[1] "ofn"        "-oTBLCA-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/BLCA-TP/15076720/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/15111049/BLCA-TP.mergedcluster.txt"

nPatients in clinical file=393, in cluster file=412, common to both=393
[1]  10 393
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
165 132  55  37 
  1   2   3   4 
165 132  55  37 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
136 107  66  84 
  1   2   3   4 
136 107  66  84 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
37 29 36  5 20 
 1  2  3  4  5 
37 29 36  5 20 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
43 38 27 19 
 1  2  3  4 
43 38 27 19 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
110 172 107 
  1   2   3 
110 172 107 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
108 109 172 
  1   2   3 
108 109 172 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
116  93 182 
  1   2   3 
116  93 182 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
85 95 94 66 51 
 1  2  3  4  5 
85 95 94 66 51 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 96  40 129 115 
  1   2   3   4 
 96  40 129 115 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
71 43 92 63 30 81 
 1  2  3  4  5  6 
71 43 92 63 30 81 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 393 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=138,	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=256,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 393 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"              "NEOPLASM_DISEASESTAGE"      
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
 [9] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  2   3 117 185  54 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     122      185       54 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  2   3 117 185  54 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     122      185       54 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
227  42  76   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
227  42  76   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
227  42  76   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
227  42  76   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=71, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=22, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 98 63
  subtype2 82 49
  subtype3 29 26
  subtype4 21 15
subtype1 subtype2 subtype3 subtype4 
     161      131       55       36 
subtype1 subtype2 subtype3 subtype4 
      63       49       26       15 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        91.63       103.50       105.70        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A5ZZ 
       34.98        49.12        66.54        33.83         7.33        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F 
       14.89        14.96         8.25         9.96        17.56        28.41 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       11.87        13.08         4.90        16.31         1.84        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ 
       19.00        16.70        16.14        17.62        15.62        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21        20.81        10.55       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 
       41.56        76.60        13.58        12.36         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       43.50        10.62        24.66         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
        0.66        14.56        13.97        14.33         0.92        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        16.77         4.01        12.62        27.98 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       17.98        25.74        46.78        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       13.35        62.86        18.81         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       10.65         8.94        30.61        15.95        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A6I1 
        7.23         6.94        64.44        21.40        17.75         8.94 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A6ZA 
        3.12         7.36        11.31        27.09        27.35        22.72 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO 
        1.51        25.02         3.45         2.76         6.38        11.80 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78P 
       21.07        14.24         1.84         3.75        12.43        67.79 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV 
      125.49         1.87        17.88        64.80        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       11.90        18.90        16.27        66.64        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       11.31        71.57        91.73        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 
       75.39         3.88        18.84         9.63         0.66         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4U 
       21.11        27.19        21.86        13.41        82.49         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        57.90        19.40         8.52         5.52 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 
       11.97         8.35        16.27        17.16        27.62         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20V 
       51.16        47.80        40.08         2.66        32.84         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
        8.35        17.16        16.18        20.48        12.82        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98         1.94         0.43        11.34         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19        21.86         2.14        18.41       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 
       10.59         2.20        13.58         7.82         8.22        48.00 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       64.18        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 
      166.03        10.49         8.65        12.03        15.35        38.83 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
        0.49        17.39         0.56         1.22        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SR 
        8.09         8.94        24.30        23.41        29.16        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       22.98        27.35         8.25        27.45        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.36         3.06         4.31        31.07        17.23 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB 
       61.94        20.12        17.62        66.02        19.46         4.50 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R 
       14.07        24.92         0.49         7.73        10.92        11.31 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73        10.65        32.98        21.34        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.48        19.07        19.40        38.60         3.06         9.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78L 
       21.24         9.07        15.42        13.48        31.56        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC 
       22.68        76.01        65.75        17.82         4.54         6.58 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMG 
       48.62         3.22        28.24        26.27         2.10       110.60 
TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN7 
        7.63         8.32         6.77        98.99        44.32        18.81 
TCGA-YF-AA3L TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       11.97        30.28        74.56        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5H 
       19.69        59.38        38.73        35.41        19.17 

$subtype3
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A3JM TCGA-BT-A20R TCGA-CU-A0YN 
       16.77        15.12        10.22         6.74         5.06        12.92 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IV TCGA-E7-A6ME TCGA-FD-A3B3 
        1.81         7.79       123.85         9.67        12.99        32.02 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TF 
       33.04        22.52         5.52         2.70        12.69         2.27 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GU-A762 TCGA-GU-A764 
       15.81        15.91        13.91         2.10         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A40E TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R 
        5.62        19.10         8.58         8.22         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-UY-A78K 
        1.74         1.81        15.32        15.58        16.67        17.62 
TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9SI TCGA-XF-A9SX 
       86.83        35.24        29.56         1.64        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 
       21.04         2.24        10.82        54.90         2.96        56.48 
TCGA-XF-AAN2 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA58 
       61.45        52.73        52.60         2.89        63.02        47.15 
TCGA-ZF-AA5P 
       10.13 

$subtype4
TCGA-4Z-AA81 TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F6 TCGA-DK-A1A6 TCGA-DK-A2I6 
       41.75         4.67        24.26        23.01        66.41        87.32 
TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A5BV 
       17.98        30.67        43.59        60.66        12.85         5.36 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3I6 
       58.92         7.10         3.25         6.48        33.01         2.24 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-K4-A5RI 
       20.98         2.20         7.00        14.27        10.59        11.70 
TCGA-PQ-A6FI TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF 
       12.23         3.58       112.83        45.04        97.45        97.12 
TCGA-XF-A8HG TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
       15.35        13.64        18.64        24.13        28.41         3.48 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.43     1.64     2.20 
subtype1 subtype2 subtype3 subtype4 
  140.81   166.03   123.85   112.83 
subtype1 subtype2 subtype3 subtype4 
   14.96    17.23    15.12    18.31 
[1] "0.1 - 140.8 (15.0)" "0.4 - 166.0 (17.2)" "1.6 - 123.8 (15.1)"
[4] "2.2 - 112.8 (18.3)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       2       59        61       41
  subtype2       2       35        37       55
  subtype3       0       18        15       22
  subtype4       0       12        14       11
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          2        2        0        0
  STAGE II        59       35       18       12
  STAGE III       61       37       15       14
  STAGE IV        41       55       22       11
[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       T0+T1+T2 T3 T4
  subtype1       55 72 26
  subtype2       39 63 19
  subtype3       16 29  5
  subtype4       11 20  3
D1V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       55       39       16       11
  T3             72       63       29       20
  T4             26       19        5        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 114  15  20   2
  subtype2  65  17  34   4
  subtype3  25   5  16   1
  subtype4  20   5   5   1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      114       65       25       20
  N1       15       17        5        5
  N2       20       34       16        5
  N3        2        4        1        1
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 91  5
  subtype2 64  3
  subtype3 18  2
  subtype4 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91    5
  subtype2   64    3
  subtype3   18    2
  subtype4   12    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       91       64       18       12
  1        5        3        2        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"
D1V7, binary
          cls
clus         0   1
  subtype1  40 125
  subtype2  34  98
  subtype3  16  39
  subtype4  11  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40  125
  subtype2   34   98
  subtype3   16   39
  subtype4   11   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       34       16       11
  MALE        125       98       39       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    26                         9   128
  subtype2    11                         8   104
  subtype3     4                         3    47
  subtype4     1                         1    32
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                           26       11        4        1
  BLACK OR AFRICAN AMERICAN        9        8        3        1
  WHITE                          128      104       47       32
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus         0   1
  subtype1   1 157
  subtype2   6 112
  subtype3   0  51
  subtype4   2  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  157
  subtype2    6  112
  subtype3    0   51
  subtype4    2   32
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        6        0        2
  NOT HISPANIC OR LATINO      157      112       51       32
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 74 61
  subtype2 73 34
  subtype3 42 23
  subtype4 43 37
subtype1 subtype2 subtype3 subtype4 
     135      107       65       80 
subtype1 subtype2 subtype3 subtype4 
      61       34       23       37 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 
       22.29       105.70        44.94        16.77        27.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       15.12        10.22         7.33        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PJ 
       19.04        12.16        14.96         5.06         8.25        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS 
        9.96        24.26        28.41         1.94         2.93         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 
       12.92         5.46        13.58        16.14        17.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
      123.85        87.32         7.82         8.22        17.72        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6T 
       20.81        10.55       140.81        41.06       166.03        12.36 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 
        7.53        43.50         1.22        14.07        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SM 
       16.77         8.94        33.04         4.01        12.62        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS 
        5.52        25.74        14.96        20.91        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
       11.01        19.33         5.69        58.92         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK 
       13.35        18.81         6.15        12.69         2.27        10.85 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3C TCGA-GC-A3WC 
        8.94         6.48        61.94        30.61         6.94        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        8.94        20.98        11.31         7.63        20.05         5.62 
TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        8.58         9.01         8.22         3.45         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
        9.07         1.74         6.38        15.32        12.23        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PB 
       14.24        12.43        31.56        37.05        67.79        29.56 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       97.45       125.49        48.62        79.66         3.22        66.41 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 
       66.64        13.74        92.98         2.96        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
        3.88         0.66        13.41        52.73        52.60        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
        2.89        60.16        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       47.15        19.17        10.13 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA80 
       11.97        91.63         8.35        16.27        17.16         0.62 
TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
       47.80        40.08         5.06         8.35        17.16        16.18 
TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A9FF 
       20.48         8.98        23.01        12.62        12.10        11.87 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19        21.86        66.41        18.41       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV 
       10.59         2.20        13.58        50.27        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6U TCGA-DK-AA6W 
       41.56        67.36        15.68        30.67        10.49         8.65 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE 
       12.03        43.59        15.35        38.83         0.49         0.56 
TCGA-E7-A6ME TCGA-E7-A8O8 TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR 
       12.99         0.43         8.09        60.66        24.30        19.79 
TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       22.98        26.73        27.45        31.07         7.13        17.23 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
       15.95        26.93        20.12        17.62        66.02        19.46 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GD-A76B 
        4.50        14.07        13.91         7.73         2.20         7.36 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA 
       10.92        32.98        19.82        20.28         8.48        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A6MB 
        1.51        19.40        38.60         3.06        21.24        15.42 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
       11.80        15.58        13.48        17.62        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HF 
       76.01       112.83        17.82         4.54         1.64        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       15.35         1.87        26.27        10.82       110.60        11.31 
TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YC-A89H TCGA-ZF-A9R0 
        7.63         6.77        98.99        18.81        18.84        18.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA51 
       30.28        74.56        82.49        19.69        38.73 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA89 TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
      103.50        33.83         2.66        17.88        19.50        14.89 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        2.04         0.46        10.95        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       13.12        12.00        11.34        13.08         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IT 
       16.31         1.84        16.70        15.62         1.81        21.30 
TCGA-DK-A3IV TCGA-DK-A6B0 TCGA-DK-AA6P TCGA-DK-AA71 TCGA-E7-A3Y1 TCGA-E7-A519 
        9.67        76.60        15.02        13.64         0.10        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H 
        0.66        13.97        14.33         0.92        13.68        12.95 
TCGA-E7-A8O7 TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A5C0 TCGA-FD-A6TA 
       15.32        23.41        46.78        27.35        18.08        62.86 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-AA3D TCGA-GC-A3OO TCGA-GD-A3OP 
        3.06        10.65        22.88        64.44        15.81         2.10 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JW TCGA-K4-A3WS TCGA-S5-A6DX TCGA-UY-A9PA 
       11.31         4.73        21.34        25.02         1.84        35.24 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN0 
       17.88        64.80        54.90        91.73        44.32        56.48 
TCGA-YC-A8S6 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RM TCGA-ZF-AA4R 
        9.63        24.13        27.19        47.84        34.06 

$subtype4
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-BL-A3JM 
       16.83        34.98        49.12        41.75        66.54         6.74 
TCGA-BT-A20N TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A47T 
       32.84         4.67        17.56        28.70         0.69        12.66 
TCGA-CF-A8HX TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-DK-AA6Q 
       11.34         2.14        19.00        17.98        38.24        13.58 
TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A677 TCGA-FD-A3N5 
       10.62        24.66         2.24        17.39        14.56        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A5BY 
       27.98        29.16        12.85         3.62         5.36         8.25 
TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A2EO 
        7.10        12.36         4.31         9.67         3.25        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS 
       33.01         7.23        21.40         2.24        15.91        24.92 
TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GU-A763 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV 
        0.49         3.12        27.09        10.65         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A54R TCGA-K4-A5RI 
       19.10        10.59        27.35        19.07        27.68        11.70 
TCGA-K4-A6FZ TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A8HB 
        1.81        21.07         3.75        65.75         3.58        45.04 
TCGA-XF-A8HC TCGA-XF-A9SV TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMQ TCGA-XF-AAMW 
        6.58        12.76        16.27         2.10        71.57         8.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       30.94        61.45        86.30        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-AA4U TCGA-ZF-AA4V 
       21.11        21.86        28.41         3.48         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA5N 
       63.02         5.52 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.43     0.10     0.49 
subtype1 subtype2 subtype3 subtype4 
  166.03   130.88   103.50    86.30 
subtype1 subtype2 subtype3 subtype4 
  14.370   17.620   15.020   14.415 
[1] "0.4 - 166.0 (14.4)" "0.4 - 130.9 (17.6)" "0.1 - 103.5 (15.0)"
[4] "0.5 - 86.3 (14.4)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       29        63       43
  subtype2       3       37        27       39
  subtype3       1       25        15       24
  subtype4       0       35        23       24
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        3        1        0
  STAGE II        29       37       25       35
  STAGE III       63       27       15       23
  STAGE IV        43       39       24       24
[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       T0+T1+T2 T3 T4
  subtype1       27 80 20
  subtype2       38 44 11
  subtype3       24 26 11
  subtype4       33 35 12
D2V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       27       38       24       33
  T3             80       44       26       35
  T4             20       11       11       12
[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       N0 N1 N2 N3
  subtype1 82 14 24  4
  subtype2 55 15 21  2
  subtype3 37  2 20  1
  subtype4 53 11 11  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       82       55       37       53
  N1       14       15        2       11
  N2       24       21       20       11
  N3        4        2        1        1
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 53  4
  subtype2 54  2
  subtype3 45  2
  subtype4 37  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53    4
  subtype2   54    2
  subtype3   45    2
  subtype4   37    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       53       54       45       37
  1        4        2        2        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 40 96
  subtype2 31 76
  subtype3 11 55
  subtype4 20 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   96
  subtype2   31   76
  subtype3   11   55
  subtype4   20   64
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       31       11       20
  MALE         96       76       55       64
[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"
D2V8, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         8   118
  subtype2    10                         6    86
  subtype3    18                         2    44
  subtype4    10                         6    63
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            5       10       18       10
  BLACK OR AFRICAN AMERICAN        8        6        2        6
  WHITE                          118       86       44       63
[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"
D2V12, binary
          cls
clus         0   1
  subtype1   2 124
  subtype2   2  94
  subtype3   0  63
  subtype4   5  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  124
  subtype2    2   94
  subtype3    0   63
  subtype4    5   73
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        0        5
  NOT HISPANIC OR LATINO      124       94       63       73
[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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 24  9
  subtype2 10 18
  subtype3 18 18
  subtype4  2  3
  subtype5  9 11
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       28       36        5       20 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       18       18        3       11 
$subtype1
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F6 
       40.08        17.88        19.50         4.67        28.70        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AA 
        0.46         0.69         5.19        16.31        21.86        19.00 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3X2 
      130.88       112.44        15.62        10.59        13.58        17.98 
TCGA-E7-A3Y1 TCGA-FD-A3NA TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM 
        0.10        60.66        10.65        17.23        17.62        21.40 
TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
        7.73        11.31        19.82         8.48        27.35        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        1.51        19.40        38.60 

$subtype2
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A42B TCGA-C4-A0F0 
        7.33         6.58         5.06         8.35        17.56         1.94 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A3WY 
       16.70        17.62         1.81         2.20        21.30       140.81 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ 
       32.02        16.77        33.04         4.01        12.62        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98         5.52        46.78        19.79        12.85 
TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WU TCGA-K4-A3WV 
        2.10        14.27         3.45        21.24 

$subtype3
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T 
        2.66         6.74        19.04        32.84        12.16        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F1 
       14.96         5.06         8.25        17.16        12.82         2.93 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AE 
        2.04         0.43         5.46         2.14        66.41        16.14 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-E5-A2PC 
        7.79       123.85         8.22        23.21        48.00        43.59 
TCGA-E7-A3X6 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-G2-A2EJ TCGA-G2-A2EO 
       24.66         8.94        22.52        29.16        30.61        35.24 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI TCGA-GV-A40E 
       33.01         2.24        17.75        24.92        10.59         8.58 

$subtype4
TCGA-BT-A0YX TCGA-BT-A2LB TCGA-DK-A3IQ TCGA-G2-A2EK TCGA-GD-A3OQ 
       13.15        16.18        17.72        15.95         3.12 

$subtype5
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IM TCGA-DK-A3IV 
       20.48         9.96         8.98        12.92         7.82         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-G2-A2EC 
       20.81        10.55        27.98        25.74        31.07        22.88 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GD-A3OS TCGA-GV-A3JW 
       61.94        26.93         7.23        20.12        20.98        21.34 
TCGA-GV-A3QF TCGA-K4-A3WS 
       20.28        25.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     1.81     0.43     3.12     7.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.88   140.81   123.85    17.72    61.94 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.880   15.485   14.925   15.950   20.645 
[1] "0.1 - 130.9 (17.9)" "1.8 - 140.8 (15.5)" "0.4 - 123.8 (14.9)"
[4] "3.1 - 17.7 (15.9)"  "7.2 - 61.9 (20.6)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       11         9       13
  subtype2       0        5         8       16
  subtype3       0        8        17       10
  subtype4       0        1         3        1
  subtype5       0       10         6        4
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        0        0        0        0
  STAGE II        11        5        8        1       10
  STAGE III        9        8       17        3        6
  STAGE IV        13       16       10        1        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       10 15  5
  subtype2        6 15  8
  subtype3        8 21  5
  subtype4        0  3  1
  subtype5        3  9  1
D3V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       10        6        8        0        3
  T3             15       15       21        3        9
  T4              5        8        5        1        1
[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       N0 N1 N2 N3
  subtype1 20  1 10  2
  subtype2 13  4 10  2
  subtype3 23  5  4  2
  subtype4  4  1  0  0
  subtype5 11  2  2  0
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       20       13       23        4       11
  N1        1        4        5        1        2
  N2       10       10        4        0        2
  N3        2        2        2        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 25  2
  subtype2 10  2
  subtype3 25  0
  subtype4  4  0
  subtype5  9  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    2
  subtype2   10    2
  subtype3   25    0
  subtype4    4    0
  subtype5    9    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       25       10       25        4        9
  1        2        2        0        0        1
[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  7 30
  subtype2 10 19
  subtype3  8 28
  subtype4  2  3
  subtype5  6 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   30
  subtype2   10   19
  subtype3    8   28
  subtype4    2    3
  subtype5    6   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        7       10        8        2        6
  MALE         30       19       28        3       14
[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, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        2       10        1       10 
 [1] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype3" "subtype5" "subtype5" "subtype1" "subtype3" "subtype5"
[13] "subtype5" "subtype3" "subtype5" "subtype3" "subtype3" "subtype5"
[19] "subtype5" "subtype1" "subtype1" "subtype3" "subtype3" "subtype5"
[25] "subtype5" "subtype1" "subtype5" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype1"
D3V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       18       22        2       13 
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype2" "subtype1" "subtype5" "subtype2" "subtype3"
[13] "subtype1" "subtype1" "subtype1" "subtype5" "subtype3" "subtype1"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[25] "subtype3" "subtype2" "subtype1" "subtype5" "subtype3" "subtype3"
[31] "subtype5" "subtype5" "subtype3" "subtype1" "subtype2" "subtype2"
[37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype5"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype5"
[49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype5"
[55] "subtype3" "subtype5" "subtype3" "subtype5" "subtype1" "subtype3"
[61] "subtype3" "subtype1" "subtype5" "subtype1" "subtype2" "subtype1"
[67] "subtype5" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[73] "subtype1" "subtype1" "subtype1" "subtype5" "subtype2"
D3V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         1    27
  subtype2     0                         2    26
  subtype3     1                         3    29
  subtype4     0                         0     5
  subtype5     0                         3    16
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            7        0        1        0        0
  BLACK OR AFRICAN AMERICAN        1        2        3        0        3
  WHITE                           27       26       29        5       16
[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"
D3V12, binary
          cls
clus        0  1
  subtype1  0 33
  subtype2  2 26
  subtype3  1 31
  subtype4  0  5
  subtype5  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    2   26
  subtype3    1   31
  subtype4    0    5
  subtype5    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        1        0        0
  NOT HISPANIC OR LATINO       33       26       31        5       19
[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 = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 26 13
  subtype2 16 21
  subtype3 12 15
  subtype4  9 10
subtype1 subtype2 subtype3 subtype4 
      39       37       27       19 
subtype1 subtype2 subtype3 subtype4 
      13       21       15       10 
$subtype1
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB 
       40.08         2.66        13.15        17.88        19.50        16.18 
TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        4.67        28.70         2.93        23.01         0.46         0.69 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        5.19        16.31        21.86         2.14        66.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      112.44        15.62        10.59        48.00        24.66         0.10 
TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY 
        8.94        60.66        17.98        17.23        20.12        17.62 
TCGA-GC-A3BM TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK 
       21.40         3.12        11.31        19.82         8.48        27.35 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE 
       19.07         1.51        38.60 

$subtype2
TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0EZ 
        7.33         5.06         8.35        20.48        17.56         8.98 
TCGA-C4-A0F0 TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK 
        1.94        16.70        17.62         1.81       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY 
       13.58         8.22        17.72        21.30        23.21       140.81 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       32.02        16.77        33.04        12.62        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-G2-A2EK 
       29.16         5.52        46.78        19.79        12.85        15.95 
TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JV TCGA-K4-A3WS TCGA-K4-A3WU 
        2.24         7.73         2.10        14.27        25.02         3.45 
TCGA-K4-A3WV 
       21.24 

$subtype3
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20T 
        6.74         6.58        19.04        32.84        12.16        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F7 
       14.96         5.06         8.25        17.16        12.82         2.04 
TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A3X2 TCGA-E5-A2PC 
        0.43         5.46       130.88        16.14        17.98        43.59 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        4.01        22.52        27.98        26.93        35.24        33.01 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A3QI 
       17.75        24.92        10.59 

$subtype4
TCGA-BT-A3PK TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IV TCGA-DK-A3WW 
        9.96        12.92         7.79         7.82         9.67        20.81 
TCGA-DK-A3WX TCGA-FD-A3SP TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.55        25.74        31.07        10.65        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-GD-A3OS TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E 
       30.61         7.23        20.98        21.34        20.28         8.58 
TCGA-H4-A2HQ 
       19.40 

subtype1 subtype2 subtype3 subtype4 
    0.10     1.81     0.43     7.23 
subtype1 subtype2 subtype3 subtype4 
  112.44   140.81   130.88    61.94 
subtype1 subtype2 subtype3 subtype4 
   17.62    16.70    16.14    19.40 
[1] "0.1 - 112.4 (17.6)" "1.8 - 140.8 (16.7)" "0.4 - 130.9 (16.1)"
[4] "7.2 - 61.9 (19.4)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       14        12       13
  subtype2       0        7        12       19
  subtype3       0        5        14        7
  subtype4       0        9         5        5
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        0        0        0
  STAGE II        14        7        5        9
  STAGE III       12       12       14        5
  STAGE IV        13       19        7        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       14 16  7
  subtype2        7 22  8
  subtype3        4 18  4
  subtype4        2  7  1
D4V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       14        7        4        2
  T3             16       22       18        7
  T4              7        8        4        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       N0 N1 N2 N3
  subtype1 24  4  9  1
  subtype2 19  6 11  2
  subtype3 19  3  4  1
  subtype4  9  0  2  2
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       24       19       19        9
  N1        4        6        3        0
  N2        9       11        4        2
  N3        1        2        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 30  1
  subtype2 18  2
  subtype3 16  0
  subtype4  9  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    1
  subtype2   18    2
  subtype3   16    0
  subtype4    9    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       30       18       16        9
  1        1        2        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  7 36
  subtype2 14 24
  subtype3  6 21
  subtype4  6 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   36
  subtype2   14   24
  subtype3    6   21
  subtype4    6   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       14        6        6
  MALE         36       24       21       13
[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"
D4V8, continuous
D4V9, continuous
D4V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         1    32
  subtype2     0                         1    35
  subtype3     1                         4    20
  subtype4     0                         3    16
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            7        0        1        0
  BLACK OR AFRICAN AMERICAN        1        1        4        3
  WHITE                           32       35       20       16
[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"
D4V12, binary
          cls
clus        0  1
  subtype1  0 38
  subtype2  3 33
  subtype3  0 24
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   38
  subtype2    3   33
  subtype3    0   24
  subtype4    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        3        0        0
  NOT HISPANIC OR LATINO       38       33       24       19
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  54  55
  subtype2 122  45
  subtype3  54  53
subtype1 subtype2 subtype3 
     109      167      107 
subtype1 subtype2 subtype3 
      55       45       53 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A13J 
       22.29         8.35        44.94        10.22         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q 
        6.74        12.39         6.58        19.04        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-DK-A1A3 
        5.06        17.16        16.18        20.48         8.98        21.86 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
        2.14       130.88        17.62         1.81        10.59       123.85 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-DK-A6B2 
        8.22        17.72        21.30        23.21       140.81        15.68 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3B8 
      166.03        12.36        43.50         1.22         4.01        12.62 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       23.41        17.98        29.16        25.74        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91        26.73        53.88        11.01 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        5.69        27.45        18.08         2.70         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
       18.81         6.15         2.27         3.06         4.31        10.85 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GD-A3OS 
        8.94         6.48        35.24         6.94        15.81        20.98 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R 
        7.63        20.05        10.65        25.02         3.45        27.68 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 
        9.07         1.74         6.38        11.80        14.24        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A8OD TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A9SI 
       31.56        17.62       112.83        29.56        97.45        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN0 
       18.90         2.24        92.98        54.90        91.73        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       27.06        18.81         3.88         0.66        28.41        74.56 
TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       52.73        34.06        35.41        19.40        47.15        19.17 
TCGA-ZF-AA5P 
       10.13 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       11.97        91.63        16.27        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 
       49.12         0.62        66.54        47.80        33.83        40.08 
TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.88         8.35         4.67        28.70        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        13.08         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG 
        1.84        66.41        18.41        19.00       112.44        15.62 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
        2.20        13.58        50.27         9.67        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U 
       41.56        76.60        67.36        30.67        15.02        10.49 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 
        7.53        13.64        12.03        10.62        38.83         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.95        15.32         0.43         8.09        60.66        24.30 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TE 
       22.98         3.62         5.36         7.10        62.86        12.36 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        9.67        31.07         7.13        10.65        17.23         3.25 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       22.88        15.95        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 
       19.46        21.40         4.50        14.07         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        7.73         2.10         2.20         7.36        10.92        11.31 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       27.09         4.73        32.98        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       19.82        20.28         8.48        10.59        27.35        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A6MB 
       22.72         1.51        19.40        38.60         3.06        15.42 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78M 
       15.58        21.07        13.48         1.84         3.75        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       86.83        76.01        17.82         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SV 
       97.12        15.35         1.87        17.88        64.80        12.76 
TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY 
       26.27       110.60         7.63        71.57         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       44.32        30.94         9.63        11.97        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RL 
       21.11        24.13        30.28        27.19        21.86        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        19.69         8.61        63.02        38.73 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
      103.50       105.70        16.77        27.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       15.12        13.15        32.84        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        12.82         9.96        24.26        28.41         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E 
        2.93         2.04         0.43        12.92         5.46        13.58 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW 
       16.70        16.14         7.79        87.32         7.82        20.81 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W 
       10.55        17.98        41.06        38.24        13.58         8.65 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 
       43.59        15.35        24.66        14.07        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        33.04        22.52        27.98         5.52 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD 
       12.85        15.58        19.33         8.25        58.92        12.69 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 
       61.94        30.61        26.93        33.01         7.23         2.24 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A42Q 
       15.91        17.75        24.92         8.94         3.12        11.31 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV 
        5.62         7.00         8.58         9.01         8.22        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI 
        2.76         9.14        11.70         1.81        15.32        12.23 
TCGA-PQ-A6FN TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       16.67        37.05        67.79        65.75         3.58        35.24 
TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       45.04       125.49        16.27        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN5 
       11.31         2.96         8.32        61.45        86.30        75.39 
TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4N 
       18.84        13.64        13.41         3.48        20.22         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        60.16        57.90         8.52         5.52 

subtype1 subtype2 subtype3 
    0.66     0.10     0.43 
subtype1 subtype2 subtype3 
  166.03   112.44   125.49 
subtype1 subtype2 subtype3 
   17.98    15.02    15.12 
[1] "0.7 - 166.0 (18.0)" "0.1 - 112.4 (15.0)" "0.4 - 125.5 (15.1)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       17        46       47
  subtype2       4       76        42       47
  subtype3       0       32        39       34
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        4        0
  STAGE II        17       76       32
  STAGE III       46       42       39
  STAGE IV        47       47       34
[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       T0+T1+T2 T3 T4
  subtype1       17 73 16
  subtype2       74 57 22
  subtype3       30 53 15
D5V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       17       74       30
  T3             73       57       53
  T4             16       22       15
[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        N0  N1  N2  N3
  subtype1  59  13  30   2
  subtype2 105  10  32   3
  subtype3  61  18  13   3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       59      105       61
  N1       13       10       18
  N2       30       32       13
  N3        2        3        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"
D5V6, binary
          cls
clus         0   1
  subtype1  38   5
  subtype2 105   3
  subtype3  46   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    5
  subtype2  105    3
  subtype3   46    2
   clus
vv  subtype1 subtype2 subtype3
  0       38      105       46
  1        5        3        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"
D5V7, binary
          cls
clus         0   1
  subtype1  27  83
  subtype2  38 134
  subtype3  36  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   83
  subtype2   38  134
  subtype3   36   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       38       36
  MALE         83      134       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"
D5V8, continuous
D5V9, continuous
D5V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         5   101
  subtype2    37                         9   120
  subtype3     3                         8    87
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3       37        3
  BLACK OR AFRICAN AMERICAN        5        9        8
  WHITE                          101      120       87
[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"
D5V12, binary
          cls
clus         0   1
  subtype1   2 104
  subtype2   2 156
  subtype3   4  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  104
  subtype2    2  156
  subtype3    4   91
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        4
  NOT HISPANIC OR LATINO      104      156       91
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 60 47
  subtype2 81 23
  subtype3 89 83
subtype1 subtype2 subtype3 
     107      104      172 
subtype1 subtype2 subtype3 
      47       23       83 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       22.29         8.35        16.27        44.94        16.83        17.16 
TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       47.80         2.66        32.84        19.50         5.06        14.89 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YO 
        8.35        16.18         4.67        23.01         0.46         4.90 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        7.20        21.86         2.14        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44        17.62         1.81        10.59         2.20        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6T TCGA-E7-A85H 
       17.72        21.30        48.00        15.68        12.36        12.95 
TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        8.09        60.66        24.30        23.41        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR 
       19.79        22.98        27.35        14.96        20.91        26.73 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
       27.45        18.08        62.86         6.15         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GC-A3RD 
       31.07        22.88        15.95        35.24        15.81        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       13.91         7.73         2.10         4.73        10.65        32.98 
TCGA-GV-A3JZ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB 
       19.82        25.02         3.45         2.76        27.68        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K 
        6.38        11.80        14.24         1.84        12.43        17.62 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HF 
       22.68        86.83       112.83        17.82         4.54        97.12 
TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ 
        1.87        64.80        66.41        12.76        11.90        28.24 
TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       26.27       110.60        54.90        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       44.32        18.84        18.64         7.36        28.41        74.56 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5P 
       34.06        19.69        38.73        35.41        10.13 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 
       11.97        91.63        34.98        49.12         0.62        66.54 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A47S 
       33.83        40.08        17.88        28.70         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IS 
        5.19        16.31         1.84        19.00        15.62        50.27 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P 
       64.18        41.56        76.60        67.36        30.67        15.02 
TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 
       10.49        13.64        12.03        10.62        38.83         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-E7-A8O8 
       13.97        12.99         0.92        13.68        15.32         0.43 
TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        3.62         5.36         7.10         7.13        10.65        17.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62        66.02        64.44        19.46        21.40 
TCGA-GC-A3RB TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 
        4.50         2.20         7.36        10.92        11.31        27.09 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       14.27        21.34        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-LT-A5Z6 
       19.07        22.72         1.51        19.40        38.60        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A9PF TCGA-XF-A8HC 
       21.07        13.48         3.75        76.01         1.64         6.58 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-AAML TCGA-XF-AAN1 TCGA-YC-A8S6 TCGA-YF-AA3L 
       15.35        17.88         7.63        30.94         9.63        11.97 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.11        24.13        30.28        27.19        82.49        47.84 
TCGA-ZF-AA4U TCGA-ZF-AA4X 
        8.61        63.02 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
      103.50       105.70        16.77        27.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       15.12        10.22         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       13.15        19.04        12.16        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F 
       17.16        20.48        12.82         9.96        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A0YN 
        8.98         1.94         2.93         2.04         0.43        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 
        5.46        13.58        16.70        16.14         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       87.32         7.82         8.22        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       10.55       140.81        17.98        41.06        38.24        13.58 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4TZ 
      166.03         8.65         7.53        43.50        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P 
       24.66        17.39        14.33         1.22        14.07        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS 
       22.52        27.98        29.16         5.52        25.74        12.85 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        11.01        19.33         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD 
       58.92         2.70         6.28        13.35        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A3EE 
       12.36         2.27         4.31        10.85         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
        6.48        61.94        30.61        26.93        33.01         7.23 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        6.94         2.24        15.91        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 
        8.94         3.12        20.98        11.31         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A40E TCGA-HQ-A2OF TCGA-HQ-A5ND 
        5.62         7.00        19.10         8.58         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        8.22        21.24         9.14         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78L 
        1.81        15.32        12.23        16.67        31.56        37.05 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB 
       67.79        65.75         3.58        35.24        29.56        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SX TCGA-XF-A9SY 
       97.45       125.49        79.66         3.22        23.64        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       92.98        11.31        71.57         2.96         8.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
        0.66        13.64        21.86        13.41         3.48        52.73 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 
       20.22         2.89        59.38        60.16        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
        8.52        47.15        19.17         5.52 

subtype1 subtype2 subtype3 
    0.46     0.10     0.43 
subtype1 subtype2 subtype3 
  130.88    91.63   166.03 
subtype1 subtype2 subtype3 
  17.980   13.825   14.665 
[1] "0.5 - 130.9 (18.0)" "0.1 - 91.6 (13.8)"  "0.4 - 166.0 (14.7)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       15        33       59
  subtype2       4       63        24       16
  subtype3       0       47        70       53
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        4        0
  STAGE II        15       63       47
  STAGE III       33       24       70
  STAGE IV        59       16       53
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       20 62 21
  subtype2       59 26 10
  subtype3       42 95 22
D6V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       20       59       42
  T3             62       26       95
  T4             21       10       22
[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        N0  N1  N2  N3
  subtype1  47  14  40   3
  subtype2  77   4  10   1
  subtype3 101  23  25   4
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       47       77      101
  N1       14        4       23
  N2       40       10       25
  N3        3        1        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 47  3
  subtype2 75  2
  subtype3 67  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    3
  subtype2   75    2
  subtype3   67    5
   clus
vv  subtype1 subtype2 subtype3
  0       47       75       67
  1        3        2        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  27  81
  subtype2  18  91
  subtype3  56 116
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   81
  subtype2   18   91
  subtype3   56  116
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       18       56
  MALE         81       91      116
[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"
D6V8, continuous
D6V9, continuous
D6V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         8    93
  subtype2    32                         3    70
  subtype3     6                        11   145
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5       32        6
  BLACK OR AFRICAN AMERICAN        8        3       11
  WHITE                           93       70      145
[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"
D6V12, binary
          cls
clus         0   1
  subtype1   1  97
  subtype2   1 102
  subtype3   6 152
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   97
  subtype2    1  102
  subtype3    6  152
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        6
  NOT HISPANIC OR LATINO       97      102      152
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  58  58
  subtype2  55  35
  subtype3 118  61
subtype1 subtype2 subtype3 
     116       90      179 
subtype1 subtype2 subtype3 
      58       35       61 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA86 TCGA-BT-A0S7 TCGA-BT-A20J 
       22.29        44.94        16.77        10.22         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X 
       12.16        19.50         5.06        14.89        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.16        16.18        17.56         1.94         0.46         0.43 
TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        4.90        13.58        21.86        16.70        16.14        17.62 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WY 
        1.81       123.85        13.58        17.72        23.21       140.81 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 
       38.24        13.58       166.03        12.36         7.53        43.50 
TCGA-E7-A6ME TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.99        14.07        14.37        32.02        16.77        12.62 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S 
       24.30        23.41        25.74        46.78        19.79        14.96 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TF 
        8.25         2.70         6.28        13.35        18.81         2.27 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK 
        3.06        10.85         8.94         6.48        22.88        15.95 
TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       15.81        17.75        13.91         7.73         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-K4-A4AC 
        7.36         7.63        20.05         4.73         7.00         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 
        9.07        11.70         6.38        11.80        14.24        12.43 
TCGA-UY-A78L TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       37.05       112.83        29.56         4.54         1.64         1.87 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
       79.66        66.41        11.90        23.64        21.04         2.24 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN0 
       13.74        92.98        10.82        91.73         2.96        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R1 
       86.30        27.06        75.39         3.88         9.63         7.36 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       74.56        13.41        60.16        35.41        57.90        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5P 
       47.15        10.13 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       11.97        91.63         8.35        27.62        49.12        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX 
       66.54        15.12        40.08         7.33         2.66        13.15 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F1 TCGA-CF-A47S 
        8.35        20.48         9.96        28.70         2.93        10.95 
TCGA-CF-A9FF TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
       11.87         7.20         5.46         5.19         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV 
      130.88        10.59        87.32         2.20        21.30        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A97Q 
       67.36        15.68        14.56        14.33         1.22         8.09 
TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 
        4.01        29.16        12.85        22.98        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH 
       58.92         7.10        62.86         6.15        12.69         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P 
        9.67        31.07        17.23        17.62        24.92        10.92 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G 
        5.62        10.65        32.98        14.27        20.28        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51        19.40        38.60        25.02         3.45         2.76 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78O 
       15.42        15.32        13.48         1.84        31.56        76.01 
TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A9SJ TCGA-XF-A9SZ TCGA-XF-A9T0 
       65.75        17.82         6.58         3.22        28.24        26.27 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YF-AA3L 
       11.31        54.90         6.77        98.99        44.32        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-ZF-AA5N 
       13.64        18.64        21.86        28.41        38.73         5.52 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      103.50       105.70        16.27        16.83        17.16        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A3JM TCGA-BT-A20N 
        0.62        41.75        47.80        33.83         6.74        32.84 
TCGA-BT-A20P TCGA-BT-A20V TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
       17.88         5.06         4.67        12.82        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         2.04         0.69        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 
       11.34        11.34        13.08        12.92        16.31        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IM 
       18.41        19.00       112.44        15.62         7.79         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 
        8.22        50.27         9.67        20.81        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P 
       17.98        41.56        76.60        41.06        30.67        15.02 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       10.49         8.65        13.64        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DU 
       16.70        17.39         0.56         0.66        13.97         0.92 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A3B5 TCGA-FD-A3B6 
       13.68        12.95        15.32         0.43         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A43P 
       22.52        27.98        60.66        17.98         5.52        27.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       20.91         3.62         5.36        12.36         7.13        10.65 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        61.94        30.61        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
        7.23        20.12        66.02        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
        2.24         4.50        15.91        14.07         0.49         8.94 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JW 
        3.12         2.20        11.31        11.31        27.09        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82         8.48        10.59        27.35         8.58 
TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A54R 
       22.72         3.06         9.01         8.22        21.24        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74         1.81        15.58        21.07        12.23        16.67 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC 
        3.75        17.62        22.68        86.83        67.79         3.58 
TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       35.24        45.04        97.45       125.49        97.12        15.35 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T4 
       17.88        48.62        64.80        12.76        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMW 
       66.64         2.10       110.60         7.63        71.57         8.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R2 
       30.94        61.45        18.81        18.84         0.66        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       24.13        30.28        27.19         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.61        59.38        63.02         8.52        19.17 

subtype1 subtype2 subtype3 
    0.43     1.22     0.10 
subtype1 subtype2 subtype3 
  166.03   130.88   125.49 
subtype1 subtype2 subtype3 
  14.925   15.220   16.700 
[1] "0.4 - 166.0 (14.9)" "1.2 - 130.9 (15.2)" "0.1 - 125.5 (16.7)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       22        43       48
  subtype2       1       23        29       39
  subtype3       3       81        55       42
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        1        3
  STAGE II        22       23       81
  STAGE III       43       29       55
  STAGE IV        48       39       42
[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       T0+T1+T2 T3 T4
  subtype1       21 76 13
  subtype2       28 45 15
  subtype3       73 63 25
D7V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       21       28       73
  T3             76       45       63
  T4             13       15       25
[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        N0  N1  N2  N3
  subtype1  60  13  35   0
  subtype2  46  13  21   4
  subtype3 120  15  20   4
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       60       46      120
  N1       13       13       15
  N2       35       21       20
  N3        0        4        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1  43   2
  subtype2  40   3
  subtype3 105   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    2
  subtype2   40    3
  subtype3  105    5
   clus
vv  subtype1 subtype2 subtype3
  0       43       40      105
  1        2        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  38  78
  subtype2  18  75
  subtype3  45 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   78
  subtype2   18   75
  subtype3   45  137
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       18       45
  MALE         78       75      137
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         7   101
  subtype2    10                         4    75
  subtype3    26                        11   133
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            7       10       26
  BLACK OR AFRICAN AMERICAN        7        4       11
  WHITE                          101       75      133
[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"
D7V12, binary
          cls
clus         0   1
  subtype1   1 111
  subtype2   4  81
  subtype3   4 160
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  111
  subtype2    4   81
  subtype3    4  160
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        4
  NOT HISPANIC OR LATINO      111       81      160
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 44 41
  subtype2 53 40
  subtype3 61 29
  subtype4 43 23
  subtype5 30 21
subtype1 subtype2 subtype3 subtype4 subtype5 
      85       93       90       66       51 
subtype1 subtype2 subtype3 subtype4 subtype5 
      41       40       29       23       21 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O 
       22.29        16.77        41.75         6.58        19.04        12.16 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PJ 
       19.50        14.89        14.96         5.06        17.16        12.82 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1AB 
       17.56        28.41         1.94         0.43         5.46        16.70 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3WW TCGA-DK-A3WX 
       16.14         7.79         7.82         8.22        20.81        10.55 
TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-E5-A2PC 
       17.98        38.24        13.58       166.03        12.36        43.59 
TCGA-E5-A4TZ TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.35        14.33        14.07        14.37         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY 
       22.52        27.98        20.91        53.88         5.69         8.25 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3I6 
        8.94        61.94        30.61        35.24        33.01         2.24 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV 
       20.98        11.31         3.06         9.01         8.22        21.24 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-PQ-A6FI TCGA-PQ-A6FN 
        9.14         9.07         1.74         1.81        12.23        16.67 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A8HE 
       17.62        37.05        67.79         3.58        35.24       125.49 
TCGA-XF-A9SG TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMT 
       48.62        21.04        18.90        66.64        13.74         2.96 
TCGA-XF-AAMW TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
        8.32        18.81         3.88        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 
       52.60        20.22         2.89        60.16        19.40         8.52 
TCGA-ZF-AA5H 
       19.17 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       11.97        91.63         8.35        27.62        49.12        51.16 
TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W 
       10.22        40.08         7.33         2.66        13.15         8.35 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F1 TCGA-CF-A47S 
       20.48         9.96        28.70        24.26         2.93        10.95 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 
        7.20         5.19         1.84         2.14       130.88        87.32 
TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6X 
        2.20        21.30        64.18        67.36        15.68         7.53 
TCGA-DK-AA74 TCGA-E7-A677 TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3SN 
       43.50        14.56         1.22         8.09         4.01        29.16 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.52        46.78        12.85        11.01        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI 
        2.70         7.10         6.15        12.69         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3YS 
       31.07        17.23        17.62        66.02        15.91        24.92 
TCGA-GC-A6I1 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
        8.94        10.92         7.63        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       32.98        14.27        20.28        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-LC-A66R TCGA-MV-A51V 
       38.60        25.02         3.45         2.76        15.32        13.48 
TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD 
        1.84        31.56        76.01        65.75        29.56        17.82 
TCGA-XF-A8HC TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-AAMH TCGA-XF-AAMJ 
        6.58         3.22        11.90        28.24        11.31        54.90 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        6.77        98.99        44.32        75.39        21.86        28.41 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA58 
       38.73        57.90        47.15 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA83 TCGA-4Z-AA89 
      103.50        44.94        16.83        34.98        66.54        33.83 
TCGA-BT-A20P TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       17.88         2.04         0.69        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA 
       11.87        13.08        12.92        16.31        66.41        19.00 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 
       15.62        10.59         9.67        41.56        76.60        24.66 
TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DU TCGA-E7-A7PW 
        0.10        16.70         0.66        13.97         0.92        13.68 
TCGA-E7-A8O7 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A6TA TCGA-FD-A6TE 
       15.32        60.66        27.35         3.62        62.86        12.36 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A3IB TCGA-G2-A3IE 
        7.13        10.65         3.25        22.88         7.23        20.12 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GD-A3OQ TCGA-GU-A42R 
       64.44        19.46        21.40         4.50         3.12        11.31 
TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3QK TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       27.09        21.34        27.35        27.68        15.58        21.07 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HG 
       22.68        86.83         4.54         1.64        45.04        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9T4 
        1.87        17.88        64.80        12.76        23.64        16.27 
TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-YC-A8S6 
        2.10         7.63        71.57        56.48        61.45         9.63 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       11.97        18.64        21.11        24.13        30.28        27.19 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA5N 
       82.49        34.06         8.61        59.38        63.02         5.52 

$subtype4
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA87 
      105.70        16.27        17.16         0.62        15.12        47.80 
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20X TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F6 
        6.74        32.84         8.25         4.67         8.98        23.01 
TCGA-CF-A47X TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6B5 
       12.62        13.58        18.41        50.27        48.00        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 
       30.67        15.02        10.49         8.65        13.64        12.03 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       10.62        38.83         0.49         2.24        17.39         0.56 
TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A8O8 TCGA-FD-A3SM TCGA-FD-A43N TCGA-FD-A43Y 
       12.99        12.95         0.43        17.98        22.98        15.58 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S TCGA-G2-A2EL TCGA-GC-A3RD 
       26.73         5.36        27.45        13.35        26.93        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A6C6 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ 
        0.49        13.91         2.20         7.00        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A5RI TCGA-K4-A6MB 
        8.48        10.59         8.58        22.72        11.70        15.42 
TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAN1 
        3.75        97.45        97.12        26.27       110.60        30.94 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9RM TCGA-ZF-AA4T 
       18.84         0.66        13.64         7.36        47.84        19.69 

$subtype5
TCGA-BT-A20R TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CU-A0YO TCGA-DK-A1A3 TCGA-DK-A1AD 
        5.06        16.18         0.46         4.90        21.86       112.44 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IU 
       17.62         1.81       123.85        13.58        17.72        23.21 
TCGA-DK-A3WY TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
      140.81        32.02        16.77        12.62        24.30        23.41 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62P TCGA-FD-A6TB 
       25.74        19.79        14.96        19.33         6.28        18.81 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EK TCGA-GC-A3OO 
        2.27         3.06        10.85         6.48        15.95        15.81 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A767 TCGA-K4-A83P 
       17.75         7.73         2.10         7.36         4.73         6.38 
TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A8OD TCGA-XF-A9SI TCGA-XF-A9SL 
       11.80        14.24        12.43       112.83        79.66        66.41 
TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-XF-AAN4 
        2.24        92.98        10.82        91.73        86.30        27.06 
TCGA-ZF-A9RC TCGA-ZF-AA52 TCGA-ZF-AA5P 
       74.56        35.41        10.13 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.43     1.22     0.10     0.43     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
  166.03   130.88   103.50   110.60   140.81 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.140   15.680   16.290   14.545   16.180 
[1] "0.4 - 166.0 (16.1)" "1.2 - 130.9 (15.7)" "0.1 - 103.5 (16.3)"
[4] "0.4 - 110.6 (14.5)" "0.5 - 140.8 (16.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       21        35       27
  subtype2       1       23        30       40
  subtype3       2       47        21       23
  subtype4       1       25        24       16
  subtype5       0       10        17       23
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        2        1        0
  STAGE II        21       23       47       25       10
  STAGE III       35       30       21       24       17
  STAGE IV        27       40       23       16       23
[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       T0+T1+T2 T3 T4
  subtype1       18 50  9
  subtype2       26 47 16
  subtype3       49 25 12
  subtype4       18 30  9
  subtype5       11 32  7
D8V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       18       26       49       18       11
  T3             50       47       25       30       32
  T4              9       16       12        9        7
[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       N0 N1 N2 N3
  subtype1 48 14 11  2
  subtype2 49 13 23  4
  subtype3 58  6 14  1
  subtype4 44  5  8  1
  subtype5 27  3 20  0
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       48       49       58       44       27
  N1       14       13        6        5        3
  N2       11       23       14        8       20
  N3        2        4        1        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"
D8V6, binary
          cls
clus        0  1
  subtype1 38  0
  subtype2 40  1
  subtype3 60  3
  subtype4 33  4
  subtype5 17  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    0
  subtype2   40    1
  subtype3   60    3
  subtype4   33    4
  subtype5   17    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       38       40       60       33       17
  1        0        1        3        4        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 28 57
  subtype2 18 77
  subtype3 20 74
  subtype4 15 51
  subtype5 20 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   57
  subtype2   18   77
  subtype3   20   74
  subtype4   15   51
  subtype5   20   31
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       28       18       20       15       20
  MALE         57       77       74       51       31
[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, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         4    72
  subtype2     8                         5    80
  subtype3    22                         5    63
  subtype4     7                         5    48
  subtype5     2                         3    46
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            4        8       22        7        2
  BLACK OR AFRICAN AMERICAN        4        5        5        5        3
  WHITE                           72       80       63       48       46
[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"
D8V12, binary
          cls
clus        0  1
  subtype1  2 77
  subtype2  2 86
  subtype3  2 84
  subtype4  2 56
  subtype5  1 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   77
  subtype2    2   86
  subtype3    2   84
  subtype4    2   56
  subtype5    1   49
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        2        2        2        1
  NOT HISPANIC OR LATINO       77       86       84       56       49
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 56 40
  subtype2 15 24
  subtype3 90 34
  subtype4 61 54
subtype1 subtype2 subtype3 subtype4 
      96       39      124      115 
subtype1 subtype2 subtype3 subtype4 
      40       24       34       54 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       22.29        16.77        27.62        41.75        15.12        10.22 
TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A3PJ TCGA-BT-A3PK 
        7.33        19.04        12.16         5.06        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS 
       17.56        24.26        28.41         1.94         2.93         0.43 
TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       12.92         7.79        87.32         7.82        20.81        10.55 
TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-E5-A4TZ TCGA-E7-A7DV 
       41.06        13.58        12.36        10.49        15.35         1.22 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.07        14.37         8.94        33.04        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
       60.66         5.52        27.35        15.58        53.88        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ 
        5.69         8.25        58.92        12.69        61.94        30.61 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A42Q 
       33.01         2.24        15.91        24.92         8.94        11.31 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC 
        7.63         5.62         8.58         9.01         8.22         9.14 
TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78P 
        9.07         1.81        15.32        12.23        16.67        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A8HE 
       65.75         3.58        35.24        29.56        97.45       125.49 
TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       48.62        23.64        21.04        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMW TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       13.74         8.32        61.45        75.39        18.84         0.66 
TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N 
       13.64        21.86        13.41        52.73        52.60         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       59.38        60.16        19.40         8.52        47.15        19.17 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J 
       11.97        91.63         8.35        51.16        40.08         2.66 
TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1AC 
       13.15         8.35        20.48         7.20         1.84       130.88 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-E7-A97Q TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5C0 
       64.18        15.68         8.09        12.85        22.98        18.08 
TCGA-FD-A62O TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV 
        7.10         4.31        31.07        10.92        10.65        14.27 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB 
       20.28        19.07         1.51        38.60         3.45         2.76 
TCGA-S5-A6DX TCGA-UY-A9PD TCGA-XF-A9SJ TCGA-XF-AAMH TCGA-XF-AAMX TCGA-XF-AAMZ 
        1.84        17.82         3.22        11.31         6.77        44.32 
TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-ZF-AA5N 
       28.41        38.73         5.52 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
      103.50        16.83        17.16        34.98        49.12         0.62 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A2LA 
       66.54        47.80        33.83        32.84        17.88        17.16 
TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C 
        4.67        28.70         8.98        23.01         2.04         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        11.34        11.34        13.08         5.19        16.31 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A3IS 
       66.41        18.41        19.00        16.14        15.62        50.27 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6P 
        9.67        17.98        41.56        76.60        67.36        15.02 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 
        8.65        13.64        12.03        10.62        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 
        0.66        14.56        12.99        13.68        12.95        15.32 
TCGA-E7-A8O8 TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FD-A6TI 
        0.43        19.79         3.62         5.36        12.36         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IE 
        7.13        10.65        17.23         3.25        26.93        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB 
       17.62        66.02        64.44        19.46        21.40         4.50 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A763 
       14.07         0.49         3.12         2.20        11.31        27.09 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
       32.98         7.00        21.34        19.10        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A54R 
       10.59        27.35        22.72        19.40         3.06        27.68 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78O 
       15.58        21.07        13.48         3.75        17.62        76.01 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T2 
       45.04         6.58        97.12        17.88        26.27        18.90 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L 
      110.60         7.63        71.57        30.94        18.81        11.97 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.11        24.13        27.19         3.48        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       20.22        19.69         8.61        63.02 

$subtype4
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20Q 
      105.70        16.27        44.94         6.74         6.58        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-CF-A1HR 
        5.06        14.89        14.96         8.25        16.18         0.46 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.10        11.87         4.90        13.58        21.86         2.14 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.70       112.44        17.62         1.81        10.59       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         8.22        17.72        21.30        23.21 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6X TCGA-DK-AA74 
      140.81        48.00        38.24       166.03         7.53        43.50 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL 
       32.02        16.77         4.01        12.62        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U 
       17.98        29.16        25.74        46.78        14.96        20.91 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       26.73        11.01        27.45         2.70         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK 
       62.86        18.81         6.15         2.27         3.06        10.85 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO 
        8.94         6.48        22.88        15.95        35.24        15.81 
TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B 
       17.75        13.91         7.73         2.10        20.98         7.36 
TCGA-GU-A764 TCGA-GU-A767 TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB 
       20.05         4.73        25.02        21.24        11.70        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
        6.38        11.80        14.24        12.43        31.56        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       22.68        86.83       112.83         4.54         1.64         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ 
       64.80        79.66        66.41        12.76        11.90        28.24 
TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
        2.24        92.98        10.82        54.90        91.73         2.96 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        56.48        86.30        27.06         3.88         9.63 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA52 TCGA-ZF-AA53 
       18.64         7.36        74.56        34.06        35.41        57.90 
TCGA-ZF-AA5P 
       10.13 

subtype1 subtype2 subtype3 subtype4 
    0.43     1.51     0.43     0.46 
subtype1 subtype2 subtype3 subtype4 
  125.49   130.88   110.60   166.03 
subtype1 subtype2 subtype3 subtype4 
  15.465   12.850   16.995   16.270 
[1] "0.4 - 125.5 (15.5)" "1.5 - 130.9 (12.8)" "0.4 - 110.6 (17.0)"
[4] "0.5 - 166.0 (16.3)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       29        34       31
  subtype2       1        4        11       23
  subtype3       2       63        36       27
  subtype4       0       23        42       48
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        1        2        0
  STAGE II        29        4       63       23
  STAGE III       34       11       36       42
  STAGE IV        31       23       27       48
[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       T0+T1+T2 T3 T4
  subtype1       26 51 10
  subtype2        9 21 10
  subtype3       59 37 18
  subtype4       24 71 15
D9V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       26        9       59       24
  T3             51       21       37       71
  T4             10       10       18       15
[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       N0 N1 N2 N3
  subtype1 57 15 11  3
  subtype2 14  6 14  3
  subtype3 87  8 14  2
  subtype4 61 12 37  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       57       14       87       61
  N1       15        6        8       12
  N2       11       14       14       37
  N3        3        3        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"
D9V6, binary
          cls
clus        0  1
  subtype1 36  2
  subtype2 14  1
  subtype3 83  3
  subtype4 48  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    2
  subtype2   14    1
  subtype3   83    3
  subtype4   48    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36       14       83       48
  1        2        1        3        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  28  68
  subtype2   9  31
  subtype3  28 101
  subtype4  36  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   68
  subtype2    9   31
  subtype3   28  101
  subtype4   36   79
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28        9       28       36
  MALE         68       31      101       79
[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"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    80
  subtype2     1                         2    36
  subtype3    28                         6    85
  subtype4     8                         6   101
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        1       28        8
  BLACK OR AFRICAN AMERICAN        7        2        6        6
  WHITE                           80       36       85      101
[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"
D9V12, binary
          cls
clus         0   1
  subtype1   3  84
  subtype2   0  37
  subtype3   3 111
  subtype4   3 109
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   84
  subtype2    0   37
  subtype3    3  111
  subtype4    3  109
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        3        3
  NOT HISPANIC OR LATINO       84       37      111      109
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 41 30
  subtype2 20 22
  subtype3 66 23
  subtype4 27 36
  subtype5 23  5
  subtype6 45 36
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      71       42       89       63       28       81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      30       22       23       36        5       36 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LB 
       22.29        44.94         6.58        19.50         5.06        16.18 
TCGA-CF-A1HR TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 
        0.46        12.10        11.87         4.90        16.31        21.86 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IT 
      112.44        17.62        10.59       123.85        13.58        21.30 
TCGA-DK-A3IU TCGA-DK-A3WY TCGA-DK-AA6X TCGA-DK-AA74 TCGA-FD-A3B3 TCGA-FD-A3B7 
       23.21       140.81         7.53        43.50        32.02         4.01 
TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S 
       12.62        24.30        23.41        25.74        19.79        14.96 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A871 
       53.88        11.01         2.27         3.06        10.85         8.94 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 
        6.48        22.88        15.95        15.81        17.75         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A764 TCGA-GU-A767 TCGA-K4-A3WS 
        2.10        20.98         7.36        20.05         4.73        25.02 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A8OD TCGA-UY-A9PE 
        6.38        11.80        14.24        12.43       112.83         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SW 
        1.64         1.87        64.80        79.66        66.41        11.90 
TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN4 TCGA-XF-AAN8 
        2.24        92.98        10.82        91.73        27.06         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R0 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA5P 
        9.63        18.64        35.41        57.90        10.13 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-BL-A0C8 
       11.97        91.63         8.35        27.62        51.16        40.08 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 TCGA-CF-A47S 
        2.66        13.15         8.35        20.48         2.93        10.95 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IK TCGA-DK-A6AV TCGA-E7-A677 
        7.20         1.84       130.88         2.20        64.18        14.56 
TCGA-E7-A97Q TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TH TCGA-FJ-A3Z7 
        8.09        12.85        58.92         7.10         4.31        31.07 
TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO 
       10.92        10.65        14.27        20.28        19.07         1.51 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A9SJ 
       38.60         3.45         2.76        65.75        17.82         3.22 
TCGA-XF-AAMH TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 
       11.31         6.77        44.32        21.86        28.41        38.73 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 
      103.50        17.16        34.98        49.12         0.62        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F7 
       15.12        47.80         4.67        28.70         8.98         2.04 
TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3IV 
       12.62         5.19        66.41        18.41        50.27         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6T 
       17.98        41.56        67.36        41.06        15.02        12.36 
TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       10.49        13.64        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       38.83         0.49         2.24        17.39         0.56        12.99 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O8 TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BV 
       13.68        12.95         0.43        22.98        27.35         5.36 
TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY 
       12.36         7.13        10.65        17.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 
       66.02        19.46         4.50        14.07         0.49        13.91 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.20        11.31        32.98        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF 
        8.48        10.59        27.35        22.72        19.40         3.06 
TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-XF-A8HB TCGA-XF-A8HC 
       27.68        15.58        13.48        17.62        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ 
       97.45        97.12        26.27       110.60         7.63        71.57 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RE 
       18.84         0.66        11.97        24.13        27.19         3.48 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA5N 
       47.84        20.22        19.69        63.02         5.52 

$subtype4
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
      105.70        16.27         6.74        19.04        32.84        17.88 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F6 TCGA-CU-A72E 
       14.89        14.96         5.06         8.25        23.01        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3X1 
        2.14        16.70        16.14         1.81        17.72        48.00 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-FD-A3B4 TCGA-FD-A3SM 
       15.68        38.24       166.03         8.65        16.77        17.98 
TCGA-FD-A3SQ TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ 
       46.78        15.58        26.73        19.33         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TI TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-AATQ 
        9.67        26.93        35.24        11.31         5.62         7.00 
TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-S5-A6DX TCGA-SY-A9G5 
        9.01        21.24        11.70        15.42         1.84        31.56 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-XF-A9SV TCGA-XF-A9SZ 
       37.05        22.68        86.83        76.01        12.76        28.24 
TCGA-XF-A9T2 TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAN3 TCGA-YF-AA3M 
       18.90        54.90         2.96        98.99        86.30        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9RC TCGA-ZF-AA4R 
        7.36        74.56        34.06 

$subtype5
TCGA-4Z-AA7O TCGA-4Z-AA89 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       16.83        33.83         0.69        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM TCGA-DK-A1AA 
       12.26        12.00        11.34        11.34        13.08        19.00 
TCGA-DK-A1AG TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A8O7 
       15.62        76.60        24.66        16.70         0.66        15.32 
TCGA-FD-A43X TCGA-GC-A3BM TCGA-GU-A763 TCGA-LT-A8JT TCGA-S5-AA26 TCGA-XF-A8HI 
        3.62        21.40        27.09        21.07         3.75        17.88 
TCGA-XF-AAN1 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4U 
       30.94        21.11        82.49         8.61 

$subtype6
TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A2LA 
       16.77        41.75        10.22         7.33        12.16        17.16 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       12.82         9.96        17.56        24.26        28.41         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN 
        0.43        12.92         7.79        87.32         7.82         8.22 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6Q TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P 
       20.81        10.55        13.58         1.22        14.07        14.37 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN 
        8.94        33.04        22.52        27.98        60.66        29.16 
TCGA-FD-A3SO TCGA-FD-A43U TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TD TCGA-FT-A3EE 
        5.52        20.91         5.69         2.70        12.69         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC 
       61.94        30.61        33.01        64.44         2.24        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A762 TCGA-GV-A40E TCGA-HQ-A5NE 
       24.92         8.94         3.12         7.63         8.58         8.22 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
        9.14         9.07         1.81        15.32        12.23        16.67 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HE TCGA-XF-A9SG 
       67.79         3.58        35.24        29.56       125.49        48.62 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       23.64        21.04        16.27        66.64         2.10        13.74 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-ZF-A9RD 
        8.32        56.48        61.45        75.39        18.81        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 
       52.73        52.60         2.89        59.38        60.16        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.52        47.15        19.17 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.46     1.51     0.43     1.81     0.66     0.43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  140.81   130.88   110.60   166.03    82.49   125.49 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   15.81    13.00    17.23    17.72    15.47    15.91 
[1] "0.5 - 140.8 (15.8)" "1.5 - 130.9 (13.0)" "0.4 - 110.6 (17.2)"
[4] "1.8 - 166.0 (17.7)" "0.7 - 82.5 (15.5)"  "0.4 - 125.5 (15.9)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       18        25       27
  subtype2       1        8        12       21
  subtype3       2       40        23       27
  subtype4       0       12        25       25
  subtype5       1       20         6        2
  subtype6       0       21        32       27
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          0        1        2        0        1        0
  STAGE II        18        8       40       12       20       21
  STAGE III       25       12       23       25        6       32
  STAGE IV        27       21       27       25        2       27
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       17 42  8
  subtype2       11 22  9
  subtype3       36 28 11
  subtype4       13 38 10
  subtype5       21  4  4
  subtype6       20 46 11
D10V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T0+T1+T2       17       11       36       13       21       20
  T3             42       22       28       38        4       46
  T4              8        9       11       10        4       11
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 39  4 23  0
  subtype2 18  6 13  3
  subtype3 53  6 14  2
  subtype4 36 11 15  0
  subtype5 25  0  1  0
  subtype6 48 14 10  3
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       39       18       53       36       25       48
  N1        4        6        6       11        0       14
  N2       23       13       14       15        1       10
  N3        0        3        2        0        0        3
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 30  2
  subtype2 19  0
  subtype3 51  6
  subtype4 26  2
  subtype5 25  0
  subtype6 30  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    2
  subtype2   19    0
  subtype3   51    6
  subtype4   26    2
  subtype5   25    0
  subtype6   30    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       30       19       51       26       25       30
  1        2        0        6        2        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 23 48
  subtype2 10 33
  subtype3 22 70
  subtype4 18 45
  subtype5  5 25
  subtype6 23 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   48
  subtype2   10   33
  subtype3   22   70
  subtype4   18   45
  subtype5    5   25
  subtype6   23   58
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       23       10       22       18        5       23
  MALE         48       33       70       45       25       58
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         3    63
  subtype2     3                         2    36
  subtype3    13                         6    66
  subtype4     2                         4    53
  subtype5    13                         2    14
  subtype6     4                         4    70
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        3       13        2       13
  BLACK OR AFRICAN AMERICAN        3        2        6        4        2
  WHITE                           63       36       66       53       14
                           clus
vv                          subtype6
  ASIAN                            4
  BLACK OR AFRICAN AMERICAN        4
  WHITE                           70
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus        0  1
  subtype1  1 68
  subtype2  1 37
  subtype3  3 77
  subtype4  2 57
  subtype5  0 28
  subtype6  2 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   68
  subtype2    1   37
  subtype3    3   77
  subtype4    2   57
  subtype5    0   28
  subtype6    2   74
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        3        2        0        2
  NOT HISPANIC OR LATINO       68       37       77       57       28       74
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
