[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/19775332/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/20139336/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=368, in cluster file=440, common to both=368
[1] "Reduce the number of clustering variables from 10 to 8."
[1]   8 368
[1] "CN_CNMF"
[1] 3
  1   2   3 
106 122 134 
  1   2   3 
106 122 134 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 83 167 118 
  1   2   3 
 83 167 118 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
59 97 70 68 68 
 1  2  3  4  5 
59 97 70 68 68 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 53  56 114  84  55 
  1   2   3   4   5 
 53  56 114  84  55 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
 62 128  50 123 
  1   2   3   4 
 62 128  50 123 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 41  97  56 122  47 
  1   2   3   4   5 
 41  97  56 122  47 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 93  86 118  41 
  1   2   3   4 
 93  86 118  41 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
66 87 99 34 52 
 1  2  3  4  5 
66 87 99 34 52 
[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 368 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	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=235,	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=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'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 368 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=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 182  92  78  13 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  183    92    78    13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 182  92  78  13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  183    92    78    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 71 35
  subtype2 67 53
  subtype3 91 41
subtype1 subtype2 subtype3 
     106      120      132 
subtype1 subtype2 subtype3 
      35       53       41 
$subtype1
TCGA-2Y-A9GW TCGA-2Y-A9H1 TCGA-2Y-A9H5 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       41.79        40.41        18.25         1.18         8.55        13.02 
TCGA-5C-A9VH TCGA-5R-AA1C TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 
       10.59        17.10        48.99        46.78         2.99        44.42 
TCGA-CC-A3MC TCGA-CC-A7IH TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 
       11.93        12.00         6.94        79.73        53.33         7.33 
TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39V 
       90.71        11.47        12.95        45.11         6.02        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NK 
        5.62        19.76        17.59         0.36        30.97        39.78 
TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACI 
        0.30        22.78       114.35        76.41        12.53        53.19 
TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       69.11        58.16        14.20        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADI 
       18.54        21.63        44.22        40.54        39.52        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADU 
       34.49         0.39        29.52        15.06        14.33        18.21 
TCGA-DD-AAE1 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
       18.15        23.74        15.72        25.08        23.64        25.78 
TCGA-DD-AAEI TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ 
       50.33        89.69        59.93        76.18        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A8O6 
       66.25        49.48        53.69        13.35         9.73         1.84 
TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       18.74         0.62         9.96        22.85        14.40        23.97 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
        8.12        81.73         0.39        22.13        19.53        20.42 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV2 TCGA-G3-AAV5 TCGA-HP-A5MZ TCGA-K7-A6G5 
       11.87        15.78        12.23         8.75         2.99        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        21.60        31.27        13.97        12.03         9.57 
TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V TCGA-RC-A7SF TCGA-WQ-AB4B TCGA-YA-A8S7 
       24.56        20.71        17.69        19.04        12.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       35.77        12.99        45.57        11.21 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H8 
       23.80        24.89        27.88       120.82        56.91        20.81 
TCGA-2Y-A9H9 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
       22.92        10.13        27.52        27.52        23.38         1.12 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        45.93         0.26        22.36        17.98        14.60 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3MA 
        0.66         4.24         3.19         4.24         3.35         9.96 
TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
       10.36         8.94         7.13        21.34         9.83        13.12 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A118 
        8.61         9.14        11.31         9.17         8.15       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A3A7 
        2.60        21.76        49.15        33.04        13.64        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AA3A 
       30.61        30.51        29.56        73.81         9.30        13.48 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
        0.53        75.65        63.48        12.00        15.42         6.41 
TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       42.81        13.64        59.31        51.35        51.52        50.33 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       42.58        22.09        40.08        40.83        13.97        40.47 
TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADV TCGA-DD-AADW 
        3.78        20.91        14.89        66.67        18.87        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEE 
       18.25        18.25        18.61         4.64        21.83        26.63 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A7PY 
       35.08        79.07        72.39        80.71        29.92        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A23B 
        0.20        13.15        13.35        20.61        19.59        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25X 
       19.10        27.88         6.38         0.03        13.68        58.49 
TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 
       14.86        25.25        20.78        11.80         2.14        11.87 
TCGA-LG-A6GG TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       12.72        26.27        21.01        15.39        15.52        36.10 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
        0.76        17.59        16.44        15.98         7.04        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-XR-A8TF TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       11.34         0.99        20.22        22.78        25.15        40.80 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GV TCGA-2Y-A9GX TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       53.39        63.75        83.24        80.28        49.84        47.74 
TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-5R-AA1D 
       11.74        38.40         8.61        10.78         0.66        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A69I 
        1.51        27.91        37.32        25.32        69.57        12.72 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 
       18.48        44.81        13.45        36.66         2.86         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IJ TCGA-CC-A8HT 
        3.32         9.86        11.41         9.99        12.56         4.60 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       37.78        83.57         0.46        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EK TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A3A0 
       19.79        75.65        18.35        27.19        55.69        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA 
        7.66        70.06        20.12       102.74       107.11        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        90.28        30.15        26.83        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E 
       12.26        80.75        78.84        23.93        23.05         1.45 
TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACO 
       35.67        11.41        55.40         0.30         3.52        61.68 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AAE2 
       46.82         5.59        37.64        35.05        15.58        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAW1 
       19.99        21.17        18.90        82.62        56.48        65.39 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E 
       26.93        28.08        13.91         0.20        14.04        13.41 
TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A3RK TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T 
        0.20        19.99        11.93        12.03         0.33        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        30.74        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M8 
       19.23        22.95        17.10        22.06        14.70        14.14 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        1.84        15.65        13.55         0.89        22.92         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 
        2.20        37.71        20.75        17.06         2.14        29.79 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 
       16.67        22.95         7.53        10.85        58.88         3.09 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WX-AA46 
       21.04        19.33        19.76         1.71        10.32        24.85 
TCGA-WX-AA47 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CF 
       18.28        25.71        23.21        35.87         0.69        79.30 

subtype1 subtype2 subtype3 
    0.30     0.03     0.20 
subtype1 subtype2 subtype3 
  114.35   120.82   108.76 
subtype1 subtype2 subtype3 
  18.890   18.430   21.105 
[1] "0.3 - 114.3 (18.9)" "0.0 - 120.8 (18.4)" "0.2 - 108.8 (21.1)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      58       25         0         14          1          0        1
  subtype2      49       34         1         22          3          2        2
  subtype3      64       26         2         24          4          5        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          58       49       64
  STAGE II         25       34       26
  STAGE III         0        1        2
  STAGE IIIA       14       22       24
  STAGE IIIB        1        3        4
  STAGE IIIC        0        2        5
  STAGE IV          1        2        0
  STAGE IVA         1        0        0
  STAGE IVB         0        1        1
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    61 26 17  1
  subtype2    52 37 27  6
  subtype3    69 29 30  5
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       61       52       69
  T2          26       37       29
  T3          17       27       30
  T4           1        6        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 73  1
  subtype2 87  1
  subtype3 90  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    1
  subtype2   87    1
  subtype3   90    1
   clus
vv  subtype1 subtype2 subtype3
  0       73       87       90
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 77  1
  subtype2 92  2
  subtype3 92  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77    1
  subtype2   92    2
  subtype3   92    1
   clus
vv  subtype1 subtype2 subtype3
  0       77       92       92
  1        1        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 23 83
  subtype2 44 78
  subtype3 48 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   83
  subtype2   44   78
  subtype3   48   86
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       44       48
  MALE         83       78       86
[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  95   3
  subtype2 114   2
  subtype3 127   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    3
  subtype2  114    2
  subtype3  127    2
     clus
vv    subtype1 subtype2 subtype3
  NO        95      114      127
  YES        3        2        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                      104
  subtype2                       0                      119
  subtype3                       2                      130
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                3
  subtype3                                2
D1V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        0        2
  HEPATOCELLULAR CARCINOMA              104      119      130
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        3        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  95   6   1   3
  subtype2 105   6   0  10
  subtype3 118   3   0   8
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       95      105      118
  R1        6        6        3
  R2        1        0        0
  RX        3       10        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    49                         5
  subtype2                                0    64                         4
  subtype3                                0    44                         8
          vv
clus       WHITE
  subtype1    46
  subtype2    53
  subtype3    78
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  49       64       44
  BLACK OR AFRICAN AMERICAN               5        4        8
  WHITE                                  46       53       78
[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   5  96
  subtype2   6 113
  subtype3   2 123
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   96
  subtype2    6  113
  subtype3    2  123
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        6        2
  NOT HISPANIC OR LATINO       96      113      123
[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  54  27
  subtype2 105  61
  subtype3  73  44
subtype1 subtype2 subtype3 
      81      166      117 
subtype1 subtype2 subtype3 
      27       61       44 
$subtype1
TCGA-2Y-A9GV TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-5R-AA1D 
       83.24        41.79        80.28        24.89        56.91        14.76 
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3EP TCGA-CC-5260 
       48.99        27.91        25.32        69.57        13.45         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A5UC TCGA-CC-A7II TCGA-CC-A7IJ 
        3.39         3.32         9.86        11.41        13.12        12.56 
TCGA-CC-A8HT TCGA-DD-A114 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EL 
        4.60        37.78        90.71        19.79        75.65        13.64 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NL 
      107.11        33.14        32.52        90.28        30.15        56.25 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73C TCGA-DD-AACC 
      108.76        12.26         0.30        80.75        23.05        55.40 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        3.52        58.16         5.62        21.63        42.58        44.22 
TCGA-DD-AADK TCGA-DD-AAE8 TCGA-DD-AAEK TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       34.49        21.83        35.08        26.93        28.08        13.91 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        14.04        13.41         0.20        11.93        14.40 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M6 
       51.06        28.27        30.74         5.92        22.95        20.78 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 
       14.14         1.84        13.55        22.92         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       20.75        17.06        16.83        11.80        29.79        13.97 
TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-RG-A7D4 TCGA-T1-A6J8 
       16.67        20.71         7.53        10.85        36.10         0.76 
TCGA-UB-AA0V TCGA-WX-AA46 TCGA-YA-A8S7 
       10.32        24.85        13.55 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       23.80        53.39        27.88       120.82        40.41        47.74 
TCGA-2Y-A9H7 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-4R-AA8I 
       38.40        22.92         1.18         8.55        13.02         8.61 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AAAM TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        0.66        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-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5263 
       17.98        12.72        18.48        44.81         0.66         4.24 
TCGA-CC-5264 TCGA-CC-A3MB TCGA-CC-A5UE TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
        3.35        10.36         8.94        12.00         8.61         9.14 
TCGA-CC-A8HU TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       11.31         8.15        83.57         2.60        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       79.40        11.47        45.11        33.04        18.35        21.14 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ 
      102.74         0.36        30.97        26.37        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       39.78        78.84        23.93        22.78         1.45        35.67 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
        0.53        75.65        76.41        63.48        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACV 
       69.11         0.30        13.64        14.20        51.52        50.33 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD 
        5.59        47.67         4.50        22.09        40.08        40.47 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
        3.78        37.64        20.91         0.39        29.52        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV TCGA-DD-AAE1 
       14.33        66.67        15.58        18.21        18.87        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 
       20.98        18.61        19.99         4.64        21.17        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVU 
       18.90        15.72        26.63        25.78        50.33        72.39 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
       65.39        49.48        53.69         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR 
       20.61         0.62         9.96        22.85        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z 
        8.12         6.38         0.03        13.68        53.79        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       22.13        19.53        19.23        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       22.06        14.70        15.78        15.65        11.80        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-KR-A7K0 TCGA-KR-A7K2 
        0.89         8.75         1.02         2.20         2.14        21.60 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 TCGA-PD-A5DF 
       31.27        12.72        22.95        24.56        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD 
        3.09        19.33        19.04        15.52        16.44         1.71 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY 
       10.75        11.34        12.99        22.78        35.77        25.71 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        12.99        40.80        79.30 

$subtype3
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H8 TCGA-5C-A9VG 
       63.75        49.84        18.25        11.74        20.81        10.78 
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H 
       10.59        37.32        10.13         2.99         5.03        14.60 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-A123 TCGA-CC-A3MA 
       36.66         4.24         8.22         3.19         7.20         9.96 
TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HS 
       11.93         9.99         7.13        21.34         9.83         9.86 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        9.17         6.94        79.73        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X 
        0.46        66.31        12.95        49.15         6.02        55.69 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NN 
       17.59        20.12        13.78        30.61        21.70        29.56 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACD 
       73.81         9.30       114.35        13.48        11.41        12.53 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACS TCGA-DD-AACT 
       15.42        53.19        42.81        61.68        59.31        51.35 
TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADE 
       46.82        18.54        40.54        40.83        13.97        39.52 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       35.67        35.05        14.89        19.30        18.25        18.25 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.08        23.64        79.07        89.69        82.62        59.93 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       29.92        13.35         9.73        12.82        13.15        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 
        1.84        19.59        60.89        27.88        12.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI 
       81.73         0.39        58.49        14.86        25.64        25.25 
TCGA-G3-A7M7 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-NI-A8LF 
       11.87         2.14        11.87        12.03         9.57        26.27 
TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       17.69        21.04        15.39        17.59        19.76        15.98 
TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-WX-AA47 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        7.04         0.99        20.22        18.28        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.15        45.57        11.21 

subtype1 subtype2 subtype3 
    0.20     0.03     0.33 
subtype1 subtype2 subtype3 
  108.76   120.82   114.35 
subtype1 subtype2 subtype3 
  20.780   19.645   18.540 
[1] "0.2 - 108.8 (20.8)" "0.0 - 120.8 (19.6)" "0.3 - 114.3 (18.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      39       16         0         17          3          4        0
  subtype2      80       40         2         25          4          3        1
  subtype3      53       29         1         21          1          2        2
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          39       80       53
  STAGE II         16       40       29
  STAGE III         0        2        1
  STAGE IIIA       17       25       21
  STAGE IIIB        3        4        1
  STAGE IIIC        4        3        2
  STAGE IV          0        1        2
  STAGE IVA         0        1        0
  STAGE IVB         0        1        1
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    41 18 20  3
  subtype2    86 43 30  7
  subtype3    56 31 28  3
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       41       86       56
  T2          18       43       31
  T3          20       30       28
  T4           3        7        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1  56   1
  subtype2 112   2
  subtype3  85   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    1
  subtype2  112    2
  subtype3   85    1
   clus
vv  subtype1 subtype2 subtype3
  0       56      112       85
  1        1        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1  58   0
  subtype2 120   1
  subtype3  89   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    0
  subtype2  120    1
  subtype3   89    3
   clus
vv  subtype1 subtype2 subtype3
  0       58      120       89
  1        0        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus         0   1
  subtype1  29  54
  subtype2  42 125
  subtype3  47  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   54
  subtype2   42  125
  subtype3   47   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       42       47
  MALE         54      125       71
[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  77   1
  subtype2 158   2
  subtype3 107   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77    1
  subtype2  158    2
  subtype3  107    4
     clus
vv    subtype1 subtype2 subtype3
  NO        77      158      107
  YES        1        2        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                       2                       79
  subtype2                       0                      165
  subtype3                       0                      115
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                2
  subtype3                                3
D2V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 2        0        0
  HEPATOCELLULAR CARCINOMA               79      165      115
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        2        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  68   3   0   8
  subtype2 150   6   0   8
  subtype3 105   6   1   6
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       68      150      105
  R1        3        6        6
  R2        0        0        1
  RX        8        8        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    26                         8
  subtype2                                1    68                         8
  subtype3                                0    66                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    86
  subtype3    48
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  26       68       66
  BLACK OR AFRICAN AMERICAN               8        8        1
  WHITE                                  46       86       48
[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   2  77
  subtype2   5 151
  subtype3   7 109
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   77
  subtype2    5  151
  subtype3    7  109
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        7
  NOT HISPANIC OR LATINO       77      151      109
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 28 30
  subtype2 65 32
  subtype3 42 26
  subtype4 46 21
  subtype5 47 21
subtype1 subtype2 subtype3 subtype4 subtype5 
      58       97       68       67       68 
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       32       26       21       21 
$subtype1
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10U 
       23.80        24.89       120.82         0.66        27.91        27.52 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
        2.99         5.03        44.42        45.93        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
       18.48        13.45         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-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A4NA 
       45.11        13.64         5.62         7.66        13.78        33.14 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       12.26         0.30        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN TCGA-DD-AADQ TCGA-ED-A459 
        3.52         5.62        44.22        29.52        14.33        29.92 
TCGA-ED-A7PZ TCGA-EP-A2KA TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        0.20        20.61         8.12        81.73        13.68        22.95 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-K7-AAU7 
       20.78         1.84        11.87         1.02        17.06        11.80 
TCGA-KR-A7K7 TCGA-MI-A75I TCGA-RG-A7D4 TCGA-WJ-A86L 
       31.27        20.71        36.10        11.34 

$subtype2
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9H9 TCGA-2Y-A9HB 
       53.39        83.24        27.88        47.74        22.92         8.55 
TCGA-3K-AAZ8 TCGA-4R-AA8I TCGA-5R-AAAM TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y 
       13.02         8.61         1.51        46.78        27.52        23.38 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-A3MB 
        1.12         0.26        17.98        44.81         0.66        10.36 
TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
       83.57         2.60         0.46        21.76        51.29        66.31 
TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NJ 
       18.35        70.06       102.74        21.70        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       39.78        56.25        73.81        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACO TCGA-DD-AACQ 
       23.05        35.67        63.48        12.00        61.68        14.20 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF 
       59.31        50.33        47.67        42.58        40.08         3.78 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AAE2 
       20.91         0.39        66.67        15.58        18.87        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEH TCGA-DD-AAEI 
       18.61        19.99        21.17        18.90        25.78        50.33 
TCGA-ED-A7XO TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A496 
       14.04        22.85        23.97        19.10         6.38         0.33 
TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI 
       53.79        21.53        22.13        25.64         5.92        25.25 
TCGA-G3-A5SK TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A9DB 
       24.46        14.70        14.14        15.78        15.65         2.20 
TCGA-HP-A5N0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75G TCGA-MR-A520 
       37.71        29.79        12.72        12.03        22.95         7.53 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK 
       58.88        21.01         3.09        19.33        19.04        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MB TCGA-WX-AA46 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZS-A9CE 
        0.76        19.76        24.85        25.71        23.21        40.80 
TCGA-ZS-A9CF 
       79.30 

$subtype3
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H7 TCGA-2Y-A9H8 TCGA-5C-A9VG 
       63.75        49.84        18.25        38.40        20.81        10.78 
TCGA-5C-A9VH TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A123 TCGA-CC-A5UC TCGA-CC-A7IE 
       10.59         4.24         3.19         7.20        11.41         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       21.34         9.83         9.86        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
        8.15        79.73       113.00        12.95        49.15        33.04 
TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73G 
       19.76        17.59        30.61        30.15        29.56       114.35 
TCGA-DD-AACC TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AADA TCGA-DD-AADB 
       55.40        42.81        13.64        46.82        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY 
       13.97        35.67        35.05        14.89        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAVQ TCGA-DD-AAVS 
       18.25        18.15         4.64        25.08        89.69        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       72.39        76.18        62.47        28.08        13.35         9.73 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B TCGA-G3-A25Y 
       12.82        13.35         1.84        19.59        60.89        14.86 
TCGA-G3-AAV6 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-A7MF 
        2.14        21.04        15.39        17.59        15.98         7.04 
TCGA-WQ-A9G7 TCGA-ZP-A9D0 
        0.99        35.87 

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H6 TCGA-5R-AA1D TCGA-BC-4072 
       41.79        80.28        56.91        11.74        14.76        48.99 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3ER TCGA-CC-5260 
       37.32        10.13        25.32        69.57        36.66         2.86 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1EI 
        3.39         9.96        11.93         7.33        19.79         6.02 
TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NS TCGA-DD-AA3A 
       55.69       107.11        32.52        90.28        80.75        13.48 
TCGA-DD-AAC9 TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADK 
       11.41        51.35        51.52        18.54        21.63        34.49 
TCGA-DD-AADP TCGA-DD-AAEG TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAW0 TCGA-ED-A4XI 
       15.06        23.64        82.62        80.71        66.25        26.93 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3JL TCGA-ES-A2HT 
       13.91         0.20        13.41         0.20         9.96        14.40 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X 
       27.88        12.03         0.03        51.06        28.27        58.49 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 
       17.10        11.87        22.92         2.99        20.75        16.83 
TCGA-KR-A7K2 TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-UB-AA0U TCGA-UB-AA0V 
       21.60        16.67        10.85        17.69        10.75        10.32 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       12.99        20.22        13.55        35.77         0.69        25.15 
TCGA-ZS-A9CD 
       45.57 

$subtype5
TCGA-2Y-A9H1 TCGA-2Y-A9HA TCGA-5R-AA1C TCGA-BC-A69I TCGA-CC-A5UD TCGA-CC-A7IH 
       40.41         1.18        17.10        12.72         9.99        12.00 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE 
        8.61         9.14        53.33        79.40        75.65        11.47 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG 
       21.14        27.19        20.12         0.36        30.97        26.37 
TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB 
      108.76        22.78         1.45         0.53        75.65        76.41 
TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD 
       12.53        69.11         5.59         4.50        22.09        40.47 
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 
       79.07        56.48        64.77        65.39        49.48        53.69 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A4ZQ 
       13.15        18.74        19.99         0.62        11.93         0.39 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV2 
       19.53        19.23        20.42        22.06        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-MI-A75C 
       13.55         0.89         8.75         2.14        13.97         9.57 
TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WX-AA47 TCGA-XR-A8TF 
       24.56        26.27        16.44         1.71        18.28        22.78 
TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.26     0.99     0.03     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  120.82   102.74   114.35   107.11   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.660   22.130   18.250   19.790   18.985 
[1] "0.2 - 120.8 (13.7)" "0.3 - 102.7 (22.1)" "1.0 - 114.3 (18.2)"
[4] "0.0 - 107.1 (19.8)" "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      15       21         0         12          3          3        1
  subtype2      56       16         1         12          2          0        0
  subtype3      31       17         1         14          1          2        1
  subtype4      35       13         0         10          0          3        1
  subtype5      31       17         1         15          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
  subtype4         0         0
  subtype5         0         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          15       56       31       35       31
  STAGE II         21       16       17       13       17
  STAGE III         0        1        1        0        1
  STAGE IIIA       12       12       14       10       15
  STAGE IIIB        3        2        1        0        1
  STAGE IIIC        3        0        2        3        1
  STAGE IV          1        0        1        1        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        1        1        0        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    15 25 15  4
  subtype2    60 17 15  4
  subtype3    34 17 18  1
  subtype4    38 15 12  3
  subtype5    32 17 17  1
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       15       60       34       38       32
  T2          25       17       17       15       17
  T3          15       15       18       12       17
  T4           4        4        1        3        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 35  1
  subtype2 64  1
  subtype3 58  2
  subtype4 40  0
  subtype5 51  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35    1
  subtype2   64    1
  subtype3   58    2
  subtype4   40    0
  subtype5   51    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       35       64       58       40       51
  1        1        1        2        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 42  0
  subtype2 67  1
  subtype3 59  2
  subtype4 40  1
  subtype5 53  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    0
  subtype2   67    1
  subtype3   59    2
  subtype4   40    1
  subtype5   53    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       42       67       59       40       53
  1        0        1        2        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 17 42
  subtype2 26 71
  subtype3 37 33
  subtype4 28 40
  subtype5  9 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   42
  subtype2   26   71
  subtype3   37   33
  subtype4   28   40
  subtype5    9   59
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17       26       37       28        9
  MALE         42       71       33       40       59
[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 57  1
  subtype2 91  0
  subtype3 65  0
  subtype4 61  2
  subtype5 62  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57    1
  subtype2   91    0
  subtype3   65    0
  subtype4   61    2
  subtype5   62    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        57       91       65       61       62
  YES        1        0        0        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                       57
  subtype2                       0                       97
  subtype3                       0                       69
  subtype4                       2                       62
  subtype5                       0                       68
          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        2        0
  HEPATOCELLULAR CARCINOMA               57       97       69       62       68
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        0        1        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 48  5  0  5
  subtype2 84  3  0  8
  subtype3 65  1  0  4
  subtype4 54  6  1  5
  subtype5 66  0  0  0
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       48       84       65       54       66
  R1        5        3        1        6        0
  R2        0        0        0        1        0
  RX        5        8        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                                0    24                         6
  subtype2                                0    35                         5
  subtype3                                0    45                         1
  subtype4                                0    23                         2
  subtype5                                1    30                         3
          vv
clus       WHITE
  subtype1    27
  subtype2    52
  subtype3    23
  subtype4    41
  subtype5    34
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  24       35       45       23       30
  BLACK OR AFRICAN AMERICAN               6        5        1        2        3
  WHITE                                  27       52       23       41       34
[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  3 51
  subtype2  5 86
  subtype3  2 67
  subtype4  3 62
  subtype5  1 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    5   86
  subtype3    2   67
  subtype4    3   62
  subtype5    1   65
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        5        2        3        1
  NOT HISPANIC OR LATINO       51       86       67       62       65
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 23 29
  subtype2 39 17
  subtype3 72 42
  subtype4 54 27
  subtype5 40 15
subtype1 subtype2 subtype3 subtype4 subtype5 
      52       56      114       81       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       17       42       27       15 
$subtype1
TCGA-2Y-A9GY TCGA-2Y-A9H2 TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W 
       24.89        56.91        48.99        27.91        37.32         2.99 
TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT 
        5.03        14.60         8.22         2.86         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ 
        9.86         9.96         8.94         9.83        13.12        12.56 
TCGA-CC-A8HT TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A3A7 
        4.60         9.17        37.78         5.62       107.11        13.78 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-AA3A TCGA-DD-AACH 
       33.14        30.15        12.26         0.30        13.48         6.41 
TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADN TCGA-ED-A7PX TCGA-ED-A82E 
        3.52         5.62        44.22        29.52         0.20        13.41 
TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
        0.20        20.61        27.88        81.73        51.06        58.49 
TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-K7-AAU7 TCGA-UB-A7MA 
       22.95        20.78         1.84        11.87        11.80        17.59 
TCGA-WQ-A9G7 TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9D2 
        0.99        20.22        13.55        25.15 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5R-AAAM 
       23.80        41.79        80.28         8.55        13.02         1.51 
TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5262 
       46.78        25.32        69.57        13.45        36.66         3.39 
TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A4ND TCGA-DD-A4NJ TCGA-DD-A4NL 
       10.36        45.11         6.02        90.28        30.51        56.25 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACT TCGA-DD-AACU 
       73.81        80.75        11.41        55.40        51.35        51.52 
TCGA-DD-AACY TCGA-DD-AAD3 TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AAE7 TCGA-ED-A627 
       47.67        42.58         0.39        15.06        21.17        13.91 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25V 
        9.96        14.40        23.97         8.12         0.03        28.27 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-GJ-A3OU TCGA-HP-A5MZ 
       21.53        22.13        17.10        11.87        22.92         2.99 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-LG-A9QD TCGA-MI-A75E TCGA-O8-A75V TCGA-RC-A7SK 
       20.75        16.83        12.03        16.67        17.69        15.52 
TCGA-T1-A6J8 TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
        0.76        10.75        10.32        12.99        35.77        25.71 
TCGA-ZP-A9D1 TCGA-ZS-A9CD 
        0.69        45.57 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 
       53.39        83.24        27.88       120.82        40.41        47.74 
TCGA-2Y-A9H9 TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       22.92         8.61         0.66        27.52        27.52        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        44.42        45.93         0.26        22.36        17.98 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5264 TCGA-CC-A7IF TCGA-CC-A7IL 
       18.48        44.81         0.66         3.35        21.34         9.14 
TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        6.94        79.73        83.57         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       51.29        66.31        18.35        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NV 
       17.59       102.74        21.70        26.83        39.78        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-AACD TCGA-DD-AACE 
       23.93         9.30        23.05        35.67        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS 
       12.00        69.11         0.30        61.68        14.20        59.31 
TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADQ 
       50.33         5.59        40.08         3.78        20.91        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADV TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 
       66.67        15.58        18.87        18.25        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI 
       19.99         4.64        18.90        25.08        25.78        50.33 
TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7XO TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3R2 
       72.39        29.92        14.04        22.85        19.10         6.38 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI 
        0.33        13.68        53.79        25.64         5.92        25.25 
TCGA-G3-A5SK TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 
       24.46        14.70        14.14        15.78        15.65         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
        2.20        37.71        17.06        21.60        29.79        12.72 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-NI-A4U2 TCGA-PD-A5DF 
        9.57        22.95        20.71         7.53        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-UB-A7MB TCGA-UB-A7MF 
        3.09        21.04        19.33        19.04        19.76         7.04 
TCGA-WJ-A86L TCGA-WX-AA46 TCGA-XR-A8TF TCGA-ZP-A9CZ TCGA-ZS-A9CE TCGA-ZS-A9CF 
       11.34        24.85        22.78        23.21        40.80        79.30 

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

$subtype5
TCGA-5R-AA1C TCGA-BC-A69I TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IK TCGA-DD-A116 
       17.10        12.72         9.99        12.00         8.61        53.33 
TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       79.40        75.65        11.47        13.64        21.14        27.19 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E 
        0.36        30.97        26.37       108.76        22.78         1.45 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AAD0 TCGA-DD-AADG TCGA-DD-AADU TCGA-DD-AAE9 
        0.53        75.65         4.50        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        79.07        56.48        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       65.39        49.48        53.69        13.15        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
        0.62        11.93        19.53        19.23        20.42        22.06 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 
       11.80        12.23        13.55         0.89         8.75         2.14 
TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-UB-A7MD TCGA-ZP-A9D4 
       13.97        24.56        26.27        16.44         1.71        12.99 
TCGA-ZS-A9CG 
       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 
  13.265   19.220   21.025   19.590   18.740 
[1] "0.2 - 107.1 (13.3)" "0.0 - 90.3 (19.2)"  "0.3 - 120.8 (21.0)"
[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       15         0         15          4          3        0
  subtype2      32       10         0          3          1          2        1
  subtype3      61       25         1         17          1          1        0
  subtype4      40       19         1         17          0          2        2
  subtype5      24       15         1         11          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
  subtype4         0         1
  subtype5         0         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          11       32       61       40       24
  STAGE II         15       10       25       19       15
  STAGE III         0        0        1        1        1
  STAGE IIIA       15        3       17       17       11
  STAGE IIIB        4        1        1        0        1
  STAGE IIIC        3        2        1        2        1
  STAGE IV          0        1        0        2        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    11 18 20  4
  subtype2    38 11  5  2
  subtype3    62 28 18  5
  subtype4    43 19 21  1
  subtype5    25 15 13  1
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       11       38       62       43       25
  T2          18       11       28       19       15
  T3          20        5       18       21       13
  T4           4        2        5        1        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 33  1
  subtype2 30  1
  subtype3 76  0
  subtype4 66  2
  subtype5 43  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    1
  subtype2   30    1
  subtype3   76    0
  subtype4   66    2
  subtype5   43    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       33       30       76       66       43
  1        1        1        0        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 38  0
  subtype2 32  0
  subtype3 81  1
  subtype4 66  3
  subtype5 44  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    0
  subtype2   32    0
  subtype3   81    1
  subtype4   66    3
  subtype5   44    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       38       32       81       66       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 30
  subtype2 13 43
  subtype3 34 80
  subtype4 40 44
  subtype5  7 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   30
  subtype2   13   43
  subtype3   34   80
  subtype4   40   44
  subtype5    7   48
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       23       13       34       40        7
  MALE         30       43       80       44       48
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus         0   1
  subtype1  51   1
  subtype2  52   0
  subtype3 106   1
  subtype4  76   2
  subtype5  51   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    1
  subtype2   52    0
  subtype3  106    1
  subtype4   76    2
  subtype5   51    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        51       52      106       76       51
  YES        1        0        1        2        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       48
  subtype2                       0                       56
  subtype3                       0                      112
  subtype4                       2                       82
  subtype5                       0                       55
          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        2        0
  HEPATOCELLULAR CARCINOMA               48       56      112       82       55
  HEPATOCHOLANGIOCARCINOMA (MIXED)        5        0        2        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  42   6   0   4
  subtype2  46   4   0   4
  subtype3 100   4   0   8
  subtype4  76   1   1   6
  subtype5  53   0   0   0
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       42       46      100       76       53
  R1        6        4        4        1        0
  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    25                         1
  subtype2                                0    14                         4
  subtype3                                0    45                         6
  subtype4                                0    50                         2
  subtype5                                1    23                         4
          vv
clus       WHITE
  subtype1    26
  subtype2    35
  subtype3    57
  subtype4    32
  subtype5    27
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  25       14       45       50       23
  BLACK OR AFRICAN AMERICAN               1        4        6        2        4
  WHITE                                  26       35       57       32       27
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus        0  1
  subtype1  3 49
  subtype2  4 51
  subtype3  5 98
  subtype4  2 80
  subtype5  0 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   49
  subtype2    4   51
  subtype3    5   98
  subtype4    2   80
  subtype5    0   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        4        5        2        0
  NOT HISPANIC OR LATINO       49       51       98       80       53
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 38 23
  subtype2 79 48
  subtype3 29 20
  subtype4 85 37
subtype1 subtype2 subtype3 subtype4 
      61      127       49      122 
subtype1 subtype2 subtype3 subtype4 
      23       48       20       37 
$subtype1
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       23.80        53.39        24.89       120.82        22.92         1.18 
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       27.91        23.38         1.12        44.81        13.45         0.66 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11D TCGA-DD-A1EG TCGA-DD-A1EK 
        3.39         3.32        83.57        51.29        45.11        18.35 
TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACQ 
        5.62       102.74        13.78        35.67        75.65        14.20 
TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL TCGA-DD-AADV TCGA-DD-AAE2 
       40.08         3.78        37.64        20.91        18.87        20.98 
TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A3JL 
       19.99        21.83        26.63        14.04        13.35         9.96 
TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25S 
       11.93        23.97        19.10         8.12         0.03        13.68 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A7M6 TCGA-G3-A7M8 
       30.74        21.53        22.13         5.92        20.78        14.14 
TCGA-G3-A7M9 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75I TCGA-RC-A7SF TCGA-RC-A7SK 
        1.84         2.20        29.79        20.71        19.04        15.52 
TCGA-T1-A6J8 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZS-A9CE 
        0.76        17.59         1.71        11.34        25.71        40.80 
TCGA-ZS-A9CF 
       79.30 

$subtype2
TCGA-2Y-A9GU TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H7 TCGA-3K-AAZ8 
       63.75        27.88        40.41        47.74        38.40        13.02 
TCGA-4R-AA8I TCGA-5R-AA1C TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 
        8.61        17.10        27.52         2.99        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-CC-5263 TCGA-CC-5264 
        0.26        22.36        17.98        18.48         4.24         3.35 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
        9.99         8.94         8.61         9.14         9.86         4.60 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        8.15        79.73        53.33         2.60         0.46        21.76 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V 
       79.40        66.31        19.79        11.47        13.64        21.14 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.76         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
        0.36        30.97        26.37       108.76        12.26         0.30 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       23.93         9.30        23.05        22.78         1.45         0.53 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACP 
       12.53        63.48        12.00        69.11         0.30        13.64 
TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD5 
       59.31        50.33         5.59         5.62         4.50        44.22 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADE TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADO 
       22.09        40.83        39.52        35.05        29.52        14.89 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 
       14.33        66.67        15.58        18.21        18.61        23.74 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAVP 
       18.90        15.72        25.08        25.78        50.33        79.07 
TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66Y 
       72.39        64.77        65.39        49.48        29.92         9.73 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A496 
        1.84        18.74        19.99        19.59        22.85         0.33 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       81.73        53.79        19.53        19.23        25.25        22.95 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.42        22.06        14.70        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-LG-A9QC 
        0.89         8.75         2.14         1.02        12.72        13.97 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-QA-A7B7 
        9.57        22.95        24.56        58.88        26.27         3.09 
TCGA-RC-A7SB TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF TCGA-XR-A8TF TCGA-ZP-A9D4 
       19.33        19.76        16.44         7.04        22.78        12.99 
TCGA-ZS-A9CG 
       11.21 

$subtype3
TCGA-2Y-A9GV TCGA-2Y-A9H8 TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 
       83.24        20.81        48.99        27.52        25.32        69.57 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A123 TCGA-CC-A3M9 
       14.60        12.72         4.24         8.22         7.20         9.86 
TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A8HV 
       10.36        11.41         7.13        12.00        13.12         9.17 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-AA3A TCGA-DD-AACB 
       75.65        49.15        33.04        27.19        13.48        76.41 
TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADD 
       55.40        15.42         3.52        51.35        46.82        40.47 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVZ 
       18.15         4.64        35.08        59.93        56.48        62.47 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B TCGA-FV-A4ZQ TCGA-G3-A5SK 
       53.69        13.35         0.20        60.89         0.39        24.46 
TCGA-K7-A5RG TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-WX-AA46 
       17.06        11.80        31.27        21.04        36.10        24.85 
TCGA-WX-AA47 
       18.28 

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       41.79        80.28        56.91        49.84        18.25        11.74 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D TCGA-5R-AAAM 
        8.55        10.78        10.59         0.66        14.76         1.51 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A112 TCGA-BD-A3ER TCGA-CC-5260 
       37.32        10.13        46.78         5.03        36.66         2.86 
TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IJ 
        3.19         9.96        11.93        21.34         9.83        12.56 
TCGA-CC-A8HU TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EF 
       11.31         6.94        37.78       113.00         7.33        12.95 
TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
        6.02        55.69        25.81        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN 
       90.28        21.70        30.15        26.83        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACH 
       73.81        80.75        78.84       114.35        11.41         6.41 
TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACU TCGA-DD-AACY 
       53.19        58.16        42.81        61.68        51.52        47.67 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADI 
       18.54        21.63        42.58        40.54        13.97        35.67 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       34.49         0.39        15.06        19.30        18.25        18.25 
TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW 
       21.17        23.64        89.69        82.62        80.71        76.18 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       66.25        26.93        28.08        13.91         0.20        12.82 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT 
       13.15        13.41         0.20        20.61         0.62        14.40 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       27.88        51.06        28.27        58.49        14.86        25.64 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       17.10        11.87        15.78        15.65        11.87        22.92 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.99        37.71        20.75        16.83         2.14        21.60 
TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A520 TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF 
       12.03        16.67         7.53        10.85        17.69        21.01 
TCGA-RC-A7SH TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        15.98        10.75        10.32         0.99        12.99 
TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       20.22        13.55        35.77        23.21        35.87         0.69 
TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       25.15        45.57 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.26     0.20     0.20 
subtype1 subtype2 subtype3 subtype4 
  120.82   108.76    83.24   114.35 
subtype1 subtype2 subtype3 subtype4 
  19.990   19.330   21.040   20.415 
[1] "0.0 - 120.8 (20.0)" "0.3 - 108.8 (19.3)" "0.2 - 83.2 (21.0)" 
[4] "0.2 - 114.3 (20.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      32        8         1          9          3          1        1
  subtype2      60       32         0         26          3          3        0
  subtype3      19       13         2         11          0          2        1
  subtype4      58       31         0         16          2          3        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         0
  subtype3         0         0
  subtype4         0         1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          32       60       19       58
  STAGE II          8       32       13       31
  STAGE III         1        0        2        0
  STAGE IIIA        9       26       11       16
  STAGE IIIB        3        3        0        2
  STAGE IIIC        1        3        2        3
  STAGE IV          1        0        1        1
  STAGE IVA         1        0        0        0
  STAGE IVB         1        0        0        1
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    35 11 13  3
  subtype2    61 33 29  4
  subtype3    22 13 13  2
  subtype4    62 34 22  4
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       35       61       22       62
  T2          11       33       13       34
  T3          13       29       13       22
  T4           3        4        2        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 40  1
  subtype2 91  1
  subtype3 37  1
  subtype4 82  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    1
  subtype2   91    1
  subtype3   37    1
  subtype4   82    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       40       91       37       82
  1        1        1        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus         0   1
  subtype1  36   1
  subtype2 101   0
  subtype3  39   1
  subtype4  88   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    1
  subtype2  101    0
  subtype3   39    1
  subtype4   88    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36      101       39       88
  1        1        0        1        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 19 43
  subtype2 33 95
  subtype3 20 30
  subtype4 43 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   43
  subtype2   33   95
  subtype3   20   30
  subtype4   43   80
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       33       20       43
  MALE         43       95       30       80
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1  58   0
  subtype2 117   4
  subtype3  47   1
  subtype4 115   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    0
  subtype2  117    4
  subtype3   47    1
  subtype4  115    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        58      117       47      115
  YES        0        4        1        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       61
  subtype2                       0                      128
  subtype3                       0                       48
  subtype4                       2                      117
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                2
  subtype4                                4
D5V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        0        0        2
  HEPATOCELLULAR CARCINOMA               61      128       48      117
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        0        2        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  49   4   0   5
  subtype2 116   4   0   7
  subtype3  44   2   0   4
  subtype4 109   5   1   6
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       49      116       44      109
  R1        4        4        2        5
  R2        0        0        0        1
  RX        5        7        4        6
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    20                         4
  subtype2                                1    58                         6
  subtype3                                0    27                         3
  subtype4                                0    55                         4
          vv
clus       WHITE
  subtype1    36
  subtype2    60
  subtype3    20
  subtype4    59
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                  20       58       27       55
  BLACK OR AFRICAN AMERICAN               4        6        3        4
  WHITE                                  36       60       20       59
[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"
D5V12, binary
          cls
clus         0   1
  subtype1   2  56
  subtype2   3 119
  subtype3   1  47
  subtype4   8 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   56
  subtype2    3  119
  subtype3    1   47
  subtype4    8  110
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        1        8
  NOT HISPANIC OR LATINO       56      119       47      110
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 22 18
  subtype2 63 34
  subtype3 28 26
  subtype4 81 40
  subtype5 37 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      40       97       54      121       47 
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       34       26       40       10 
$subtype1
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 TCGA-BC-4073 
       24.89       120.82        22.92         1.18        48.99        27.91 
TCGA-BC-A10Z TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        1.12        13.45         0.66         3.39         4.24         3.32 
TCGA-CC-A5UC TCGA-CC-A7IK TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL 
       11.41         8.61        83.57        45.11        18.35        13.64 
TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       35.67        75.65        76.41        40.47         3.78        37.64 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADU TCGA-DD-AADV TCGA-ED-A7PZ TCGA-ED-A8O5 
       35.05        20.91        18.21        18.87         0.20        13.35 
TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB 
        9.96         0.03        13.68        20.78         1.84         2.20 
TCGA-MI-A75I TCGA-RC-A7SK TCGA-UB-A7MD TCGA-WJ-A86L 
       20.71        15.52         1.71        11.34 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H4 TCGA-2Y-A9HB 
       23.80        53.39        83.24        27.88        47.74         8.55 
TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
        8.61        10.13        46.78        27.52        27.52        23.38 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 
        5.03        45.93        22.36        17.98        18.48        44.81 
TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-DD-A113 
       10.36         9.99         8.94        12.56         4.60        79.73 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A3A1 TCGA-DD-A3A2 
        2.60        21.76        51.29        66.31         7.66        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73A 
      102.74        13.78        26.37        12.26        78.84        23.93 
TCGA-DD-A73C TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACV 
       23.05        53.19         0.30        14.20        59.31        50.33 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADY 
       47.67         5.62        40.08         0.39        66.67        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEG 
       20.98        18.61        19.99        21.83        26.63        23.64 
TCGA-DD-AAEI TCGA-DD-AAVV TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ 
       50.33        80.71        20.61         0.62        11.93        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.10         8.12         0.33        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A5SK 
       58.49        21.53        22.13         5.92        22.95        24.46 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 
       17.10        14.70        14.14        15.78        15.65        11.87 
TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MR-A520 
        1.02        17.06        21.60        29.79        12.72         7.53 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-T1-A6J8 
       58.88        21.01         3.09        19.33        19.04         0.76 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       17.59        19.76        25.71        23.21         0.69        40.80 
TCGA-ZS-A9CF 
       79.30 

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

$subtype4
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-5C-A9VG 
       41.79        80.28        56.91        18.25        11.74        10.78 
TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X 
       10.59        14.76         1.51        37.32         2.99        25.32 
TCGA-BC-A110 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       69.57        14.60        36.66         4.24         8.22         2.86 
TCGA-CC-A123 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IE TCGA-CC-A7IF 
        7.20         9.86         9.96        11.93         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A8HV TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EC 
        9.83        13.12         9.17        37.78         7.33        19.79 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39W TCGA-DD-A39X 
       75.65        49.15         6.02        33.04        27.19        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A4 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       25.81        20.12        30.61        33.14        32.52        90.28 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       21.70        30.15        26.83        56.25        29.56        73.81 
TCGA-DD-A4NS TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG 
       80.75       114.35        13.48        11.41        55.40        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACT TCGA-DD-AACW 
        3.52        58.16        42.81        61.68        51.35        46.82 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK 
       18.54        21.63        42.58        40.54        35.67        34.49 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       15.06        14.33        19.30        18.25        18.15         4.64 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        89.69        82.62        59.93        72.39        76.18 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X 
       62.47        66.25        29.92        26.93        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HS 
        0.20        14.04        13.15        13.41         0.20        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y 
       14.40        60.89        27.88         0.39        51.06        14.86 
TCGA-G3-A3CH TCGA-G3-A7M7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       25.64        11.87        22.92         2.99        37.71        20.75 
TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V 
       11.80        31.27        12.03        16.67        10.85        17.69 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 
       21.04        15.39        36.10        10.75        10.32         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV 
       12.99        20.22        24.85        18.28        22.78        35.77 
TCGA-ZS-A9CD 
       45.57 

$subtype5
TCGA-5R-AA1C TCGA-BC-A3KF TCGA-BC-A69I TCGA-CC-A7IH TCGA-CC-A7IL TCGA-DD-A116 
       17.10         0.26        12.72        12.00         9.14        53.33 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP 
       79.40        11.47        21.14         0.36        30.97       108.76 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ 
       22.78         1.45         0.53        12.53        63.48        69.11 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADE TCGA-DD-AAE9 TCGA-DD-AAEB 
        5.59         4.50        22.09        39.52        23.74        15.72 
TCGA-DD-AAVP TCGA-DD-AAVY TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-EP-A12J 
       79.07        64.77        65.39        49.48        53.69        18.74 
TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 
       19.99        19.53        19.23        20.42        22.06        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC 
       12.23        13.55         0.89         8.75         2.14        13.97 
TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       24.56        26.27        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 
  14.600   21.530   16.405   21.340   18.740 
[1] "0.0 - 120.8 (14.6)" "0.3 - 102.7 (21.5)" "0.3 - 113.0 (16.4)"
[4] "0.2 - 114.3 (21.3)" "0.3 - 108.8 (18.7)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      20        6         0         11          1          1        0
  subtype2      44       23         1         11          4          1        1
  subtype3      26       14         0         12          1          1        0
  subtype4      56       29         2         20          1          5        2
  subtype5      23       12         0          8          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         0
  subtype4         0         1
  subtype5         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          20       44       26       56       23
  STAGE II          6       23       14       29       12
  STAGE III         0        1        0        2        0
  STAGE IIIA       11       11       12       20        8
  STAGE IIIB        1        4        1        1        1
  STAGE IIIC        1        1        1        5        1
  STAGE IV          0        1        0        2        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         1        0        0        1        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    20  7 12  2
  subtype2    49 26 17  5
  subtype3    28 14 14  0
  subtype4    59 32 25  5
  subtype5    24 12  9  1
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       20       49       28       59       24
  T2           7       26       14       32       12
  T3          12       17       14       25        9
  T4           2        5        0        5        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 30  0
  subtype2 58  1
  subtype3 39  1
  subtype4 86  2
  subtype5 37  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2   58    1
  subtype3   39    1
  subtype4   86    2
  subtype5   37    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       30       58       39       86       37
  1        0        1        1        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 26  1
  subtype2 65  0
  subtype3 42  0
  subtype4 92  3
  subtype5 39  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   65    0
  subtype3   42    0
  subtype4   92    3
  subtype5   39    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       26       65       42       92       39
  1        1        0        0        3        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 13 28
  subtype2 29 68
  subtype3 19 37
  subtype4 48 74
  subtype5  6 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   28
  subtype2   29   68
  subtype3   19   37
  subtype4   48   74
  subtype5    6   41
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       29       19       48        6
  MALE         28       68       37       74       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  39   0
  subtype2  93   0
  subtype3  51   0
  subtype4 111   4
  subtype5  43   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   93    0
  subtype3   51    0
  subtype4  111    4
  subtype5   43    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        39       93       51      111       43
  YES        0        0        0        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                       41
  subtype2                       0                       95
  subtype3                       0                       55
  subtype4                       2                      116
  subtype5                       0                       47
          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        2        0
  HEPATOCELLULAR CARCINOMA               41       95       55      116       47
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        2        1        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  32   3   0   3
  subtype2  83   5   0   6
  subtype3  50   1   0   5
  subtype4 107   6   1   8
  subtype5  46   0   0   0
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       32       83       50      107       46
  R1        3        5        1        6        0
  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    17                         5
  subtype2                                0    34                         5
  subtype3                                0    32                         2
  subtype4                                0    56                         4
  subtype5                                1    21                         1
          vv
clus       WHITE
  subtype1    19
  subtype2    52
  subtype3    21
  subtype4    59
  subtype5    24
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  17       34       32       56       21
  BLACK OR AFRICAN AMERICAN               5        5        2        4        1
  WHITE                                  19       52       21       59       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"
D6V12, binary
          cls
clus         0   1
  subtype1   1  39
  subtype2   4  86
  subtype3   3  51
  subtype4   6 112
  subtype5   0  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   39
  subtype2    4   86
  subtype3    3   51
  subtype4    6  112
  subtype5    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        4        3        6        0
  NOT HISPANIC OR LATINO       39       86       51      112       44
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 51 41
  subtype2 55 30
  subtype3 83 35
  subtype4 25 14
subtype1 subtype2 subtype3 subtype4 
      92       85      118       39 
subtype1 subtype2 subtype3 subtype4 
      41       30       35       14 
$subtype1
TCGA-2Y-A9GU TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-5C-AAPD 
       63.75        24.89       120.82        49.84        38.40         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-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NA 
       33.04        13.64         5.62        17.59        13.78        33.14 
TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       21.70        26.37        30.15        29.56        73.81        12.26 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACP TCGA-DD-AACZ 
      114.35         0.53        12.53         6.41        13.64         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADN 
       44.22        22.09        40.83        13.97        35.05        29.52 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEI 
       14.89        19.30        18.25        18.90        25.08        50.33 
TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 
       89.69        29.92        28.08         9.73        12.82        13.35 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP TCGA-G3-A25S 
        1.84        20.61        19.59        11.93        81.73        13.68 
TCGA-G3-A25W TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAV6 TCGA-G3-AAV7 
       30.74        25.25        22.95        20.78         2.14        11.87 
TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        1.02        17.06        21.60        31.27        12.72         9.57 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WX-AA44 
       21.01         3.09        17.59        15.98         7.04        20.22 
TCGA-WX-AA47 TCGA-YA-A8S7 
       18.28        13.55 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 
       23.80        41.79        80.28        56.91        18.25        11.74 
TCGA-2Y-A9HB TCGA-5C-A9VG TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10R 
        8.55        10.78        14.76         1.51        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3EP TCGA-BD-A3ER 
       27.52        25.32        69.57         5.03        13.45        36.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-CC-A7IF 
        2.86         3.19         3.39         9.96        11.93        21.34 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A6 
       37.78         7.33        45.11         6.02        55.69       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACN 
       30.61        80.75        11.41        53.19        58.16        42.81 
TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADI TCGA-DD-AADK 
       51.52        18.54        21.63        42.58        35.67        34.49 
TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVR TCGA-DD-AAVV 
       15.06        18.25        21.17        23.64        82.62        80.71 
TCGA-DD-AAW0 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3JL 
       66.25         0.20        14.04        13.41         0.20         9.96 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-G3-A25T TCGA-G3-A25V 
       14.40        23.97        27.88         8.12        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M7 
       58.49        14.86        22.13        25.64        17.10        11.87 
TCGA-G3-AAV3 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-AAU7 
       13.55        22.92         2.20         2.99        20.75        11.80 
TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SH TCGA-UB-AA0U 
       29.79        16.67        10.85        17.69        15.39        10.75 
TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       10.32        12.99        35.77        23.21         0.69        25.15 
TCGA-ZS-A9CD 
       45.57 

$subtype3
TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H9 
       53.39        83.24        27.88        40.41        47.74        22.92 
TCGA-2Y-A9HA TCGA-4R-AA8I TCGA-5R-AA1C TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10Y 
        1.18         8.61        17.10        46.78        27.52        23.38 
TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A2L6 TCGA-CC-A7IH TCGA-CC-A7IK 
        1.12         0.26        17.98        44.81        12.00         8.61 
TCGA-CC-A9FS TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        6.94        83.57        53.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK 
       51.29        79.40        66.31        75.65        11.47        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A4NF 
       21.14        19.76        25.81         7.66       102.74        30.97 
TCGA-DD-A4NI TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       26.83       108.76        23.93         9.30        23.05        22.78 
TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK 
       35.67        75.65        63.48        12.00        69.11         0.30 
TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACV TCGA-DD-AACX TCGA-DD-AACY 
       61.68        14.20        59.31        50.33         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD8 TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADL 
        4.50        40.08        39.52         3.78        37.64        20.91 
TCGA-DD-AADM TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADV 
        0.39        14.33        66.67        15.58        18.21        18.87 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99        21.83        23.74        15.72 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW1 
       26.63        25.78        79.07        72.39        56.48        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       49.48        53.69        13.15        18.74        19.99         0.62 
TCGA-FV-A2QR TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ 
       19.10         0.33        53.79        21.53         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       19.23        24.46        20.42        15.78        15.65        12.23 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD 
        0.89         8.75        37.71         2.14        13.97        12.03 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-RC-A7SB TCGA-RC-A7SF 
       22.95        24.56        20.71        58.88        19.33        19.04 
TCGA-RC-A7SK TCGA-T1-A6J8 TCGA-UB-A7MD TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZP-A9D0 
       15.52         0.76         1.71        11.34        25.71        35.87 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        40.80        79.30        11.21 

$subtype4
TCGA-2Y-A9H8 TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A123 
       20.81        10.59        48.99        14.60         4.24         7.20 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A5UC TCGA-CC-A7II TCGA-CC-A8HV TCGA-DD-A1EH 
        9.86        10.36        11.41        13.12         9.17        49.15 
TCGA-DD-A39W TCGA-DD-A4ND TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG 
       27.19        90.28        13.48        76.41        55.40        15.42 
TCGA-DD-AACL TCGA-DD-AACT TCGA-DD-AACW TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AAE1 
        3.52        51.35        46.82        40.54        40.47        18.15 
TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-ED-A4XI 
        4.64        35.08        59.93        76.18        62.47        26.93 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B TCGA-FV-A495 TCGA-FV-A4ZQ 
       13.91        13.35         0.20        60.89         0.03         0.39 
TCGA-G3-A7M9 TCGA-RG-A7D4 TCGA-WQ-A9G7 
        1.84        36.10         0.99 

subtype1 subtype2 subtype3 subtype4 
    0.53     0.20     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 
  120.82   107.11   108.76    90.28 
subtype1 subtype2 subtype3 subtype4 
   17.92    20.75    21.06    15.42 
[1] "0.5 - 120.8 (17.9)" "0.2 - 107.1 (20.8)" "0.3 - 108.8 (21.1)"
[4] "0.0 - 90.3 (15.4)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      34       22         0         26          5          5        0
  subtype2      37       21         0         12          0          3        2
  subtype3      66       27         1         12          0          0        0
  subtype4      18       11         2          7          1          0        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
  subtype4         0         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          34       37       66       18
  STAGE II         22       21       27       11
  STAGE III         0        0        1        2
  STAGE IIIA       26       12       12        7
  STAGE IIIB        5        0        0        1
  STAGE IIIC        5        3        0        0
  STAGE IV          0        2        0        1
  STAGE IVA         0        1        0        0
  STAGE IVB         0        1        1        0
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    35 23 30  5
  subtype2    42 24 15  5
  subtype3    70 30 14  2
  subtype4    19 11 11  0
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       35       42       70       19
  T2          23       24       30       11
  T3          30       15       14       11
  T4           5        5        2        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 65  3
  subtype2 54  1
  subtype3 83  0
  subtype4 32  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65    3
  subtype2   54    1
  subtype3   83    0
  subtype4   32    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       65       54       83       32
  1        3        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 73  0
  subtype2 52  2
  subtype3 89  1
  subtype4 36  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    0
  subtype2   52    2
  subtype3   89    1
  subtype4   36    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       73       52       89       36
  1        0        2        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 40 53
  subtype2 29 57
  subtype3 27 91
  subtype4 16 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   53
  subtype2   29   57
  subtype3   27   91
  subtype4   16   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       29       27       16
  MALE         53       57       91       25
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1  87   3
  subtype2  80   1
  subtype3 109   3
  subtype4  37   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   87    3
  subtype2   80    1
  subtype3  109    3
  subtype4   37    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        87       80      109       37
  YES        3        1        3        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                       90
  subtype2                       1                       82
  subtype3                       0                      118
  subtype4                       0                       40
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                3
  subtype2                                3
  subtype3                                0
  subtype4                                1
D7V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        1        0        0
  HEPATOCELLULAR CARCINOMA               90       82      118       40
  HEPATOCHOLANGIOCARCINOMA (MIXED)        3        3        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  79   5   0   6
  subtype2  71   7   1   5
  subtype3 111   2   0   4
  subtype4  36   1   0   4
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       79       71      111       36
  R1        5        7        2        1
  R2        0        1        0        0
  RX        6        5        4        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    45                         4
  subtype2                                0    35                         4
  subtype3                                1    50                         7
  subtype4                                0    24                         1
          vv
clus       WHITE
  subtype1    43
  subtype2    43
  subtype3    55
  subtype4    16
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                  45       35       50       24
  BLACK OR AFRICAN AMERICAN               4        4        7        1
  WHITE                                  43       43       55       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
          cls
clus         0   1
  subtype1   6  82
  subtype2   3  80
  subtype3   3 107
  subtype4   1  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   82
  subtype2    3   80
  subtype3    3  107
  subtype4    1   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            6        3        3        1
  NOT HISPANIC OR LATINO       82       80      107       40
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 33 31
  subtype2 55 32
  subtype3 66 32
  subtype4 18 15
  subtype5 42 10
subtype1 subtype2 subtype3 subtype4 subtype5 
      64       87       98       33       52 
subtype1 subtype2 subtype3 subtype4 subtype5 
      31       32       32       15       10 
$subtype1
TCGA-2Y-A9GU TCGA-2Y-A9H3 TCGA-2Y-A9H7 TCGA-5C-AAPD TCGA-BC-A10U TCGA-BC-A10W 
       63.75        49.84        38.40         0.66        27.52         2.99 
TCGA-BC-A216 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-CC-A7IE 
       44.42         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-A4NE 
       19.79        12.95         5.62        17.59       107.11        21.70 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI 
       30.15        29.56        12.26        12.53         6.41        53.19 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADB 
       61.68        13.64        51.52         5.62        44.22        40.83 
TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAEA TCGA-DD-AAED 
       13.97        29.52        14.89        14.33        18.90        25.08 
TCGA-DD-AAEG TCGA-DD-AAVQ TCGA-DD-AAVV TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y 
       23.64        89.69        80.71        29.92        28.08         9.73 
TCGA-ED-A7PY TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A5SJ 
       12.82         1.84        20.61        19.59        81.73        22.95 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WX-AA44 
        2.14        11.87        17.59        15.98         7.04        20.22 
TCGA-WX-AA47 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D0 
       18.28        13.55        35.77        35.87 

$subtype2
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GV TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H4 
       23.80        53.39        83.24        24.89        27.88        47.74 
TCGA-2Y-A9HB TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y 
        8.55         8.61        10.13        46.78        27.52        23.38 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO 
       45.93        22.36        17.98        18.48        44.81         0.66 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A9FS TCGA-DD-A113 
        9.99         8.94         8.61         4.60         6.94        79.73 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB 
      113.00         2.60         0.46        21.76        51.29        66.31 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NI 
       25.81         7.66       102.74        13.78        26.37        26.83 
TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACS 
      108.76        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-AAE8 TCGA-DD-AAEI TCGA-ED-A7XO 
       18.25        20.98        19.99        21.83        50.33        14.04 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 
        0.62        11.93        23.97        19.10         8.12         0.33 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A5SI 
       53.79        30.74        21.53        22.13         5.92        25.25 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 TCGA-K7-A5RG 
       24.46        17.10        15.78        15.65         1.02        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75I TCGA-NI-A4U2 TCGA-PD-A5DF 
       21.60        29.79        12.72        20.71        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-T1-A6J8 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        3.09        19.33        19.04         0.76        25.71        23.21 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        40.80        79.30 

$subtype3
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9H2 TCGA-2Y-A9H5 TCGA-2Y-A9H6 TCGA-2Y-A9H8 
       41.79        80.28        56.91        18.25        11.74        20.81 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q TCGA-BC-A10X 
       10.78        10.59        14.76         1.51        37.32        25.32 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 
       69.57         5.03        14.60        36.66         4.24         8.22 
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-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
       33.04        27.19        55.69        30.61        33.14        90.28 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC 
       73.81        80.75       114.35        13.48        11.41        55.40 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACT TCGA-DD-AACW 
       15.42         3.52        58.16        42.81        51.35        46.82 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP 
       18.54        21.63        40.54        35.67        34.49        15.06 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAEK 
       19.30        18.25        18.15         4.64        21.17        35.08 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI 
       82.62        59.93        76.18        62.47        66.25        26.93 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT 
       13.91        13.35         0.20        13.41         0.20        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X 
       60.89        27.88         0.39        51.06        28.27        58.49 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A7M7 TCGA-GJ-A3OU TCGA-HP-A5MZ TCGA-HP-A5N0 
       14.86        25.64        11.87        22.92         2.99        37.71 
TCGA-K7-A5RF TCGA-K7-AAU7 TCGA-KR-A7K7 TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V 
       20.75        11.80        31.27        16.67        10.85        17.69 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        36.10        10.75        10.32         0.99        12.99 
TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       25.15        45.57 

$subtype4
TCGA-2Y-A9H0 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z 
      120.82        22.92         1.18        48.99        27.91         1.12 
TCGA-BD-A3EP TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A5UC TCGA-DD-A115 TCGA-DD-A1EG 
       13.45         3.39         3.32        11.41        83.57        45.11 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADF 
       18.35        13.64        35.67        76.41        40.47         3.78 
TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADV TCGA-ED-A7PZ TCGA-ED-A8O5 
       37.64        35.05        20.91        18.87         0.20        13.35 
TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB 
        9.96         0.03        13.68        20.78         1.84         2.20 
TCGA-RC-A7SK TCGA-UB-A7MD TCGA-WJ-A86L 
       15.52         1.71        11.34 

$subtype5
TCGA-2Y-A9H1 TCGA-5R-AA1C TCGA-BC-A3KF TCGA-CC-A7IH TCGA-DD-A116 TCGA-DD-A1EA 
       40.41        17.10         0.26        12.00        53.33        79.40 
TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A4NF TCGA-DD-A73B TCGA-DD-A73D 
       11.47        21.14        19.76        30.97         9.30        22.78 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACX 
        0.53        75.65        63.48        12.00        69.11         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADE TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 
        4.50        22.09        39.52        15.58        18.21        18.61 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVU 
       23.74        15.72        26.63        25.78        79.07        72.39 
TCGA-DD-AAVX TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J 
       56.48        65.39        49.48        53.69        13.15        18.74 
TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-AAV2 TCGA-G3-AAV3 
       19.99        19.53        19.23        20.42        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        0.89         8.75         2.14        13.97        12.03         9.57 
TCGA-MI-A75G TCGA-MI-A75H TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       22.95        24.56        12.99        11.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.66     0.30     0.20     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11   113.00   114.35   120.82    79.40 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.935   21.760   20.780   13.680   19.380 
[1] "0.7 - 107.1 (17.9)" "0.3 - 113.0 (21.8)" "0.2 - 114.3 (20.8)"
[4] "0.0 - 120.8 (13.7)" "0.3 - 79.4 (19.4)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      25       15         0         20          1          1        0
  subtype2      38       20         1         11          4          1        1
  subtype3      46       25         2         12          0          5        2
  subtype4      19        4         0          8          1          1        0
  subtype5      27       17         0          6          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
  subtype4         0         1
  subtype5         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          25       38       46       19       27
  STAGE II         15       20       25        4       17
  STAGE III         0        1        2        0        0
  STAGE IIIA       20       11       12        8        6
  STAGE IIIB        1        4        0        1        0
  STAGE IIIC        1        1        5        1        0
  STAGE IV          0        1        2        0        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    27 16 22  1
  subtype2    43 23 16  5
  subtype3    49 28 17  4
  subtype4    19  4  9  2
  subtype5    28 17  6  0
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       27       43       49       19       28
  T2          16       23       28        4       17
  T3          22       16       17        9        6
  T4           1        5        4        2        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 47  1
  subtype2 51  1
  subtype3 69  2
  subtype4 26  0
  subtype5 41  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    1
  subtype2   51    1
  subtype3   69    2
  subtype4   26    0
  subtype5   41    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       47       51       69       26       41
  1        1        1        2        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 51  0
  subtype2 59  0
  subtype3 73  3
  subtype4 22  1
  subtype5 45  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    0
  subtype2   59    0
  subtype3   73    3
  subtype4   22    1
  subtype5   45    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       51       59       73       22       45
  1        0        0        3        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 24 42
  subtype2 26 61
  subtype3 41 58
  subtype4 12 22
  subtype5  9 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   42
  subtype2   26   61
  subtype3   41   58
  subtype4   12   22
  subtype5    9   43
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       26       41       12        9
  MALE         42       61       58       22       43
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 59  3
  subtype2 83  0
  subtype3 92  1
  subtype4 32  0
  subtype5 47  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    3
  subtype2   83    0
  subtype3   92    1
  subtype4   32    0
  subtype5   47    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        59       83       92       32       47
  YES        3        0        1        0        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                       64
  subtype2                       0                       86
  subtype3                       1                       94
  subtype4                       0                       34
  subtype5                       0                       52
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                1
  subtype3                                4
  subtype4                                0
  subtype5                                0
D8V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        1        0        0
  HEPATOCELLULAR CARCINOMA               64       86       94       34       52
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        1        4        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 59  4  0  3
  subtype2 75  3  0  7
  subtype3 85  5  1  8
  subtype4 27  3  0  1
  subtype5 51  0  0  0
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       59       75       85       27       51
  R1        4        3        5        3        0
  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                                0    42                         1
  subtype2                                0    27                         7
  subtype3                                0    45                         4
  subtype4                                0    13                         3
  subtype5                                1    27                         1
          vv
clus       WHITE
  subtype1    23
  subtype2    47
  subtype3    47
  subtype4    18
  subtype5    22
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  42       27       45       13       27
  BLACK OR AFRICAN AMERICAN               1        7        4        3        1
  WHITE                                  23       47       47       18       22
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus        0  1
  subtype1  5 60
  subtype2  3 77
  subtype3  2 93
  subtype4  1 32
  subtype5  2 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   60
  subtype2    3   77
  subtype3    2   93
  subtype4    1   32
  subtype5    2   47
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        3        2        1        2
  NOT HISPANIC OR LATINO       60       77       93       32       47
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
