
       50.33         5.59        47.67         4.50        40.08        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADQ TCGA-DD-AADR 
        3.78        37.64        20.91         0.39        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       15.58        18.21        18.87        20.98        18.61        19.99 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
       21.83        23.74        15.72        16.37        25.78        79.07 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP 
       72.39        56.48        65.39        49.48        53.69        13.15 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25U 
       18.74        19.99         0.62        19.10         0.33        53.79 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL 
       21.53         5.92        19.53        19.23        24.46        20.42 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-HP-A5N0 
       11.24         8.55         9.70         0.89         8.75        37.91 
TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        2.14        13.97        12.03        18.38        12.85        20.71 
TCGA-NI-A4U2 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MD 
       58.88        19.33        19.04        15.52         0.76         1.71 
TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       11.34        25.71        23.57        12.99        40.80        79.30 
TCGA-ZS-A9CG 
       11.21 

$subtype4
TCGA-2Y-A9H8 TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3M9 
       20.81        10.59        48.99        14.60         0.07         0.10 
TCGA-CC-A3MB TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-A4ND TCGA-DD-AA3A TCGA-DD-AACB 
        0.10        49.15        27.19        90.28        13.48        76.41 
TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADA 
       55.40        15.42         3.52        51.35        46.82        40.54 
TCGA-DD-AADD TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW 
       40.47        18.15         4.64        35.08        59.93        76.18 
TCGA-DD-AAVZ TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B 
       62.47        12.69        13.91        13.35         0.20        60.89 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A7M9 TCGA-RG-A7D4 TCGA-WQ-A9G7 
        0.03         0.39         1.84        24.13         0.99 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.07     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 
  120.82   107.11   108.76    90.28 
subtype1 subtype2 subtype3 subtype4 
  17.325   18.395   20.710   18.150 
[1] "0.2 - 120.8 (17.3)" "0.1 - 107.1 (18.4)" "0.3 - 108.8 (20.7)"
[4] "0.0 - 90.3 (18.1)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      33       22         0         25          5          5        0
  subtype2      36       20         0         12          0          3        2
  subtype3      66       27         1         12          0          0        0
  subtype4      18       11         2          7          1          0        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
  subtype4         0         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          33       36       66       18
  STAGE II         22       20       27       11
  STAGE III         0        0        1        2
  STAGE IIIA       25       12       12        7
  STAGE IIIB        5        0        0        1
  STAGE IIIC        5        3        0        0
  STAGE IV          0        2        0        1
  STAGE IVA         0        1        0        0
  STAGE IVB         0        1        1        0
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    34 23 29  5
  subtype2    41 23 15  5
  subtype3    70 30 14  2
  subtype4    19 11 11  0
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       34       41       70       19
  T2          23       23       30       11
  T3          29       15       14       11
  T4           5        5        2        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"
D7V5, binary
          cls
clus        0  1
  subtype1 65  3
  subtype2 53  1
  subtype3 83  0
  subtype4 32  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65    3
  subtype2   53    1
  subtype3   83    0
  subtype4   32    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       65       53       83       32
  1        3        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 73  0
  subtype2 51  2
  subtype3 89  1
  subtype4 36  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    0
  subtype2   51    2
  subtype3   89    1
  subtype4   36    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       73       51       89       36
  1        0        2        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 38 53
  subtype2 29 55
  subtype3 27 91
  subtype4 16 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   53
  subtype2   29   55
  subtype3   27   91
  subtype4   16   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       38       29       27       16
  MALE         53       55       91       25
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       88
  subtype2                       1                       80
  subtype3                       0                      118
  subtype4                       0                       40
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                3
  subtype2                                3
  subtype3                                0
  subtype4                                1
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        1        0        0
  HEPATOCELLULAR CARCINOMA               88       80      118       40
  HEPATOCHOLANGIOCARCINOMA (MIXED)        3        3        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  78   5   0   5
  subtype2  70   7   1   4
  subtype3 111   2   0   4
  subtype4  36   1   0   4
D7V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       78       70      111       36
  R1        5        7        2        1
  R2        0        1        0        0
  RX        5        4        4        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    45                         4
  subtype2                                0    34                         4
  subtype3                                1    50                         7
  subtype4                                0    24                         1
          vv
clus       WHITE
  subtype1    41
  subtype2    42
  subtype3    55
  subtype4    16
D7V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                  45       34       50       24
  BLACK OR AFRICAN AMERICAN               4        4        7        1
  WHITE                                  41       42       55       16
[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"
D7V11, binary
          cls
clus         0   1
  subtype1   5  81
  subtype2   3  78
  subtype3   3 107
  subtype4   1  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   81
  subtype2    3   78
  subtype3    3  107
  subtype4    1   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        3        3        1
  NOT HISPANIC OR LATINO       81       78      107       40
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 30 23
  subtype2 55 27
  subtype3 67 27
  subtype4 18 14
  subtype5 41 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      53       82       94       32       51 
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       27       27       14       10 
$subtype1
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-5C-AAPD TCGA-BC-A10U TCGA-BC-A10W 
       63.75        41.33        37.25         0.66        27.52         2.99 
TCGA-BC-A216 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A1EC TCGA-DD-A1EF 
       44.42         4.24         0.10         0.13        19.79        12.95 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A6 TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN 
        5.62        17.59       107.11        21.70        30.15        29.56 
TCGA-DD-A4NQ TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP 
       12.26        12.53         6.41        53.19        61.68        13.64 
TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADN 
       51.52         5.62        44.22        40.83        13.97        29.52 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAVQ 
       14.89        14.33        18.90        25.08        23.64        89.69 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-EP-A2KA 
       13.41        15.85         9.73        12.82         1.84        20.61 
TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A5SJ TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MA 
       19.59        81.73        22.95         2.14         3.02        17.59 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D0 
       15.98         7.04        13.55        35.77        23.57 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H4 
       23.80        53.39        83.24        24.89        27.88        47.74 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y 
        8.55         8.61        10.13        46.78        27.52        23.34 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       13.84        22.36        17.98        18.48        44.81         0.66 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       79.73       113.00         2.60         0.46        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG 
       66.31        25.81         7.66       102.74        13.78        26.37 
TCGA-DD-A4NI TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACK TCGA-DD-AACQ 
       26.83       108.76        23.93        23.05         0.30        14.20 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADM 
       59.31        50.33        47.67        42.58        40.08         0.39 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEI 
       66.67        18.25        20.98        19.99        21.83        50.33 
TCGA-ED-A7XO TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       14.04         0.62        11.93        23.97        19.10         8.12 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
        0.33        53.79        30.74        21.53        22.13         5.92 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 
       25.25        24.46        17.10        11.24         8.55         1.02 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75I TCGA-NI-A4U2 
       17.06        11.84        24.36        12.72        20.71        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-T1-A6J8 TCGA-ZP-A9CY 
       21.01         3.09        19.33        19.04         0.76        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.21         0.69        40.80        79.30 

$subtype3
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H8 
       41.79        80.28        56.91        18.25        11.74        20.81 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10X 
       10.78        10.59        11.08         1.51        37.32        25.32 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 
       69.57         5.03        14.60        36.66         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A119 
        2.86         3.19         0.07         0.10        37.78         7.33 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-A39X 
       75.65        49.15         6.02        33.04        27.19        55.69 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A73G 
       30.61        33.14        90.28        73.81        80.75       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM 
       13.48        11.41        55.40        15.42         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADA 
       42.81        51.35        46.82        18.54        21.63        40.54 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       35.67        34.49        15.06        19.30        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
        4.64        21.17        35.08        82.62        59.93        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       62.47        66.25        12.69        13.91        13.35         0.20 
TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ 
       13.41         0.20        14.40        60.89        27.88         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A7M7 
       51.06        28.27        58.49        14.86        25.64         5.98 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-MI-A75E 
        2.99        37.91        20.75         3.72        13.38        16.67 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V 
       10.85        17.69        15.39        24.13        10.75        10.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D2 TCGA-ZS-A9CD 
        0.99        12.99        24.43        45.57 

$subtype4
TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z 
      120.82        14.99         1.18        48.99        27.91         1.12 
TCGA-BD-A3EP TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK 
       13.45         3.39         3.32        83.57        45.11        18.35 
TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       13.64        35.67        76.41        40.47         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADV TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A3JL 
       35.05        20.91        18.87         0.20        13.35         9.96 
TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB TCGA-RC-A7SK 
        0.03        13.68        12.03         1.84         2.20        15.52 
TCGA-UB-A7MD TCGA-WJ-A86L 
        1.71        11.34 

$subtype5
TCGA-2Y-A9H1 TCGA-5R-AA1C TCGA-BC-A3KF TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE 
       40.41        11.97         0.26        53.33        79.40        11.47 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A4NF TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AAC8 
       21.14        19.76        30.97         9.30        22.78         0.53 
TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 
       75.65        63.48        12.00        69.11         5.59         4.50 
TCGA-DD-AAD6 TCGA-DD-AADE TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 
       22.09        39.52        15.58        18.21        18.61        23.74 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX 
       15.72        16.37        25.78        79.07        72.39        56.48 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       65.39        49.48        53.69        13.15        18.74        19.99 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       19.53        19.23        20.42         9.70         9.17         0.89 
TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
        8.75         2.14        13.97        12.03         9.57        18.38 
TCGA-MI-A75H TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.85        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.30     0.07     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11   113.00   114.35   120.82    79.40 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.590   21.980   20.025   13.660   18.610 
[1] "0.1 - 107.1 (17.6)" "0.3 - 113.0 (22.0)" "0.1 - 114.3 (20.0)"
[4] "0.0 - 120.8 (13.7)" "0.3 - 79.4 (18.6)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      24       14         0         19          1          1        0
  subtype2      38       20         1         11          4          1        1
  subtype3      45       25         2         12          0          5        2
  subtype4      19        4         0          8          1          1        0
  subtype5      27       17         0          6          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
  subtype4         0         1
  subtype5         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          24       38       45       19       27
  STAGE II         14       20       25        4       17
  STAGE III         0        1        2        0        0
  STAGE IIIA       19       11       12        8        6
  STAGE IIIB        1        4        0        1        0
  STAGE IIIC        1        1        5        1        0
  STAGE IV          0        1        2        0        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 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       T0+T1 T2 T3 T4
  subtype1    26 15 21  1
  subtype2    43 23 16  5
  subtype3    48 28 17  4
  subtype4    19  4  9  2
  subtype5    28 17  6  0
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       26       43       48       19       28
  T2          15       23       28        4       17
  T3          21       16       17        9        6
  T4           1        5        4        2        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"
D8V5, binary
          cls
clus        0  1
  subtype1 46  1
  subtype2 51  1
  subtype3 69  2
  subtype4 26  0
  subtype5 41  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    1
  subtype2   51    1
  subtype3   69    2
  subtype4   26    0
  subtype5   41    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       46       51       69       26       41
  1        1        1        2        0        0
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 50  0
  subtype2 59  0
  subtype3 73  3
  subtype4 22  1
  subtype5 45  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    0
  subtype2   59    0
  subtype3   73    3
  subtype4   22    1
  subtype5   45    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       50       59       73       22       45
  1        0        0        3        1        0
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 22 41
  subtype2 26 61
  subtype3 41 57
  subtype4 12 22
  subtype5  9 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   41
  subtype2   26   61
  subtype3   41   57
  subtype4   12   22
  subtype5    9   43
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       26       41       12        9
  MALE         41       61       57       22       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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       61
  subtype2                       0                       86
  subtype3                       1                       93
  subtype4                       0                       34
  subtype5                       0                       52
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                1
  subtype3                                4
  subtype4                                0
  subtype5                                0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        1        0        0
  HEPATOCELLULAR CARCINOMA               61       86       93       34       52
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        1        4        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 57  4  0  2
  subtype2 75  3  0  7
  subtype3 85  5  1  7
  subtype4 27  3  0  1
  subtype5 51  0  0  0
D8V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       57       75       85       27       51
  R1        4        3        5        3        0
  R2        0        0        1        0        0
  RX        2        7        7        1        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    41                         1
  subtype2                                0    27                         7
  subtype3                                0    45                         4
  subtype4                                0    13                         3
  subtype5                                1    27                         1
          vv
clus       WHITE
  subtype1    21
  subtype2    47
  subtype3    46
  subtype4    18
  subtype5    22
D8V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  41       27       45       13       27
  BLACK OR AFRICAN AMERICAN               1        7        4        3        1
  WHITE                                  21       47       46       18       22
[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"
D8V11, binary
          cls
clus        0  1
  subtype1  4 58
  subtype2  3 77
  subtype3  2 92
  subtype4  1 32
  subtype5  2 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   58
  subtype2    3   77
  subtype3    2   92
  subtype4    1   32
  subtype5    2   47
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        3        2        1        2
  NOT HISPANIC OR LATINO       58       77       92       32       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"
