[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/22506983/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/22542932/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=377, in cluster file=440, common to both=377
[1] "Reduce the number of clustering variables from 10 to 8."
[1]   8 377
[1] "CN_CNMF"
[1] 3
  1   2   3 
 93 151 126 
  1   2   3 
 93 151 126 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 93 163 121 
  1   2   3 
 93 163 121 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
68 88 74 71 70 
 1  2  3  4  5 
68 88 74 71 70 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 55  56 116  87  57 
  1   2   3   4   5 
 55  56 116  87  57 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
40 64 92 85 50 41 
 1  2  3  4  5  6 
40 64 92 85 50 41 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 44  97  57 126  48 
  1   2   3   4   5 
 44  97  57 126  48 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
110  81 104  51 
  1   2   3   4 
110  81 104  51 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 73  84 101  34  54 
  1   2   3   4   5 
 73  84 101  34  54 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 377 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=124,	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=222,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 377 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
 [4] "PATHOLOGY_N_STAGE" "PATHOLOGY_M_STAGE" "GENDER"           
 [7] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[10] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=64, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
185  95  81  13 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
185  95  81  13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
185  95  81  13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
185  95  81  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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, 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 64 26
  subtype2 91 59
  subtype3 80 44
subtype1 subtype2 subtype3 
      90      150      124 
subtype1 subtype2 subtype3 
      26       59       44 
$subtype1
TCGA-4R-AA8I TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-AAE7 TCGA-G3-A25W TCGA-K7-A5RF 
        8.61        69.57        36.66        21.17        30.74        20.75 
TCGA-KR-A7K0 TCGA-MI-A75H TCGA-UB-AA0V TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX 
        2.14        24.56        10.32        53.39        63.75        80.28 
TCGA-2Y-A9H4 TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A69I 
       47.74        14.76         1.51        27.91        25.32        12.72 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A5UD TCGA-DD-A1EA TCGA-DD-A1EC 
        2.86         3.39         9.86         9.99        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       75.65        18.35        27.19        70.06        20.12       107.11 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       32.52        30.97        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACD TCGA-DD-AACK 
       78.84        23.05         1.45        11.41        12.53         0.30 
TCGA-DD-AACX TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADE TCGA-DD-AADS TCGA-DD-AAE4 
        5.59        18.54        21.63        39.52        15.58        19.99 
TCGA-DD-AAEI TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       50.33        56.48        65.39        26.93        28.08        13.91 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-ES-A2HT TCGA-FV-A3R3 
        9.73        13.41        18.74        19.99        14.40        12.03 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A7M7 
       51.06        28.27         5.92        19.23        22.95        11.87 
TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-HP-A5N0 
       14.14        15.65        12.23        13.55        28.90        37.71 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A520 
       16.83        11.80        12.03         9.57        16.67         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-UB-A7MD 
       10.85        58.88         3.09         0.72         0.49         1.71 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZS-A9CF 
       24.85        18.28        30.41        35.77        25.71        79.30 

$subtype2
TCGA-2Y-A9GV TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       83.24         5.03        17.98        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-T1-A6J8 
       21.83        18.90         8.12         1.84        12.72         0.76 
TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       29.52        40.80        23.80        24.89        27.88       120.82 
TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-BC-4072 
       49.84        20.81        22.92         1.18         0.66        48.99 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       37.32        10.13        27.52        27.52        23.38         1.12 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 
       13.45         0.66         4.24         3.19         4.24         3.35 
TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE 
        3.32        10.36        11.93        11.41         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU 
       21.34        13.12        12.56         8.61         4.60        11.31 
TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        9.17        37.78        83.57       113.00         2.60        21.76 
TCGA-DD-A1EB TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 
       66.31         6.02        33.04        13.64         5.62        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NQ 
      102.74        30.61        33.14        30.15        30.51        12.26 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        9.30        35.67        75.65        55.40        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACT 
       15.42         3.52        58.16        61.68        14.20        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
       51.52        50.33         5.62        42.58        22.09        40.08 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADN 
       40.83        40.47         3.78        37.64        20.91        29.52 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 
       66.67        19.30        18.25        18.25        20.98        18.61 
TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A7PX 
        4.64        26.63        35.08        80.71        29.92         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-FV-A2QR 
        0.20        14.04        13.15        13.35         0.20        19.10 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
       27.88         0.03         0.33        53.79        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-AAV1 
       21.53        25.64        17.10        14.70        20.78        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K8 
        0.89        11.87         1.02         2.20        17.06        29.79 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A6M6 TCGA-RC-A7SB 
       22.95        20.71        26.27        21.01         0.30        19.33 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U 
       15.52        36.10        19.76        16.44        15.98        10.75 
TCGA-WJ-A86L TCGA-WX-AA44 TCGA-XR-A8TD TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9D2 
       11.34        20.22        33.86        22.78        13.55        25.15 

$subtype3
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-DD-A3A8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       11.74        38.40         0.36        23.64         9.96        22.62 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-KR-A7K7 TCGA-UB-A7MF 
        6.38        81.73        22.13        22.06        31.27         7.04 
TCGA-ZP-A9D1 TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9HB 
        0.69        41.79        40.41        56.91        18.25         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-BC-A10S TCGA-BC-A10W 
       13.02        10.78        10.59        17.10        46.78         2.99 
TCGA-BC-A216 TCGA-CC-A3MA TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A9FS 
       44.42         9.96         9.83        12.00         9.14         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
        8.15        79.73        53.33         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39V 
       90.71        11.47        12.95        45.11        49.15        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NK 
       55.69        19.76         7.66        17.59        13.78        39.78 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AA3A 
       29.56        73.81        23.93        22.78       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACN 
        0.53        76.41         6.41        53.19        69.11        42.81 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD5 
       13.64        59.31        46.82        47.67         4.50        44.22 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       40.54        13.97        35.67        35.05        34.49         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE9 
       14.89        15.06        14.33        18.21        18.15        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.72        25.08        25.78        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        72.39        76.18        64.77        62.47        66.25 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-EP-A2KA 
       60.99        53.69        13.35        12.82         1.84        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A4ZQ 
       19.59         0.62        11.93        60.89        23.97         0.39 
TCGA-G3-A25S TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAUZ TCGA-G3-AAV5 
       13.68        19.53        25.25        20.42        15.78        11.64 
TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A9QC TCGA-O8-A75V TCGA-RC-A7S9 
        2.14         2.99        27.25        13.97        17.69        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ 
       19.04        15.39        27.88         0.99        12.99        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.87        12.99        45.57        11.21 

subtype1 subtype2 subtype3 
    0.30     0.03     0.36 
subtype1 subtype2 subtype3 
  108.76   120.82   114.35 
subtype1 subtype2 subtype3 
  19.890   19.315   20.515 
[1] "0.3 - 108.8 (19.9)" "0.0 - 120.8 (19.3)" "0.4 - 114.3 (20.5)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      47       16         1         18          1          3        0
  subtype2      60       42         1         26          5          4        0
  subtype3      66       29         1         18          3          0        2
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         1
  subtype3         0         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          47       60       66
  STAGE II         16       42       29
  STAGE III         1        1        1
  STAGE IIIA       18       26       18
  STAGE IIIB        1        5        3
  STAGE IIIC        3        4        0
  STAGE IV          0        0        2
  STAGE IVA         1        0        0
  STAGE IVB         1        1        0
[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       T1 T2 T3 T4
  subtype1 50 16 20  4
  subtype2 63 49 32  7
  subtype3 70 30 25  1
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       50       63       70
  T2       16       49       30
  T3       20       32       25
  T4        4        7        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 63  1
  subtype2 99  2
  subtype3 92  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    1
  subtype2   99    2
  subtype3   92    0
   clus
vv  subtype1 subtype2 subtype3
  0       63       99       92
  1        1        2        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1  58   1
  subtype2 112   1
  subtype3  96   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    1
  subtype2  112    1
  subtype3   96    2
   clus
vv  subtype1 subtype2 subtype3
  0       58      112       96
  1        1        1        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 29 64
  subtype2 52 99
  subtype3 37 89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   64
  subtype2   52   99
  subtype3   37   89
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       52       37
  MALE         64       99       89
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1  83   3
  subtype2 139   3
  subtype3 116   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   83    3
  subtype2  139    3
  subtype3  116    3
     clus
vv    subtype1 subtype2 subtype3
  NO        83      139      116
  YES        3        3        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       3                       89
  subtype2                       0                      148
  subtype3                       0                      123
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                3
  subtype3                                3
D1V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 3        0        0
  HEPATOCELLULAR CARCINOMA               89      148      123
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        3        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  79   4   0   7
  subtype2 131   7   0  11
  subtype3 114   6   1   3
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       79      131      114
  R1        4        7        6
  R2        0        0        1
  RX        7       11        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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    27                         6
  subtype2                                0    73                         8
  subtype3                                1    58                         3
          vv
clus       WHITE
  subtype1    58
  subtype2    68
  subtype3    57
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                  27       73       58
  BLACK OR AFRICAN AMERICAN               6        8        3
  WHITE                                  58       68       57
[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"
D1V12, binary
          cls
clus         0   1
  subtype1   2  85
  subtype2  10 135
  subtype3   4 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   85
  subtype2   10  135
  subtype3    4  115
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2       10        4
  NOT HISPANIC OR LATINO       85      135      115
[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  57  33
  subtype2 105  57
  subtype3  77  42
subtype1 subtype2 subtype3 
      90      162      119 
subtype1 subtype2 subtype3 
      33       57       42 
$subtype1
TCGA-2Y-A9GV TCGA-BC-A110 TCGA-DD-A4ND TCGA-DD-AAE8 TCGA-FV-A3I1 TCGA-G3-A25W 
       83.24        69.57        90.28        21.83         8.12        30.74 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-UB-AA0V TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
        1.84        20.75        10.32        41.79        80.28        24.89 
TCGA-2Y-A9H2 TCGA-5C-AAPD TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       56.91         0.66        14.76        48.99        27.91        37.32 
TCGA-BC-A10X TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       25.32        13.45         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-DD-A114 
        9.86        11.41        13.12        12.56         4.60        37.78 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A3A6 
       90.71        19.79        75.65        45.11        13.64       107.11 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       33.14        32.52        30.15        56.25       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-AACC TCGA-DD-AACL 
        0.30        80.75        23.05        35.67        55.40         3.52 
TCGA-DD-AACM TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADC 
       58.16         5.62        21.63        42.58        44.22        13.97 
TCGA-DD-AADK TCGA-DD-AAEK TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7XO 
       34.49        35.08        26.93        28.08        13.91        14.04 
TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A495 TCGA-G3-A25T 
       13.41         0.20        11.93        14.40         0.03        51.06 
TCGA-G3-A25V TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M8 TCGA-G3-AAV3 
       28.27         5.92        22.95        20.78        14.14        13.55 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
       28.90         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-RC-A6M5 
       29.79        16.67        20.71         7.53        10.85         0.49 
TCGA-RC-A6M6 TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 
        0.30        36.10         1.71        33.86        30.41        13.55 

$subtype2
TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-A4NI TCGA-DD-AADV 
       38.40         8.61        17.98         0.36        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A4ZP 
       21.17        18.90         9.96        22.62         6.38        81.73 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
       22.13        22.06         2.14        31.27        12.72        24.56 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GZ 
       29.52         0.69        40.80        23.80        53.39        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
      120.82        40.41        47.74        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       13.02        17.10         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 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A3MB 
       12.72        18.48        44.81         0.66         3.35        10.36 
TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A115 
       12.00         8.61         9.14        11.31         8.15        83.57 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EJ 
        2.60        21.76        51.29        79.40        11.47        33.04 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        21.14        27.19         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NJ 
        7.66        70.06       102.74        30.97        26.37        30.51 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       39.78        78.84        23.93        22.78         1.45         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ 
       75.65        76.41        71.80        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-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       66.67        15.58        18.21        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       19.99         4.64        23.74        15.72        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       50.33        72.39        56.48        65.39        60.99        53.69 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-FV-A2QQ 
        0.20        18.74        19.99        20.61         0.62        23.97 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK 
       19.10        13.68        53.79        21.53        19.53        19.23 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV0 
       24.46        20.42        17.10        14.70        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.80        12.23         0.89        11.64         1.02         2.20 
TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       27.25        22.95        58.88        21.01         3.09         0.72 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L 
       19.33        19.04        15.52        16.44        10.75        11.34 
TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       12.99        22.78        35.77        25.71        12.99        79.30 

$subtype3
TCGA-2Y-A9H6 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-AAEG TCGA-T1-A6J8 TCGA-UB-A7MF 
       11.74         5.03        36.66        23.64         0.76         7.04 
TCGA-XR-A8TC TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-5C-A9VG 
       44.02        63.75        49.84        18.25        20.81        10.78 
TCGA-5C-A9VH TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 
       10.59        10.13         2.99        14.60         4.24         8.22 
TCGA-CC-5261 TCGA-CC-A123 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A5UE 
        3.19         7.20         9.96        11.93         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HS TCGA-CC-A8HV TCGA-CC-A9FS 
        7.13        21.34         9.83         9.86         9.17         6.94 
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-AADE TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO 
       40.54        40.83        39.52        35.67        35.05        14.89 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAED TCGA-DD-AAVP TCGA-DD-AAVQ 
       19.30        18.25        18.25        25.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ 
       82.62        59.93        80.71        76.18        64.77        62.47 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       66.25        29.92        13.35         9.73         0.20        12.82 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 
       13.15        13.35         1.84        19.59        60.89        27.88 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       12.03         0.33         0.39        58.49        14.86        25.64 
TCGA-G3-A5SI TCGA-G3-A7M7 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-LG-A9QC TCGA-LG-A9QD 
       25.25        11.87         2.14        11.87        13.97        12.03 
TCGA-MI-A75C TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA 
        9.57        26.27        17.69        21.04        15.39        27.88 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       19.76        15.98         0.99        20.22        24.85        18.28 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        35.87        25.15        45.57        11.21 

subtype1 subtype2 subtype3 
    0.03     0.20     0.20 
subtype1 subtype2 subtype3 
  108.76   120.82   114.35 
subtype1 subtype2 subtype3 
  20.765   20.205   18.280 
[1] "0.0 - 108.8 (20.8)" "0.2 - 120.8 (20.2)" "0.2 - 114.3 (18.3)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      42       19         0         19          4          4        0
  subtype2      79       38         2         26          3          3        0
  subtype3      54       30         1         20          2          2        2
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          42       79       54
  STAGE II         19       38       30
  STAGE III         0        2        1
  STAGE IIIA       19       26       20
  STAGE IIIB        4        3        2
  STAGE IIIC        4        3        2
  STAGE IV          0        0        2
  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       T1 T2 T3 T4
  subtype1 43 22 23  3
  subtype2 84 41 31  6
  subtype3 58 32 27  4
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       84       58
  T2       22       41       32
  T3       23       31       27
  T4        3        6        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1  65   2
  subtype2 107   1
  subtype3  85   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65    2
  subtype2  107    1
  subtype3   85    1
   clus
vv  subtype1 subtype2 subtype3
  0       65      107       85
  1        2        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"
D2V6, binary
          cls
clus         0   1
  subtype1  64   0
  subtype2 117   1
  subtype3  91   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64    0
  subtype2  117    1
  subtype3   91    3
   clus
vv  subtype1 subtype2 subtype3
  0       64      117       91
  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  34  59
  subtype2  40 123
  subtype3  48  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   59
  subtype2   40  123
  subtype3   48   73
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       40       48
  MALE         59      123       73
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus         0   1
  subtype1  85   1
  subtype2 152   4
  subtype3 108   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   85    1
  subtype2  152    4
  subtype3  108    4
     clus
vv    subtype1 subtype2 subtype3
  NO        85      152      108
  YES        1        4        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       3                       87
  subtype2                       0                      162
  subtype3                       0                      118
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                3
  subtype2                                1
  subtype3                                3
D2V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 3        0        0
  HEPATOCELLULAR CARCINOMA               87      162      118
  HEPATOCHOLANGIOCARCINOMA (MIXED)        3        1        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  76   5   0   8
  subtype2 145   8   0   7
  subtype3 109   4   1   7
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       76      145      109
  R1        5        8        4
  R2        0        0        1
  RX        8        7        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                                0    29                         9
  subtype2                                1    66                         7
  subtype3                                1    66                         1
          vv
clus       WHITE
  subtype1    52
  subtype2    85
  subtype3    50
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                  29       66       66
  BLACK OR AFRICAN AMERICAN               9        7        1
  WHITE                                  52       85       50
[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"
D2V12, binary
          cls
clus         0   1
  subtype1   4  84
  subtype2   6 146
  subtype3   8 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   84
  subtype2    6  146
  subtype3    8  110
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        6        8
  NOT HISPANIC OR LATINO       84      146      110
[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 33 32
  subtype2 59 29
  subtype3 46 26
  subtype4 48 22
  subtype5 49 21
subtype1 subtype2 subtype3 subtype4 subtype5 
      65       88       72       70       70 
subtype1 subtype2 subtype3 subtype4 subtype5 
      32       29       26       22       21 
$subtype1
TCGA-BC-A112 TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-KR-A7K7 TCGA-LG-A6GG 
        5.03         8.12        81.73         1.84        31.27        12.72 
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-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
        2.99        44.42        45.93        22.36        14.60        18.48 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
       13.45         0.66         8.22         4.24         3.35         3.32 
TCGA-CC-A3M9 TCGA-CC-A5UE TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-DD-A114 
        9.86         8.94        13.12        12.56         4.60        37.78 
TCGA-DD-A1EC TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A1 
       19.79        45.11        18.35        13.64         5.62         7.66 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-AACG TCGA-DD-AACH 
       13.78        33.14        12.26         0.30        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN 
       53.19         0.30         3.52         5.62        44.22        29.52 
TCGA-DD-AADQ TCGA-ED-A459 TCGA-EP-A2KA TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-A7M6 
       14.33        29.92        20.61        13.68        22.95        20.78 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-MI-A75I TCGA-QA-A7B7 
       11.87         1.02        17.06        11.80        20.71         3.09 
TCGA-RC-A6M6 TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-WJ-A86L TCGA-YA-A8S7 
        0.30        19.04        36.10        11.34        13.55 

$subtype2
TCGA-2Y-A9GV TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAEA TCGA-ES-A2HS 
       83.24        17.98        26.83        18.87        18.90        22.62 
TCGA-FV-A3R2 TCGA-G3-A3CG TCGA-T1-A6J8 TCGA-XR-A8TG TCGA-ZS-A9CE TCGA-2Y-A9GT 
        6.38        22.13         0.76        29.52        40.80        53.39 
TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5R-AAAM 
       27.88        47.74        22.92         8.55        13.02         1.51 
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-CC-A3MB 
       27.52        23.38         1.12         0.26        44.81        10.36 
TCGA-CC-A7IL TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
        9.14        83.57         2.60         0.46        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NJ TCGA-DD-A4NK 
       66.31        70.06       102.74        21.70        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       56.25        73.81        78.84        23.93         9.30        23.05 
TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACV 
       35.67        71.80        12.00        14.20        59.31        50.33 
TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM 
       47.67        42.58        40.08         3.78        20.91         0.39 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEH 
       66.67        15.58        20.98        18.61        19.99        25.78 
TCGA-DD-AAEI TCGA-ED-A7XO TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25U 
       50.33        14.04        23.97        19.10         0.33        53.79 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A7M5 
       21.53        25.64         5.92        25.25        24.46        14.70 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-KR-A7K8 
       14.14        15.78        15.65         2.20        37.71        29.79 
TCGA-LG-A9QD TCGA-MI-A75G TCGA-MR-A520 TCGA-NI-A4U2 TCGA-RC-A7SB TCGA-RC-A7SK 
       12.03        22.95         7.53        58.88        19.33        15.52 
TCGA-UB-A7MB TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZS-A9CF 
       19.76        24.85        25.71        79.30 

$subtype3
TCGA-2Y-A9H7 TCGA-UB-A7MF TCGA-XR-A8TC TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       38.40         7.04        44.02        63.75        49.84        18.25 
TCGA-2Y-A9H8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A123 
       20.81        10.78        10.59         4.24         3.19         7.20 
TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HS TCGA-CC-A8HU 
       11.41         7.13        21.34         9.83         9.86        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EF 
        9.17         6.94         8.15        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-AACO TCGA-DD-AACP 
       29.56       114.35        55.40        42.81        61.68        13.64 
TCGA-DD-AACW TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ 
       46.82        40.54        40.83        13.97        35.67        35.05 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       14.89        19.30        18.25        18.25        18.15         4.64 
TCGA-DD-AAED TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       25.08        89.69        59.93        72.39        76.18        62.47 
TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 
       28.08        13.35         9.73        12.82         0.20        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-G3-A25Y TCGA-G3-AAV6 TCGA-RC-A7S9 
        1.84        19.59        60.89        14.86         2.14        21.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       15.39        27.88        15.98         0.99        23.21        35.87 

$subtype4
TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-DD-AAEG 
       11.74        69.57        36.66        90.28        21.17        23.64 
TCGA-EP-A3JL TCGA-K7-A5RF TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GW TCGA-2Y-A9GX 
        9.96        20.75        10.32         0.69        41.79        80.28 
TCGA-2Y-A9H2 TCGA-5R-AA1D TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       56.91        14.76        48.99        37.32        10.13        46.78 
TCGA-BC-A10X TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A119 
       25.32         2.86         3.39         9.96        11.93         7.33 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NS TCGA-DD-AA3A 
        6.02        55.69       107.11        32.52        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-AAVR TCGA-DD-AAVV TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 
       15.06        82.62        80.71        66.25        26.93        13.91 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A3R3 
        0.20        13.41         0.20        14.40        27.88        12.03 
TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 
        0.03        51.06        28.27        58.49        17.10        11.87 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-MI-A75E TCGA-MR-A8JO 
       28.90         2.99        16.83        27.25        16.67        10.85 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M5 TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-WX-AA44 
       17.69        21.01         0.49        10.75        12.99        20.22 
TCGA-XR-A8TD TCGA-ZP-A9CV TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       33.86        35.77        25.15        45.57 

$subtype5
TCGA-4R-AA8I TCGA-DD-A3A8 TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-MI-A75H TCGA-2Y-A9H1 
        8.61         0.36        22.06         2.14        24.56        40.41 
TCGA-2Y-A9HA TCGA-5R-AA1C TCGA-BC-A69I TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IK 
        1.18        17.10        12.72         9.99        12.00         8.61 
TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39W 
       53.33        79.40        75.65        11.47        21.14        27.19 
TCGA-DD-A3A4 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E 
       20.12        30.97        26.37       108.76        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACX 
        0.53        75.65        76.41        12.53        69.11         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADG TCGA-DD-AADU TCGA-DD-AAE9 
        4.50        22.09        40.47        37.64        18.21        23.74 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVX TCGA-DD-AAVY 
       15.72        26.63        35.08        90.48        56.48        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       65.39        60.99        53.69        13.15        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL 
        0.62        11.93         0.39        19.53        19.23        20.42 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-LG-A9QC 
       11.80        12.23        13.55         0.89        11.64        13.97 
TCGA-MI-A75C TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WX-AA47 
        9.57        26.27         0.72        16.44         1.71        18.28 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       30.41        22.78        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.30     0.26     0.20     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   22.935   19.445   20.880   18.985 
[1] "0.3 - 120.8 (13.6)" "0.3 - 102.7 (22.9)" "0.2 - 114.3 (19.4)"
[4] "0.0 - 107.1 (20.9)" "0.4 - 108.8 (19.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      17       25         0         14          3          3        0
  subtype2      55       13         1         12          1          0        0
  subtype3      33       17         1         14          1          2        1
  subtype4      35       13         0          9          2          3        1
  subtype5      31       18         1         16          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         0         1
  subtype4         1         0
  subtype5         0         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          17       55       33       35       31
  STAGE II         25       13       17       13       18
  STAGE III         0        1        1        0        1
  STAGE IIIA       14       12       14        9       16
  STAGE IIIB        3        1        1        2        1
  STAGE IIIC        3        0        2        3        1
  STAGE IV          0        0        1        1        0
  STAGE IVA         0        0        0        1        0
  STAGE IVB         1        0        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       T1 T2 T3 T4
  subtype1 17 29 17  5
  subtype2 57 14 14  2
  subtype3 37 18 18  1
  subtype4 38 15 13  4
  subtype5 32 18 18  1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       17       57       37       38       32
  T2       29       14       18       15       18
  T3       17       14       18       13       18
  T4        5        2        1        4        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 40  1
  subtype2 61  0
  subtype3 59  2
  subtype4 41  1
  subtype5 51  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    1
  subtype2   61    0
  subtype3   59    2
  subtype4   41    1
  subtype5   51    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       40       61       59       41       51
  1        1        0        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"
D3V6, binary
          cls
clus        0  1
  subtype1 46  1
  subtype2 64  0
  subtype3 61  2
  subtype4 43  1
  subtype5 52  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    1
  subtype2   64    0
  subtype3   61    2
  subtype4   43    1
  subtype5   52    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       46       64       61       43       52
  1        1        0        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 20 48
  subtype2 23 65
  subtype3 38 36
  subtype4 30 41
  subtype5 10 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   48
  subtype2   23   65
  subtype3   38   36
  subtype4   30   41
  subtype5   10   60
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       20       23       38       30       10
  MALE         48       65       36       41       60
[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"
D3V8, binary
          cls
clus        0  1
  subtype1 64  1
  subtype2 81  1
  subtype3 69  0
  subtype4 63  2
  subtype5 62  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64    1
  subtype2   81    1
  subtype3   69    0
  subtype4   63    2
  subtype5   62    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        64       81       69       63       62
  YES        1        1        0        2        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       66
  subtype2                       0                       88
  subtype3                       0                       73
  subtype4                       3                       64
  subtype5                       0                       70
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                0
  subtype3                                1
  subtype4                                4
  subtype5                                0
D3V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        3        0
  HEPATOCELLULAR CARCINOMA               66       88       73       64       70
  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 54  6  0  7
  subtype2 78  3  0  6
  subtype3 69  1  0  4
  subtype4 56  6  1  5
  subtype5 67  1  0  0
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       54       78       69       56       67
  R1        6        3        1        6        1
  R2        0        0        0        1        0
  RX        7        6        4        5        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                                1    25                         8
  subtype2                                0    32                         3
  subtype3                                0    48                         1
  subtype4                                0    24                         2
  subtype5                                1    29                         3
          vv
clus       WHITE
  subtype1    32
  subtype2    48
  subtype3    24
  subtype4    43
  subtype5    37
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        1
  ASIAN                                  25       32       48       24       29
  BLACK OR AFRICAN AMERICAN               8        3        1        2        3
  WHITE                                  32       48       24       43       37
[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"
D3V12, binary
          cls
clus        0  1
  subtype1  4 58
  subtype2  6 76
  subtype3  3 70
  subtype4  3 64
  subtype5  2 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   58
  subtype2    6   76
  subtype3    3   70
  subtype4    3   64
  subtype5    2   66
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        6        3        3        2
  NOT HISPANIC OR LATINO       58       76       70       64       66
[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 24 29
  subtype2 39 17
  subtype3 74 42
  subtype4 56 27
  subtype5 42 15
subtype1 subtype2 subtype3 subtype4 subtype5 
      53       56      116       83       57 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       17       42       27       15 
$subtype1
TCGA-BC-A112 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-BC-4072 
        5.03        81.73         1.84        24.89        56.91        48.99 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A69H TCGA-CC-5259 TCGA-CC-5260 
       27.91        37.32         2.99        14.60         8.22         2.86 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UE TCGA-CC-A7IG 
        4.24         3.32         9.86         9.96         8.94         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A39Y 
       13.12        12.56         4.60         9.17        37.78         5.62 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NQ TCGA-DD-A4NR 
      107.11        13.78        33.14        30.15        12.26         0.30 
TCGA-DD-AA3A TCGA-DD-AACH TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN 
       13.48         6.41         3.52         5.62        44.22        29.52 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-G3-A25T 
        0.20        13.41         0.20        20.61        27.88        51.06 
TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAV7 TCGA-K7-AAU7 TCGA-RC-A6M6 
       58.49        22.95        20.78        11.87        11.80         0.30 
TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9D2 
       27.88         0.99        20.22        13.55        25.15 

$subtype2
TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-AAE7 TCGA-EP-A3JL TCGA-FV-A3I1 
       69.57        36.66        90.28        21.17         9.96         8.12 
TCGA-G3-A3CG TCGA-K7-A5RF TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-ZP-A9D1 TCGA-2Y-A9GS 
       22.13        20.75         0.76        10.32         0.69        23.80 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5R-AAAM TCGA-BC-A10S 
       41.79        80.28         8.55        13.02         1.51        46.78 
TCGA-BC-A10X TCGA-BD-A3EP TCGA-CC-5262 TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A1EI 
       25.32        13.45         3.39        10.36        45.11         6.02 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACC 
       30.51        56.25        73.81        80.75        11.41        55.40 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AADM TCGA-DD-AADP 
       51.35        51.52        47.67        42.58         0.39        15.06 
TCGA-ED-A627 TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A495 TCGA-G3-A25V TCGA-G3-A25Z 
       13.91        14.40        23.97         0.03        28.27        21.53 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QD 
       17.10        11.87        28.90         2.99        16.83        12.03 
TCGA-MI-A75E TCGA-O8-A75V TCGA-RC-A7SK TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-ZP-A9CV 
       16.67        17.69        15.52        10.75        12.99        35.77 
TCGA-ZP-A9CY TCGA-ZS-A9CD 
       25.71        45.57 

$subtype3
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAEA 
       83.24         8.61        17.98        26.83        18.87        18.90 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-LG-A6GG TCGA-UB-A7MF TCGA-XR-A8TG TCGA-ZS-A9CE 
       22.62         6.38        12.72         7.04        29.52        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       53.39        27.88       120.82        40.41        47.74        22.92 
TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
        0.66        27.52        27.52        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93         0.26        22.36        18.48        44.81         0.66 
TCGA-CC-5264 TCGA-CC-A7IF TCGA-CC-A7IL TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 
        3.35        21.34         9.14         6.94        79.73        83.57 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EK 
        2.60         0.46        21.76        51.29        66.31        18.35 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NE 
       19.76         7.66        70.06        17.59       102.74        21.70 
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        71.80        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-AADY TCGA-DD-AAE2 
       20.91        14.33        66.67        15.58        18.25        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI 
       18.61        19.99         4.64        25.08        25.78        50.33 
TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7XO TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25S 
       72.39        29.92        14.04        19.10         0.33        13.68 
TCGA-G3-A25U TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A7M5 
       53.79        25.64         5.92        25.25        24.46        14.70 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
       14.14        15.78        15.65         1.02         2.20        37.71 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I 
       17.06        27.25        29.79         9.57        22.95        20.71 
TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB 
        7.53        58.88        21.01         3.09        21.04        19.33 
TCGA-RC-A7SF TCGA-UB-A7MB TCGA-WJ-A86L TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TF 
       19.04        19.76        11.34        24.85        33.86        22.78 
TCGA-ZP-A9CZ TCGA-ZS-A9CF 
       23.21        79.30 

$subtype4
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-DD-AAEG TCGA-KR-A7K7 TCGA-XR-A8TC TCGA-2Y-A9GU 
       11.74        38.40        23.64        31.27        44.02        63.75 
TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9HA TCGA-5C-A9VG TCGA-5C-A9VH 
       49.84        18.25        20.81         1.18        10.78        10.59 
TCGA-5R-AA1D TCGA-BC-A10R TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A123 TCGA-CC-A3MC 
       14.76        10.13         4.24         3.19         7.20        11.93 
TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A118 
       11.41         7.13         9.86        11.31         8.15       113.00 
TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X 
        7.33        19.79        12.95        49.15        33.04        55.69 
TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NN TCGA-DD-A73G TCGA-DD-AACB 
       20.12        30.61        32.52        29.56       114.35        76.41 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AAD1 
       15.42        53.19        42.81        13.64        46.82        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       21.63        22.09        40.54        40.83        13.97        40.47 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 
       35.67        35.05        34.49        14.89        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW 
       18.15        89.69        82.62        59.93        80.71        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       62.47        66.25        26.93        28.08        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B 
       12.82         0.20        13.35         1.84        19.59        60.89 
TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25Y TCGA-G3-AAV6 TCGA-MR-A8JO TCGA-RC-A6M5 
       12.03         0.39        14.86         2.14        10.85         0.49 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-WX-AA47 TCGA-ZP-A9D0 
       15.39        36.10        15.98        18.28        35.87 

$subtype5
TCGA-DD-A3A8 TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-MI-A75H TCGA-5R-AA1C TCGA-BC-A69I 
        0.36        22.06         2.14        24.56        17.10        12.72 
TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IK TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED 
        9.99        12.00         8.61        53.33        79.40        75.65 
TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A4NF TCGA-DD-A4NG 
       11.47        13.64        21.14        27.19        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        26.63        35.08 
TCGA-DD-AAVP TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       90.48        56.48        64.77        65.39        60.99        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-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       19.23        20.42        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-LG-A9QC TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-UB-A7MC TCGA-UB-A7MD 
       11.64        13.97        26.27         0.72        16.44         1.71 
TCGA-XR-A8TE TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       30.41        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.03     0.26     0.20     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11    90.28   120.82   114.35   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
   13.12    19.22    21.19    19.59    18.74 
[1] "0.2 - 107.1 (13.1)" "0.0 - 90.3 (19.2)"  "0.3 - 120.8 (21.2)"
[4] "0.2 - 114.3 (19.6)" "0.4 - 108.8 (18.7)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      11       17         0         15          4          3        0
  subtype2      33       10         0          3          1          2        0
  subtype3      62       25         1         17          2          1        0
  subtype4      41       19         1         17          0          2        2
  subtype5      24       15         1         13          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         0
  subtype3         0         1
  subtype4         1         1
  subtype5         0         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          11       33       62       41       24
  STAGE II         17       10       25       19       15
  STAGE III         0        0        1        1        1
  STAGE IIIA       15        3       17       17       13
  STAGE IIIB        4        1        2        0        1
  STAGE IIIC        3        2        1        2        1
  STAGE IV          0        0        0        2        0
  STAGE IVA         0        0        0        1        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       T1 T2 T3 T4
  subtype1 11 20 20  4
  subtype2 37 11  5  2
  subtype3 63 28 19  5
  subtype4 45 20 21  1
  subtype5 25 15 15  1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       11       37       63       45       25
  T2       20       11       28       20       15
  T3       20        5       19       21       15
  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 31  0
  subtype3 77  0
  subtype4 67  3
  subtype5 44  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    1
  subtype2   31    0
  subtype3   77    0
  subtype4   67    3
  subtype5   44    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       33       31       77       67       44
  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"
D4V6, binary
          cls
clus        0  1
  subtype1 39  0
  subtype2 32  0
  subtype3 83  1
  subtype4 68  3
  subtype5 44  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   32    0
  subtype3   83    1
  subtype4   68    3
  subtype5   44    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       39       32       83       68       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 23 32
  subtype2 13 43
  subtype3 35 81
  subtype4 42 45
  subtype5  8 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   32
  subtype2   13   43
  subtype3   35   81
  subtype4   42   45
  subtype5    8   49
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       23       13       35       42        8
  MALE         32       43       81       45       49
[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"
D4V8, binary
          cls
clus         0   1
  subtype1  52   1
  subtype2  52   0
  subtype3 107   2
  subtype4  77   2
  subtype5  51   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    1
  subtype2   52    0
  subtype3  107    2
  subtype4   77    2
  subtype5   51    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        52       52      107       77       51
  YES        1        0        2        2        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       50
  subtype2                       0                       56
  subtype3                       0                      114
  subtype4                       3                       84
  subtype5                       0                       57
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                5
  subtype2                                0
  subtype3                                2
  subtype4                                0
  subtype5                                0
D4V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        3        0
  HEPATOCELLULAR CARCINOMA               50       56      114       84       57
  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  43   7   0   4
  subtype2  46   4   0   4
  subtype3 102   4   0   8
  subtype4  79   1   1   6
  subtype5  54   1   0   0
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       43       46      102       79       54
  R1        7        4        4        1        1
  R2        0        0        0        1        0
  RX        4        4        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    26                         1
  subtype2                                0    14                         4
  subtype3                                0    45                         6
  subtype4                                1    50                         2
  subtype5                                1    23                         4
          vv
clus       WHITE
  subtype1    27
  subtype2    35
  subtype3    59
  subtype4    34
  subtype5    29
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        1
  ASIAN                                  26       14       45       50       23
  BLACK OR AFRICAN AMERICAN               1        4        6        2        4
  WHITE                                  27       35       59       34       29
[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"
D4V12, binary
          cls
clus        0  1
  subtype1  3 51
  subtype2  4 51
  subtype3  7 98
  subtype4  3 80
  subtype5  1 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    4   51
  subtype3    7   98
  subtype4    3   80
  subtype5    1   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        4        7        3        1
  NOT HISPANIC OR LATINO       51       51       98       80       54
[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 21 17
  subtype2 41 23
  subtype3 66 26
  subtype4 57 27
  subtype5 30 19
  subtype6 23 16
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      38       64       92       84       49       39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      17       23       26       27       19       16 
$subtype1
TCGA-DD-AADV TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-G3-A7M9 TCGA-2Y-A9GY TCGA-2Y-A9H0 
       18.87         9.96         8.12         1.84        24.89       120.82 
TCGA-2Y-A9HA TCGA-BC-4073 TCGA-BC-A10Z TCGA-BC-A216 TCGA-BD-A3EP TCGA-BW-A5NO 
        1.18        27.91         1.12        44.42        13.45         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A7IK TCGA-DD-A115 TCGA-DD-A1EG 
        3.39         4.24         3.32         8.61        83.57        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AADD 
       18.35        13.64        35.67        75.65        76.41        40.47 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-ED-A7PZ TCGA-ED-A8O5 
        3.78        37.64        35.05        20.91         0.20        13.35 
TCGA-G3-A25S TCGA-G3-A7M6 TCGA-GJ-A9DB TCGA-MI-A75I TCGA-RC-A7SK TCGA-UB-A7MD 
       13.68        20.78         2.20        20.71        15.52         1.71 
TCGA-WJ-A86L TCGA-XR-A8TD 
       11.34        33.86 

$subtype2
TCGA-4R-AA8I TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-XR-A8TG 
        8.61        30.74        22.13        12.72         0.76        29.52 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-BC-A10U 
       40.80        23.80        47.74        22.92         8.55        27.52 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-5264 
       23.38        45.93        22.36        18.48        44.81         3.35 
TCGA-CC-A8HT TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
        4.60        79.73       113.00         2.60        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG 
       66.31         5.62         7.66       102.74        13.78        26.37 
TCGA-DD-A4NQ TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       12.26        23.93        23.05         6.41        53.19         0.30 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AAE2 
       14.20        59.31        40.08         0.39        66.67        20.98 
TCGA-DD-AAE3 TCGA-DD-AAEI TCGA-EP-A2KA TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR 
       18.61        50.33        20.61        11.93        23.97        19.10 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
       53.79        21.53        25.25        22.95        17.10        14.70 
TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB 
        1.02        17.06        58.88        21.01         3.09        19.33 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MB TCGA-ZS-A9CF 
       19.04        27.88        19.76        79.30 

$subtype3
TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI 
       11.74        69.57         5.03        36.66        90.28        26.83 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-UB-AA0V 
       21.17        21.83        23.64        20.75         2.14        10.32 
TCGA-ZP-A9D1 TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-5C-A9VG TCGA-5C-A9VH 
        0.69        53.39        41.79        80.28        10.78        10.59 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-CC-5260 
       14.76         1.51        10.13        27.52        25.32         2.86 
TCGA-CC-5261 TCGA-CC-A3MC TCGA-CC-A7IF TCGA-CC-A8HU TCGA-DD-A114 TCGA-DD-A119 
        3.19        11.93        21.34        11.31        37.78         7.33 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NL 
        6.02        55.69        25.81        30.61        32.52        56.25 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACE 
       73.81        80.75        78.84       114.35        11.41        71.80 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADC 
       42.81        61.68        18.54        21.63        42.58        13.97 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AAE4 TCGA-DD-AAVR TCGA-DD-AAVV 
       35.67        34.49        15.06        19.99        82.62        80.71 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP 
       66.25        26.93        13.91         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-EP-A2KC TCGA-ES-A2HT TCGA-FV-A495 TCGA-G3-A25V TCGA-G3-A25X 
       13.41         0.62        14.40         0.03        28.27        58.49 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       25.64         5.92        11.87        14.14        15.78        15.65 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 
       28.90         2.99        37.71        16.83        27.25        29.79 
TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A6M5 TCGA-UB-AA0U 
       16.67         7.53        10.85        17.69         0.49        10.75 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       12.99        20.22        24.85        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CD 
       35.87        45.57 

$subtype4
TCGA-2Y-A9H7 TCGA-BC-A5W4 TCGA-DD-A3A8 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-G3-A6UC 
       38.40        17.98         0.36        18.90        22.62        22.06 
TCGA-MI-A75H TCGA-UB-A7MF TCGA-2Y-A9GU TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-3K-AAZ8 
       24.56         7.04        63.75        27.88        40.41        13.02 
TCGA-5R-AA1C TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-A5UD TCGA-CC-A5UE 
       17.10         2.99         0.26        12.72         9.99         8.94 
TCGA-CC-A7IH TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A9FS TCGA-DD-A116 
       12.00        12.56         9.14         9.86         6.94        53.33 
TCGA-DD-A11B TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A3A2 TCGA-DD-A3A3 
        0.46        79.40        11.47        21.14        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-A73D 
       20.12       107.11        30.97       108.76         9.30        22.78 
TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACP 
        1.45         0.53        12.53        12.00        69.11        13.64 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 
       50.33         5.59        47.67         5.62         4.50        22.09 
TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
       40.83        39.52        29.52        14.89        15.58        18.21 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVX 
       23.74        15.72        26.63        25.78        90.48        56.48 
TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-EP-A12J TCGA-EP-A26S 
       64.77        65.39        60.99        53.69        18.74        19.99 
TCGA-EP-A2KB TCGA-FV-A496 TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-AAV1 
       19.59         0.33        19.53        19.23        20.42        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-LG-A9QC TCGA-MI-A75C 
       12.23        13.55         0.89        11.64        13.97         9.57 
TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-UB-A7MC TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       22.95        26.27         0.72        16.44        12.99        11.21 

$subtype5
TCGA-2Y-A9GV TCGA-KR-A7K7 TCGA-XR-A8TC TCGA-2Y-A9H8 TCGA-BC-4072 TCGA-BC-A10S 
       83.24        31.27        44.02        20.81        48.99        46.78 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A123 TCGA-CC-A3M9 TCGA-CC-A3MB 
       14.60         4.24         8.22         7.20         9.86        10.36 
TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7II TCGA-CC-A8HV TCGA-DD-A1ED TCGA-DD-A1EH 
       11.41         7.13        13.12         9.17        75.65        49.15 
TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
       33.04        27.19        13.48        55.40        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AADQ TCGA-DD-AAE1 
       58.16        51.35        51.52        46.82        14.33        18.15 
TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
        4.64        35.08        59.93        72.39        76.18        62.47 
TCGA-ED-A459 TCGA-ED-A66X TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A5SK 
       29.92        13.35        60.89        27.88         0.39        24.46 
TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-WX-AA47 TCGA-XR-A8TE 
       11.80        12.03        21.04        36.10        18.28        30.41 
TCGA-XR-A8TF 
       22.78 

$subtype6
TCGA-FV-A4ZP TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-5C-AAPD TCGA-BC-A10Q 
       81.73        56.91        49.84        18.25         0.66        37.32 
TCGA-CC-A3MA TCGA-CC-A7IG TCGA-CC-A9FW TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39Z 
        9.96         9.83         8.15        19.79        12.95        19.76 
TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-AAD5 
       33.14        21.70        30.15        29.56         0.30        44.22 
TCGA-DD-AADA TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAED TCGA-DD-AAVQ 
       40.54        19.30        18.25        18.25        25.08        89.69 
TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-ED-A97K TCGA-G3-A25T 
       28.08         9.73        12.82         1.84         0.20        51.06 
TCGA-G3-A25Y TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-RC-A6M6 TCGA-RC-A7SH TCGA-UB-A7ME 
       14.86         2.14        11.87         0.30        15.39        15.98 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D2 
        0.99        13.55        25.15 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.20     0.30     0.03     0.26     0.39     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  120.82   113.00   114.35   108.76    83.24    89.69 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  14.600   21.945   21.255   18.095   24.460   18.250 
[1] "0.2 - 120.8 (14.6)" "0.3 - 113.0 (21.9)" "0.0 - 114.3 (21.3)"
[4] "0.3 - 108.8 (18.1)" "0.4 - 83.2 (24.5)"  "0.2 - 89.7 (18.2)" 
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      19        6         0         10          2          1        0
  subtype2      26       20         1          8          3          1        0
  subtype3      51       17         0          9          0          2        1
  subtype4      44       19         0         14          3          2        0
  subtype5      18       14         2         11          0          2        1
  subtype6      14       10         0         12          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         1         1
  subtype4         0         0
  subtype5         0         0
  subtype6         0         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          19       26       51       44       18       14
  STAGE II          6       20       17       19       14       10
  STAGE III         0        1        0        0        2        0
  STAGE IIIA       10        8        9       14       11       12
  STAGE IIIB        2        3        0        3        0        1
  STAGE IIIC        1        1        2        2        2        1
  STAGE IV          0        0        1        0        1        0
  STAGE IVA         0        0        1        0        0        0
  STAGE IVB         1        0        1        0        0        0
[1] 9 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 19  7 12  2
  subtype2 27 23 11  3
  subtype3 57 17 12  4
  subtype4 45 19 17  3
  subtype5 20 15 14  1
  subtype6 14 13 14  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       19       27       57       45       20       14
  T2        7       23       17       19       15       13
  T3       12       11       12       17       14       14
  T4        2        3        4        3        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 28  0
  subtype2 40  0
  subtype3 55  1
  subtype4 62  1
  subtype5 38  1
  subtype6 31  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   40    0
  subtype3   55    1
  subtype4   62    1
  subtype5   38    1
  subtype6   31    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       28       40       55       62       38       31
  1        0        0        1        1        1        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 24  1
  subtype2 45  0
  subtype3 60  2
  subtype4 66  0
  subtype5 40  1
  subtype6 34  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2   45    0
  subtype3   60    2
  subtype4   66    0
  subtype5   40    1
  subtype6   34    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       24       45       60       66       40       34
  1        1        0        2        0        1        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 14 26
  subtype2 18 46
  subtype3 29 63
  subtype4 16 69
  subtype5 19 31
  subtype6 23 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   26
  subtype2   18   46
  subtype3   29   63
  subtype4   16   69
  subtype5   19   31
  subtype6   23   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       14       18       29       16       19       23
  MALE         26       46       63       69       31       18
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 39  0
  subtype2 61  1
  subtype3 83  2
  subtype4 75  4
  subtype5 46  2
  subtype6 36  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   61    1
  subtype3   83    2
  subtype4   75    4
  subtype5   46    2
  subtype6   36    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        39       61       83       75       46       36
  YES        0        1        2        4        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       40
  subtype2                       0                       63
  subtype3                       3                       88
  subtype4                       0                       85
  subtype5                       0                       47
  subtype6                       0                       39
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                1
  subtype3                                1
  subtype4                                0
  subtype5                                3
  subtype6                                2
D5V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        3        0        0
  HEPATOCELLULAR CARCINOMA               40       63       88       85       47
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        1        1        0        3
                                  clus
vv                                 subtype6
  FIBROLAMELLAR CARCINOMA                 0
  HEPATOCELLULAR CARCINOMA               39
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 32  2  0  3
  subtype2 53  3  0  6
  subtype3 78  5  1  7
  subtype4 79  3  0  2
  subtype5 45  1  0  4
  subtype6 38  3  0  0
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       32       53       78       79       45       38
  R1        2        3        5        3        1        3
  R2        0        0        1        0        0        0
  RX        3        6        7        2        4        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    16                         5
  subtype2                                0    20                         4
  subtype3                                0    35                         5
  subtype4                                1    42                         2
  subtype5                                0    27                         1
  subtype6                                1    21                         0
          vv
clus       WHITE
  subtype1    19
  subtype2    36
  subtype3    47
  subtype4    40
  subtype5    22
  subtype6    18
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                  16       20       35       42       27
  BLACK OR AFRICAN AMERICAN               5        4        5        2        1
  WHITE                                  19       36       47       40       22
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                  21
  BLACK OR AFRICAN AMERICAN               0
  WHITE                                  18
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
          cls
clus        0  1
  subtype1  2 36
  subtype2  4 55
  subtype3  3 82
  subtype4  1 82
  subtype5  5 44
  subtype6  3 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   36
  subtype2    4   55
  subtype3    3   82
  subtype4    1   82
  subtype5    5   44
  subtype6    3   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        4        3        1        5        3
  NOT HISPANIC OR LATINO       36       55       82       82       44       36
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 24 18
  subtype2 63 34
  subtype3 29 26
  subtype4 84 40
  subtype5 38 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      42       97       55      124       48 
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       34       26       40       10 
$subtype1
TCGA-DD-AADV TCGA-EP-A3JL TCGA-G3-A7M9 TCGA-XR-A8TG TCGA-2Y-A9GY TCGA-2Y-A9H0 
       18.87         9.96         1.84        29.52        24.89       120.82 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-BD-A3EP 
       22.92         1.18        48.99        27.91         1.12        13.45 
TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A5UC TCGA-CC-A7IK 
        0.66         3.39         4.24         3.32        11.41         8.61 
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-ED-A7PZ TCGA-ED-A8O5 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 
       18.21         0.20        13.35         0.03        13.68        20.78 
TCGA-GJ-A9DB TCGA-MI-A75I TCGA-RC-A7SK TCGA-UB-A7MD TCGA-WJ-A86L TCGA-XR-A8TD 
        2.20        20.71        15.52         1.71        11.34        33.86 

$subtype2
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A112 TCGA-BC-A5W4 TCGA-DD-AAE8 TCGA-DD-AAEG 
       83.24         8.61         5.03        17.98        21.83        23.64 
TCGA-FV-A3I1 TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-ZP-A9D1 
        8.12        30.74        22.13        12.72         0.76         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9HB 
       40.80        23.80        53.39        27.88        47.74         8.55 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A217 
       10.13        46.78        27.52        27.52        23.38        45.93 
TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE 
       22.36        18.48        44.81        10.36         9.99         8.94 
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       12.56         4.60        79.73         2.60        21.76        51.29 
TCGA-DD-A1EB TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG 
       66.31         7.66        70.06       102.74        13.78        26.37 
TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACI TCGA-DD-AACK 
       12.26        78.84        23.93        23.05        53.19         0.30 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD8 
       14.20        59.31        50.33        47.67         5.62        40.08 
TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        0.39        66.67        18.25        20.98        18.61        19.99 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAVV TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
       26.63        50.33        80.71        20.61         0.62        11.93 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
       23.97        19.10         0.33        53.79        28.27        58.49 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M5 
       21.53         5.92        22.95        24.46        17.10        14.70 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG 
       14.14        15.78        15.65        11.87         1.02        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       27.25        29.79         7.53        58.88        21.01         3.09 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MB TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       19.33        19.04        27.88        19.76        25.71        23.21 
TCGA-ZS-A9CF 
       79.30 

$subtype3
TCGA-2Y-A9H7 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-FV-A4ZP TCGA-UB-A7MF TCGA-2Y-A9GU 
       38.40        21.17        18.90        81.73         7.04        63.75 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H8 TCGA-3K-AAZ8 TCGA-5C-AAPD TCGA-BC-A216 
       40.41        49.84        20.81        13.02         0.66        44.42 
TCGA-CC-5261 TCGA-CC-5264 TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A9FS TCGA-CC-A9FW 
        3.19         3.35         9.86        11.31         6.94         8.15 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 
      113.00         0.46        12.95         5.62        19.76        17.59 
TCGA-DD-A3A6 TCGA-DD-A4NR TCGA-DD-A73B TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACP 
      107.11         0.30         9.30        12.00         6.41        13.64 
TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO 
       51.52        44.22        40.83        13.97        29.52        14.89 
TCGA-DD-AADS TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVX TCGA-ED-A5KG TCGA-ED-A66Y 
       15.58        25.08        25.78        56.48        28.08         9.73 
TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-G3-A5SI TCGA-G3-AAV6 TCGA-K7-A6G5 
       12.82         1.84        19.59        25.25         2.14        16.83 
TCGA-MI-A75C TCGA-MI-A75G TCGA-RC-A6M6 TCGA-UB-A7ME TCGA-YA-A8S7 TCGA-ZP-A9D0 
        9.57        22.95         0.30        15.98        13.55        35.87 
TCGA-ZP-A9D2 
       25.15 

$subtype4
TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI TCGA-ES-A2HS 
       11.74        69.57        36.66        90.28        26.83        22.62 
TCGA-K7-A5RF TCGA-KR-A7K7 TCGA-UB-AA0V TCGA-XR-A8TC TCGA-2Y-A9GW TCGA-2Y-A9GX 
       20.75        31.27        10.32        44.02        41.79        80.28 
TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM 
       56.91        18.25        10.78        10.59        14.76         1.51 
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 
       37.32         2.99        25.32        14.60         4.24         8.22 
TCGA-CC-5260 TCGA-CC-A123 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IE 
        2.86         7.20         9.86         9.96        11.93         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A119 
       21.34         9.83        13.12         9.17        37.78         7.33 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39W 
       19.79        75.65        49.15         6.02        33.04        27.19 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       55.69        25.81        20.12        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS 
       21.70        30.15        56.25        29.56        73.81        80.75 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
      114.35        13.48        11.41        55.40        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AAD1 
       58.16        42.81        61.68        51.35        46.82        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP 
       21.63        42.58        40.54        35.67        34.49        15.06 
TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK 
       14.33        19.30        18.25        18.15         4.64        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       89.69        82.62        59.93        72.39        76.18        62.47 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       66.25        29.92        26.93        13.91        13.35         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A23B 
       14.04        13.15        13.41         0.20        14.40        60.89 
TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A7M7 
       27.88         0.39        51.06        14.86        25.64        11.87 
TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-LG-A9QD TCGA-MI-A75E 
       28.90         2.99        37.71        11.80        12.03        16.67 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RG-A7D4 
       10.85        17.69         0.49        21.04        15.39        36.10 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZS-A9CD 
       30.41        22.78        35.77        45.57 

$subtype5
TCGA-DD-A3A8 TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-MI-A75H TCGA-5R-AA1C TCGA-BC-A3KF 
        0.36        22.06         2.14        24.56        17.10         0.26 
TCGA-BC-A69I TCGA-CC-A7IH TCGA-CC-A7IL TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE 
       12.72        12.00         9.14        53.33        79.40        11.47 
TCGA-DD-A39V TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       21.14        30.97       108.76        22.78         1.45         0.53 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 
       12.53        71.80        69.11         5.59         4.50        22.09 
TCGA-DD-AADE TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAVP TCGA-DD-AAVY TCGA-DD-AAW1 
       39.52        23.74        15.72        90.48        64.77        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK 
       60.99        53.69        18.74        19.99        19.53        19.23 
TCGA-G3-A5SL TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       20.42        11.80        12.23        13.55         0.89        11.64 
TCGA-LG-A9QC TCGA-NI-A8LF TCGA-RC-A6M4 TCGA-UB-A7MC TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       13.97        26.27         0.72        16.44        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.30     0.30     0.20     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  120.82   102.74   113.00   114.35   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.865   21.760   15.980   21.485   17.920 
[1] "0.0 - 120.8 (16.9)" "0.3 - 102.7 (21.8)" "0.3 - 113.0 (16.0)"
[4] "0.2 - 114.3 (21.5)" "0.3 - 108.8 (17.9)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      21        7         0         11          2          1        0
  subtype2      45       23         1         11          4          1        0
  subtype3      26       14         0         12          1          1        0
  subtype4      57       30         2         21          1          5        2
  subtype5      23       12         0          9          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         0         0
  subtype4         1         1
  subtype5         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          21       45       26       57       23
  STAGE II          7       23       14       30       12
  STAGE III         0        1        0        2        0
  STAGE IIIA       11       11       12       21        9
  STAGE IIIB        2        4        1        1        1
  STAGE IIIC        1        1        1        5        1
  STAGE IV          0        0        0        2        0
  STAGE IVA         0        0        0        1        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       T1 T2 T3 T4
  subtype1 21  8 13  2
  subtype2 49 26 17  5
  subtype3 28 15 14  0
  subtype4 60 33 26  5
  subtype5 24 12 10  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       21       49       28       60       24
  T2        8       26       15       33       12
  T3       13       17       14       26       10
  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 31  0
  subtype2 59  0
  subtype3 39  1
  subtype4 88  3
  subtype5 37  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    0
  subtype2   59    0
  subtype3   39    1
  subtype4   88    3
  subtype5   37    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       31       59       39       88       37
  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"
D6V6, binary
          cls
clus        0  1
  subtype1 28  1
  subtype2 65  0
  subtype3 43  0
  subtype4 94  3
  subtype5 39  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    1
  subtype2   65    0
  subtype3   43    0
  subtype4   94    3
  subtype5   39    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       28       65       43       94       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 14 30
  subtype2 29 68
  subtype3 19 38
  subtype4 50 76
  subtype5  7 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   30
  subtype2   29   68
  subtype3   19   38
  subtype4   50   76
  subtype5    7   41
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       14       29       19       50        7
  MALE         30       68       38       76       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"
D6V8, binary
          cls
clus         0   1
  subtype1  41   1
  subtype2  93   0
  subtype3  50   1
  subtype4 113   4
  subtype5  43   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    1
  subtype2   93    0
  subtype3   50    1
  subtype4  113    4
  subtype5   43    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        41       93       50      113       43
  YES        1        0        1        4        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       44
  subtype2                       0                       95
  subtype3                       0                       56
  subtype4                       3                      119
  subtype5                       0                       48
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                2
  subtype3                                1
  subtype4                                4
  subtype5                                0
D6V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        3        0
  HEPATOCELLULAR CARCINOMA               44       95       56      119       48
  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  35   3   0   3
  subtype2  83   5   0   6
  subtype3  50   2   0   5
  subtype4 111   6   1   8
  subtype5  46   1   0   0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       35       83       50      111       46
  R1        3        5        2        6        1
  R2        0        0        0        1        0
  RX        3        6        5        8        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    18                         5
  subtype2                                0    34                         5
  subtype3                                0    32                         2
  subtype4                                1    56                         4
  subtype5                                1    21                         1
          vv
clus       WHITE
  subtype1    21
  subtype2    52
  subtype3    22
  subtype4    62
  subtype5    25
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        1
  ASIAN                                  18       34       32       56       21
  BLACK OR AFRICAN AMERICAN               5        5        2        4        1
  WHITE                                  21       52       22       62       25
[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"
D6V12, binary
          cls
clus         0   1
  subtype1   3  40
  subtype2   4  86
  subtype3   3  52
  subtype4   8 112
  subtype5   0  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   40
  subtype2    4   86
  subtype3    3   52
  subtype4    8  112
  subtype5    0   45
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        4        3        8        0
  NOT HISPANIC OR LATINO       40       86       52      112       45
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 61 46
  subtype2 52 28
  subtype3 73 31
  subtype4 34 15
subtype1 subtype2 subtype3 subtype4 
     107       80      104       49 
subtype1 subtype2 subtype3 subtype4 
      46       28       31       15 
$subtype1
TCGA-2Y-A9H7 TCGA-DD-AAEA TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-KR-A7K7 
       38.40        18.90         8.12        81.73        30.74        31.27 
TCGA-LG-A6GG TCGA-UB-A7MF TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-5C-AAPD 
       12.72         7.04        63.75        24.89       120.82         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        45.93        22.36        18.48 
TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A5UD 
        0.66         8.22         4.24         3.35         3.32         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A8HS TCGA-CC-A8HT 
        8.94         7.13         9.83        12.56         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EF 
       11.31         8.15        79.73       113.00        19.79        12.95 
TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 
       45.11        33.04        13.64         5.62         7.66        17.59 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO 
       13.78        33.14        21.70        30.15        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A73A TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACD 
       12.26        23.93        35.67       114.35         0.53        12.53 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
       12.00         6.41         0.30        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       59.31         5.62        44.22        22.09        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ 
       13.97         3.78        35.05        29.52        14.89        14.33 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVQ 
       66.67        19.30        18.25        25.08        50.33        89.69 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 
       29.92        28.08         9.73        12.82        13.35         1.84 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A496 TCGA-G3-A25S 
       20.61        19.59        11.93        23.97         0.33        13.68 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       25.25        22.95        20.78         2.14        11.87         1.02 
TCGA-KR-A7K2 TCGA-MI-A75C TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7SF 
       27.25         9.57        21.01         3.09         0.30        19.04 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WX-AA44 TCGA-WX-AA47 TCGA-YA-A8S7 
       15.98        11.34        20.22        18.28        13.55 

$subtype2
TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-AAE7 TCGA-DD-AAEG 
       11.74        69.57         5.03        36.66        21.17        23.64 
TCGA-EP-A3JL TCGA-G3-A3CG TCGA-K7-A5RF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 
        9.96        22.13        20.75        10.32        29.52         0.69 
TCGA-2Y-A9GS TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 
       23.80        41.79        80.28        56.91        49.84        18.25 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5R-AA1D TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        8.55        10.78        14.76        37.32        10.13        27.52 
TCGA-BC-A10X TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA 
       25.32        13.45         2.86         3.19         3.39         9.96 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 
       11.93        37.78         7.33         6.02        55.69        25.81 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACI TCGA-DD-AACM 
      107.11        30.61        80.75        11.41        53.19        58.16 
TCGA-DD-AACN TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADI TCGA-DD-AADK 
       42.81        18.54        21.63        42.58        35.67        34.49 
TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAW0 TCGA-ED-A7PX 
       15.06        18.25        82.62        80.71        66.25         0.20 
TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25V 
       13.41         0.20        14.40        19.10        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-GJ-A3OU 
       58.49        14.86        25.64        17.10        11.87        28.90 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V 
        2.20         2.99        29.79        16.67        10.85        17.69 
TCGA-RC-A6M5 TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CZ 
        0.49        27.88        10.75        12.99        35.77        23.21 
TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       25.15        45.57 

$subtype3
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AADV TCGA-KR-A7K0 
       83.24         8.61        17.98        26.83        18.87         2.14 
TCGA-MI-A75H TCGA-T1-A6J8 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H1 
       24.56         0.76        40.80        53.39        27.88        40.41 
TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-5R-AA1C TCGA-BC-A10S TCGA-BC-A10U 
       47.74        22.92         1.18        17.10        46.78        27.52 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-CC-A7IF TCGA-CC-A7IH 
       23.38         1.12         0.26        44.81        21.34        12.00 
TCGA-CC-A7IK TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        8.61         6.94        83.57        53.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       21.76        51.29        79.40        66.31        75.65        11.47 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A4NF TCGA-DD-A4NG 
       18.35        21.14        19.76       102.74        30.97        26.37 
TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-AACA TCGA-DD-AACE 
      108.76         9.30        23.05        22.78        75.65        71.80 
TCGA-DD-AACJ TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AADE 
       69.11        50.33         5.59        47.67         4.50        39.52 
TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 
       37.64        20.91         0.39        15.58        18.21        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       18.61        19.99        23.74        15.72        26.63        25.78 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       90.48        72.39        56.48        65.39        60.99        53.69 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-G3-A25U TCGA-G3-A25Z 
       13.15        18.74        19.99         0.62        53.79        21.53 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-AAUZ 
        5.92        19.53        19.23        24.46        20.42        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-HP-A5N0 
       15.65        12.23        13.55         0.89        11.64        37.71 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-RC-A6M4 
       13.97        12.03        22.95        20.71        58.88         0.72 
TCGA-RC-A7SB TCGA-RC-A7SK TCGA-UB-A7MD TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D4 
       19.33        15.52         1.71        25.71        35.87        12.99 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

$subtype4
TCGA-DD-A4ND TCGA-DD-AAE8 TCGA-G3-A7M9 TCGA-2Y-A9H8 TCGA-5C-A9VH TCGA-5R-AAAM 
       90.28        21.83         1.84        20.81        10.59         1.51 
TCGA-BC-4072 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A123 TCGA-CC-A3M9 TCGA-CC-A3MB 
       48.99        14.60         4.24         7.20         9.86        10.36 
TCGA-CC-A5UC TCGA-CC-A7II TCGA-CC-A8HV TCGA-DD-A1EH TCGA-DD-A39W TCGA-DD-AA3A 
       11.41        13.12         9.17        49.15        27.19        13.48 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACU 
       76.41        55.40        15.42         3.52        51.35        51.52 
TCGA-DD-AACW TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK 
       46.82        40.54        40.47        18.15         4.64        35.08 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X 
       59.93        76.18        62.47        26.93        13.91        13.35 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZQ 
        0.20        14.04        60.89        27.88         0.03         0.39 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-XR-A8TD 
       17.06        11.80        15.39        36.10         0.99        33.86 
TCGA-XR-A8TE 
       30.41 

subtype1 subtype2 subtype3 subtype4 
    0.30     0.20     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 
  120.82   107.11   108.76    90.28 
subtype1 subtype2 subtype3 subtype4 
   17.59    21.40    21.24    17.06 
[1] "0.3 - 120.8 (17.6)" "0.2 - 107.1 (21.4)" "0.3 - 108.8 (21.2)"
[4] "0.0 - 90.3 (17.1)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      47       26         0         26          5          5        0
  subtype2      38       17         0         10          0          3        1
  subtype3      51       26         1         14          0          0        0
  subtype4      21       14         2          9          2          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          47       38       51       21
  STAGE II         26       17       26       14
  STAGE III         0        0        1        2
  STAGE IIIA       26       10       14        9
  STAGE IIIB        5        0        0        2
  STAGE IIIC        5        3        0        0
  STAGE IV          0        1        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       T1 T2 T3 T4
  subtype1 48 27 30  5
  subtype2 42 20 13  5
  subtype3 55 29 16  2
  subtype4 22 15 14  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       48       42       55       22
  T2       27       20       29       15
  T3       30       13       16       14
  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 81  3
  subtype2 48  1
  subtype3 70  0
  subtype4 39  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81    3
  subtype2   48    1
  subtype3   70    0
  subtype4   39    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       81       48       70       39
  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 88  0
  subtype2 49  2
  subtype3 75  1
  subtype4 43  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   88    0
  subtype2   49    2
  subtype3   75    1
  subtype4   43    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       88       49       75       43
  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 45 65
  subtype2 27 54
  subtype3 24 80
  subtype4 19 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   65
  subtype2   27   54
  subtype3   24   80
  subtype4   19   32
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       45       27       24       19
  MALE         65       54       80       32
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1 101   3
  subtype2  73   2
  subtype3  94   4
  subtype4  47   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101    3
  subtype2   73    2
  subtype3   94    4
  subtype4   47    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       101       73       94       47
  YES        3        2        4        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                      108
  subtype2                       2                       77
  subtype3                       0                      104
  subtype4                       0                       48
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                2
  subtype3                                0
  subtype4                                3
D7V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        2        0        0
  HEPATOCELLULAR CARCINOMA              108       77      104       48
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        2        0        3
[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 96  5  0  6
  subtype2 65  8  1  5
  subtype3 97  3  0  3
  subtype4 45  1  0  5
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       96       65       97       45
  R1        5        8        3        1
  R2        0        1        0        0
  RX        6        5        3        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    56                         3
  subtype2                                0    31                         4
  subtype3                                1    40                         7
  subtype4                                0    28                         2
          vv
clus       WHITE
  subtype1    48
  subtype2    42
  subtype3    52
  subtype4    21
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                  56       31       40       28
  BLACK OR AFRICAN AMERICAN               3        4        7        2
  WHITE                                  48       42       52       21
[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"
D7V12, binary
          cls
clus        0  1
  subtype1  5 98
  subtype2  5 72
  subtype3  3 94
  subtype4  3 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   98
  subtype2    5   72
  subtype3    3   94
  subtype4    3   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        5        3        3
  NOT HISPANIC OR LATINO       98       72       94       48
[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 35 34
  subtype2 54 30
  subtype3 68 32
  subtype4 19 14
  subtype5 44 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      69       84      100       33       54 
subtype1 subtype2 subtype3 subtype4 subtype5 
      34       30       32       14       10 
$subtype1
TCGA-2Y-A9H7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-UB-A7MF 
       38.40        18.90        23.64        81.73         1.84         7.04 
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-5C-AAPD TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 
       63.75        49.84         0.66        27.52         2.99        44.42 
TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A7IE 
        8.22         4.24         3.35         9.86        11.93         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A9FW 
       21.34         9.83        12.56         9.86        11.31         8.15 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A6 TCGA-DD-A3A9 
       19.79        12.95         5.62        17.59       107.11        30.61 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-AACD TCGA-DD-AACH 
       21.70        30.15        29.56        12.26        12.53         6.41 
TCGA-DD-AACI TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 
       53.19        61.68        13.64        51.52         5.62        44.22 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       40.83        13.97        29.52        14.89        15.06        14.33 
TCGA-DD-AAED TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y 
       25.08        89.69        80.71        29.92        28.08         9.73 
TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-G3-A5SJ TCGA-G3-A7M7 
       12.82         1.84        20.61        19.59        22.95        11.87 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-RC-A6M6 TCGA-UB-A7ME TCGA-WX-AA44 TCGA-WX-AA47 
        2.14        11.87         0.30        15.98        20.22        18.28 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D2 
       13.55        35.77        25.15 

$subtype2
TCGA-2Y-A9GV TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-FV-A3I1 
       83.24         8.61        17.98        26.83        21.83         8.12 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-LG-A6GG TCGA-T1-A6J8 TCGA-XR-A8TG TCGA-ZP-A9D1 
       30.74        22.13        12.72         0.76        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H4 
       40.80        23.80        53.39        24.89        27.88        47.74 
TCGA-2Y-A9HB TCGA-BC-A10S TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO 
        8.55        46.78        23.38        45.93        22.36        18.48 
TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A8HT 
       44.81         0.66         9.99         8.94         8.61         4.60 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        6.94        79.73       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 
       51.29        66.31        25.81         7.66       102.74        13.78 
TCGA-DD-A4NG TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACS 
       26.37        23.93        23.05         0.30        14.20        59.31 
TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADR 
       50.33        47.67        42.58        40.08         0.39        66.67 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEI TCGA-ED-A7XO TCGA-EP-A2KC 
       18.25        20.98        19.99        50.33        14.04         0.62 
TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z 
       11.93        23.97        19.10         0.33        53.79        21.53 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 
        5.92        25.25        24.46        17.10        15.78        15.65 
TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MI-A75I TCGA-NI-A4U2 
        1.02        17.06        27.25        29.79        20.71        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-ZP-A9CZ TCGA-ZS-A9CF 
       21.01         3.09        19.33        19.04        23.21        79.30 

$subtype3
TCGA-2Y-A9H6 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-AAE7 
       11.74        69.57         5.03        36.66        90.28        21.17 
TCGA-K7-A5RF TCGA-KR-A7K7 TCGA-UB-AA0V TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 
       20.75        31.27        10.32        41.79        80.28        56.91 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM 
       18.25        20.81        10.78        10.59        14.76         1.51 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A69H TCGA-CC-5258 
       37.32        10.13        27.52        25.32        14.60         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A123 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A7II 
        2.86         3.19         7.20         9.96        10.36        13.12 
TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI 
        9.17        37.78         7.33        75.65        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A4NS 
       33.04        27.19        55.69        33.14        73.81        80.75 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
      114.35        13.48        11.41        55.40        15.42         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 
       58.16        42.81        51.35        46.82        18.54        21.63 
TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       40.54        35.67        34.49        19.30        18.25        18.15 
TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ 
        4.64        35.08        82.62        59.93        76.18        62.47 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A82E 
       66.25        26.93        13.91        13.35         0.20        13.41 
TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.20        14.40        60.89        27.88         0.39        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-GJ-A3OU TCGA-HP-A5MZ 
       28.27        58.49        14.86        25.64        28.90         2.99 
TCGA-HP-A5N0 TCGA-K7-AAU7 TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A6M5 
       37.71        11.80        16.67        10.85        17.69         0.49 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        36.10        27.88        10.75         0.99        12.99 
TCGA-XR-A8TE TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZS-A9CD 
       30.41        25.71        35.87        45.57 

$subtype4
TCGA-DD-AADV TCGA-EP-A3JL TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 
       18.87         9.96       120.82        22.92         1.18        48.99 
TCGA-BC-4073 TCGA-BC-A10Z TCGA-BD-A3EP TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A5UC 
       27.91         1.12        13.45         3.39         3.32        11.41 
TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACB 
       83.57        45.11        18.35        13.64        35.67        76.41 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-ED-A7PZ 
       40.47         3.78        37.64        35.05        20.91         0.20 
TCGA-ED-A8O5 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 TCGA-GJ-A9DB TCGA-RC-A7SK 
       13.35         0.03        13.68        20.78         2.20        15.52 
TCGA-UB-A7MD TCGA-WJ-A86L TCGA-XR-A8TD 
        1.71        11.34        33.86 

$subtype5
TCGA-KR-A7K0 TCGA-MI-A75H TCGA-2Y-A9H1 TCGA-5R-AA1C TCGA-BC-A3KF TCGA-CC-A7IH 
        2.14        24.56        40.41        17.10         0.26        12.00 
TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A4NF 
       53.33        79.40        11.47        21.14        19.76        30.97 
TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE 
      108.76         9.30        22.78         0.53        75.65        71.80 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADE 
       12.00        69.11         5.59         4.50        22.09        39.52 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
       15.58        18.21        18.61        23.74        15.72        26.63 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 
       25.78        90.48        72.39        56.48        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK 
       53.69        13.15        18.74        19.99        19.53        19.23 
TCGA-G3-A5SL TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-LG-A9QC 
       20.42        12.23        13.55         0.89        11.64        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-RC-A6M4 TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.03         9.57        22.95         0.72        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.30     0.30     0.20     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11   113.00   114.35   120.82   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.980   21.795   21.400   15.520   19.380 
[1] "0.3 - 107.1 (16.0)" "0.3 - 113.0 (21.8)" "0.2 - 114.3 (21.4)"
[4] "0.0 - 120.8 (15.5)" "0.3 - 108.8 (19.4)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      27       17         0         20          2          2        0
  subtype2      39       20         1         11          4          1        0
  subtype3      44       25         2         13          0          4        2
  subtype4      19        4         0          8          1          1        0
  subtype5      28       17         0          7          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         0         0
  subtype3         1         0
  subtype4         0         1
  subtype5         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          27       39       44       19       28
  STAGE II         17       20       25        4       17
  STAGE III         0        1        2        0        0
  STAGE IIIA       20       11       13        8        7
  STAGE IIIB        2        4        0        1        0
  STAGE IIIC        2        1        4        1        0
  STAGE IV          0        0        2        0        0
  STAGE IVA         0        0        1        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       T1 T2 T3 T4
  subtype1 28 19 23  3
  subtype2 42 23 15  4
  subtype3 49 28 19  3
  subtype4 19  4  9  2
  subtype5 29 17  7  0
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       28       42       49       19       29
  T2       19       23       28        4       17
  T3       23       15       19        9        7
  T4        3        4        3        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 50  1
  subtype2 51  0
  subtype3 68  3
  subtype4 27  0
  subtype5 42  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    1
  subtype2   51    0
  subtype3   68    3
  subtype4   27    0
  subtype5   42    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       50       51       68       27       42
  1        1        0        3        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 54  1
  subtype2 59  0
  subtype3 73  2
  subtype4 23  1
  subtype5 46  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54    1
  subtype2   59    0
  subtype3   73    2
  subtype4   23    1
  subtype5   46    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       54       59       73       23       46
  1        1        0        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"
D8V7, binary
          cls
clus        0  1
  subtype1 24 49
  subtype2 24 60
  subtype3 44 57
  subtype4 13 21
  subtype5 10 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   49
  subtype2   24   60
  subtype3   44   57
  subtype4   13   21
  subtype5   10   44
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       24       44       13       10
  MALE         49       60       57       21       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"
D8V8, binary
          cls
clus        0  1
  subtype1 63  3
  subtype2 79  1
  subtype3 94  1
  subtype4 32  0
  subtype5 47  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    3
  subtype2   79    1
  subtype3   94    1
  subtype4   32    0
  subtype5   47    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        63       79       94       32       47
  YES        3        1        1        0        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       72
  subtype2                       0                       83
  subtype3                       2                       94
  subtype4                       0                       34
  subtype5                       0                       54
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                1
  subtype3                                5
  subtype4                                0
  subtype5                                0
D8V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        2        0        0
  HEPATOCELLULAR CARCINOMA               72       83       94       34       54
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        1        5        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 66  4  0  3
  subtype2 73  2  0  7
  subtype3 85  7  1  8
  subtype4 27  3  0  1
  subtype5 52  1  0  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       66       73       85       27       52
  R1        4        2        7        3        1
  R2        0        0        1        0        0
  RX        3        7        8        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                                1    45                         0
  subtype2                                0    27                         7
  subtype3                                0    43                         5
  subtype4                                0    13                         3
  subtype5                                1    27                         1
          vv
clus       WHITE
  subtype1    27
  subtype2    44
  subtype3    50
  subtype4    18
  subtype5    24
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        1
  ASIAN                                  45       27       43       13       27
  BLACK OR AFRICAN AMERICAN               0        7        5        3        1
  WHITE                                  27       44       50       18       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"
D8V12, binary
          cls
clus        0  1
  subtype1  5 66
  subtype2  4 73
  subtype3  3 93
  subtype4  2 31
  subtype5  2 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   66
  subtype2    4   73
  subtype3    3   93
  subtype4    2   31
  subtype5    2   49
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        4        3        2        2
  NOT HISPANIC OR LATINO       66       73       93       31       49
[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"
