[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/19775034/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/20125359/BLCA-TP.mergedcluster.txt"

nPatients in clinical file=412, in cluster file=412, common to both=412
[1]  10 412
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
169 140  59  40 
  1   2   3   4 
169 140  59  40 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
139 117  71  85 
  1   2   3   4 
139 117  71  85 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
123 116 105 
  1   2   3 
123 116 105 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 90 122 100  32 
  1   2   3   4 
 90 122 100  32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
116 182 110 
  1   2   3 
116 182 110 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
119 113 176 
  1   2   3 
119 113 176 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
121  97 191 
  1   2   3 
121  97 191 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 89 100  95  71  54 
  1   2   3   4   5 
 89 100  95  71  54 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 99  43 136 120 
  1   2   3   4 
 99  43 136 120 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
75 47 95 66 31 84 
 1  2  3  4  5  6 
75 47 95 66 31 84 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 412 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=160,	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=271,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 412 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "NUMBER_OF_LYMPH_NODES"      
[11] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  1   3 120 196  59 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     124      196       59 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   3 120 196  59 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     124      196       59 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
238  47  76   9 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
238  47  76   9 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
238  47  76   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
238  47  76   9 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, 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=21, 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 96 71
  subtype2 81 59
  subtype3 31 28
  subtype4 21 19
subtype1 subtype2 subtype3 subtype4 
     167      140       59       40 
subtype1 subtype2 subtype3 subtype4 
      71       59       28       19 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        94.88       104.65       108.95        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I 
       34.98        50.04        66.54        29.65        17.42         7.33 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-BT-A42B 
       19.50        14.89        14.96         8.25         9.96        17.56 
TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       28.41        12.79        13.97        12.59        13.08        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-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        29.79         1.84        13.58        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       16.14        17.62        15.62        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21        20.81        10.55       163.30        53.29        76.60 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       13.58        18.81        15.35        13.64        56.15        20.32 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       29.72         0.10         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24        24.66         0.92        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SP 
       16.77         4.01        12.62        27.98        17.98        25.74 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62S TCGA-FD-A6TA 
       53.88        11.01        19.33         5.69        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       18.81         9.67        10.85        12.66        10.65         8.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C 
       48.00        15.95        26.93        59.31         7.23         6.94 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A76B 
       70.32        21.40        17.75         8.94         3.12         7.36 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS 
       11.31        32.78        27.35        22.72         1.51        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A8JT TCGA-R3-A69X 
        3.45         2.76        16.27        11.80        21.07        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78P TCGA-UY-A9PH TCGA-XF-A8HE 
        1.84        16.54        12.43        78.25        51.32       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SV 
        1.87        17.88        64.80        66.41         5.98        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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4U 
       21.11        35.84        21.86        13.41        88.87         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-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N 
       51.16        47.80         2.50        40.08         2.66        26.14 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35        17.16        16.18        20.48        12.82 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A8HY 
       28.70         8.98         1.94        12.56        12.16        11.34 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       15.12        18.48         5.19        21.86         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
      130.88       112.44        17.95         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
        8.22        66.05        64.18        67.36        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 
       38.24        15.02       166.03        19.00        13.64        11.18 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       12.03        15.35        38.83        22.16        25.58         0.56 
TCGA-E7-A6MD TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B5 
        4.24         1.22        13.68        12.95         8.09         8.94 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
       24.30        23.41        29.16        19.79         7.56        27.35 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
        8.25        27.45        18.08         6.28         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A3IE 
        3.06         4.31        31.07        17.23        61.94        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS 
       17.62        66.02        29.36        19.13        14.07        24.92 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATO 
        0.49         7.73        10.92        18.97         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G 
       32.98        21.34        19.82        20.28         8.48        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01         9.01        21.24         9.07 
TCGA-K4-A6MB TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-MV-A51V TCGA-SY-A9G5 
       15.42        35.97        46.98        44.38        13.48        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-UY-A9PE 
       37.05        22.68        76.01        69.34        17.82         6.21 
TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SZ 
        6.58        48.62         3.22        15.98         4.21        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX 
       26.27         2.10       110.60         7.63         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       98.99        44.32        18.15        11.97        30.28        94.29 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 
       47.84        20.22        34.06        19.69        59.38        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA5H 
       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-DK-AA6M TCGA-DK-AA6R 
       46.68         7.79       142.78         9.67        52.01       165.73 
TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A62N 
       24.03        32.02        33.04        22.52         5.52         2.70 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A3OP 
       12.69         2.27        15.81        15.91        13.91         2.10 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A40E TCGA-HQ-A5NE 
        7.63        20.05         5.62        19.10         8.58        12.16 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
        9.14        27.68        17.72         1.81        15.32        15.58 
TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF 
       16.67        17.62        86.83         3.91        29.56         3.85 
TCGA-XF-A9SI TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
       79.66        34.45        14.93        23.64        21.04         2.24 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9RF 
       10.82        54.90         2.96        56.48        61.45        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA58 TCGA-ZF-AA5P 
       58.72         2.89        63.02        54.21        12.23 

$subtype4
TCGA-4Z-AA81 TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A3MG TCGA-DK-A1A6 
       41.75         4.67        36.43        23.01        12.13        66.41 
TCGA-DK-A2I6 TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SS 
       87.32        17.98        36.66        43.59        60.66        12.85 
TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES 
        5.36        58.92         7.10         3.25        11.08        33.01 
TCGA-GC-A3I6 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI 
       20.71        20.98         2.20         7.00        14.27        36.49 
TCGA-K4-A5RI TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-UY-A8OC 
       11.70        52.73        50.56         1.15        12.23         3.02 
TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-YF-AA3M 
      112.83        45.04        97.45        97.12        15.35        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
       22.36        31.20        28.41         3.48 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.49     1.81     1.15 
subtype1 subtype2 subtype3 subtype4 
  163.30   166.03   165.73   112.83 
subtype1 subtype2 subtype3 subtype4 
  16.540   18.115   15.810   21.670 
[1] "0.1 - 163.3 (16.5)" "0.5 - 166.0 (18.1)" "1.8 - 165.7 (15.8)"
[4] "1.1 - 112.8 (21.7)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1       61        65       41
  subtype2       1       37        42       59
  subtype3       0       19        17       23
  subtype4       0       12        16       12
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        1        0        0
  STAGE II        61       37       19       12
  STAGE III       65       42       17       16
  STAGE IV        41       59       23       12
[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 74 27
  subtype2       40 68 21
  subtype3       17 31  6
  subtype4       11 22  4
D1V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       55       40       17       11
  T3             74       68       31       22
  T4             27       21        6        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 117  16  20   2
  subtype2  69  19  34   5
  subtype3  28   6  16   1
  subtype4  21   6   5   1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      117       69       28       21
  N1       16       19        6        6
  N2       20       34       16        5
  N3        2        5        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 92  5
  subtype2 66  4
  subtype3 20  2
  subtype4 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    5
  subtype2   66    4
  subtype3   20    2
  subtype4   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       92       66       20       14
  1        5        4        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  42 127
  subtype2  36 104
  subtype3  17  42
  subtype4  12  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42  127
  subtype2   36  104
  subtype3   17   42
  subtype4   12   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       36       17       12
  MALE        127      104       42       28
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1 151  12
  subtype2 126   3
  subtype3  50   3
  subtype4  37   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151   12
  subtype2  126    3
  subtype3   50    3
  subtype4   37    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       151      126       50       37
  YES       12        3        3        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
D1V10, continuous
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    27                         9   131
  subtype2    11                         8   112
  subtype3     4                         3    51
  subtype4     1                         2    33
D1V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                           27       11        4        1
  BLACK OR AFRICAN AMERICAN        9        8        3        2
  WHITE                          131      112       51       33
[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"
D1V13, binary
          cls
clus         0   1
  subtype1   1 161
  subtype2   6 120
  subtype3   0  55
  subtype4   2  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  161
  subtype2    6  120
  subtype3    0   55
  subtype4    2   33
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        6        0        2
  NOT HISPANIC OR LATINO      161      120       55       33
[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 73 65
  subtype2 74 43
  subtype3 40 30
  subtype4 44 41
subtype1 subtype2 subtype3 subtype4 
     138      117       70       85 
subtype1 subtype2 subtype3 subtype4 
      65       43       30       41 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 
       24.13       108.95        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        36.43        28.41         1.94         2.93        12.56 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 
       12.92        18.48        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 
      142.78        87.32         8.15         8.22        17.72        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6B5 TCGA-DK-AA6R TCGA-DK-AA6S 
       20.81        10.55       163.30        50.70       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P 
       18.81        15.35        56.15         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-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
       17.98         5.52        25.74        14.96        20.91        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N 
       53.88        11.01        19.33         5.69        58.92         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
        6.28        13.35        18.81         6.15        12.69         2.27 
TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3C 
       10.85         8.94        11.08        61.94        48.00         6.94 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 
       17.75         8.94        20.98        11.31         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A40E TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        5.62         8.58         9.01        12.16         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI 
        9.14         9.07        17.72        16.27        15.32        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78P 
       16.67        14.24        12.43        38.99        37.05        78.25 
TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ 
       29.56        97.45       125.49        48.62        79.66         3.22 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       15.98        66.41        34.45        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       28.24        18.90         2.24        66.64        13.74        92.98 
TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-ZF-A9RD 
        2.96        27.06        75.39         3.88         0.66        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA52 
       64.08        58.72        20.22         2.89        60.16        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40         8.52        54.21        19.17        12.23 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA80 
       11.97        94.88         8.35        16.27        17.16         0.62 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A20W 
       47.80         2.50        17.42        40.08         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47X 
       17.16        16.18        20.48         8.98        23.01        12.62 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.10        11.87        18.58         5.19        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41       130.88       112.44        17.95         4.80        13.58 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 
       50.27        66.05        64.18        53.29        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC 
       36.66        19.00        13.64        11.18        12.03        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A8O8 
       15.35        38.83        22.16         0.56        24.03         0.43 
TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BR 
        8.09        60.66        24.30        19.79         7.56        26.73 
TCGA-FD-A5BZ TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EK TCGA-G2-A2EL 
       27.45        31.07        12.66        17.23        15.95        26.93 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD 
       20.12        17.62        66.02        29.36        19.13        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-AATP 
       13.91         7.73         2.20         7.36        10.92        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       19.82        20.28         8.48        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N 
       38.60        64.01        21.24        15.42        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V 
       50.56        35.97        46.98        44.38        15.58        13.48 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PD 
       17.62        22.68        86.83        76.01       112.83        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SP 
        6.21         3.85        97.12        15.35         1.87        14.93 
TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMX 
       26.27        10.82       110.60        11.31         7.63         6.77 
TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       98.99        18.15        18.84        22.36        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA51 
       88.87        19.69        56.35 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA89 TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
      104.65        29.65         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        12.79        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        15.12 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IT 
       29.79         1.84        16.70        15.62        46.68        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-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
        0.66        26.24         4.24        24.66         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A5C0 
       12.95        15.32        23.41        46.78        27.35        18.08 
TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EC TCGA-G2-AA3D TCGA-GC-A3OO 
       62.86         3.06        10.65        22.88        70.32        15.81 
TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JW TCGA-K4-A3WS TCGA-KQ-A41S 
        2.10        18.97         4.73        21.34        25.02         1.15 
TCGA-S5-A6DX TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9ST 
        1.84         3.91        51.32        17.88        64.80         4.21 
TCGA-XF-A9SU TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-YC-A8S6 
        5.98        54.90        91.73        44.32        56.48         9.63 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RM TCGA-ZF-AA4R 
       31.20        35.84        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        50.04        41.75        66.54         6.74 
TCGA-BT-A20N TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A3MF 
       26.14         4.67        17.56        28.70        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A8HX TCGA-DK-A1A5 
       12.13        13.08        12.16        12.66        11.34         2.14 
TCGA-DK-A1AA TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA77 
       19.00        17.98        38.24        52.01        13.58        20.32 
TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A677 TCGA-FD-A3N5 TCGA-FD-A3N6 
       29.72         2.24        25.58        26.96        22.52        27.98 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O 
       29.16        12.85         3.62         5.36         8.25         7.10 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A2ES 
       12.36         4.31         9.67         3.25        59.31        33.01 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW 
        7.23        21.40        20.71        15.91        24.92         0.49 
TCGA-GD-A3OQ TCGA-GU-A763 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
        3.12        32.78        10.65         7.00        14.27        19.10 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ 
       36.49        27.35        19.07        27.68        11.70         1.81 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A8HB TCGA-XF-A8HC 
       21.07        16.54        69.34         3.02        45.04         6.58 
TCGA-XF-A9SV TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMQ TCGA-XF-AAMW TCGA-XF-AAN1 
       12.76        16.27         2.10        71.57         8.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       61.45        86.30        11.97        13.64        25.41        21.11 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       21.86        28.41         3.48         8.61        59.38        63.02 
TCGA-ZF-AA5N 
        5.52 

subtype1 subtype2 subtype3 subtype4 
    0.66     0.43     0.10     0.49 
subtype1 subtype2 subtype3 subtype4 
  166.03   130.88   104.65    86.30 
subtype1 subtype2 subtype3 subtype4 
   15.78    18.84    15.47    16.83 
[1] "0.7 - 166.0 (15.8)" "0.4 - 130.9 (18.8)" "0.1 - 104.7 (15.5)"
[4] "0.5 - 86.3 (16.8)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       30        65       44
  subtype2       1       39        34       41
  subtype3       1       26        18       26
  subtype4       0       36        24       25
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        1        0
  STAGE II        30       39       26       36
  STAGE III       65       34       18       24
  STAGE IV        44       41       26       25
[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 82 21
  subtype2       38 51 13
  subtype3       25 28 13
  subtype4       34 35 12
D2V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       27       38       25       34
  T3             82       51       28       35
  T4             21       13       13       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 83 16 24  4
  subtype2 62 16 21  3
  subtype3 39  4 20  1
  subtype4 54 11 11  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       83       62       39       54
  N1       16       16        4       11
  N2       24       21       20       11
  N3        4        3        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 54  4
  subtype2 58  3
  subtype3 46  2
  subtype4 38  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54    4
  subtype2   58    3
  subtype3   46    2
  subtype4   38    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       54       58       46       38
  1        4        3        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 99
  subtype2 34 83
  subtype3 13 58
  subtype4 21 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   99
  subtype2   34   83
  subtype3   13   58
  subtype4   21   64
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       34       13       21
  MALE         99       83       58       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, binary
          cls
clus         0   1
  subtype1 126   5
  subtype2 106   2
  subtype3  60   5
  subtype4  74   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  126    5
  subtype2  106    2
  subtype3   60    5
  subtype4   74    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       126      106       60       74
  YES        5        2        5        7
[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"
D2V9, continuous
D2V10, continuous
D2V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         8   121
  subtype2    11                         7    93
  subtype3    18                         2    49
  subtype4    10                         6    64
D2V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            5       11       18       10
  BLACK OR AFRICAN AMERICAN        8        7        2        6
  WHITE                          121       93       49       64
[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"
D2V13, binary
          cls
clus         0   1
  subtype1   2 127
  subtype2   2 103
  subtype3   0  67
  subtype4   5  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  127
  subtype2    2  103
  subtype3    0   67
  subtype4    5   74
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        0        5
  NOT HISPANIC OR LATINO      127      103       67       74
[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 55 68
  subtype2 79 36
  subtype3 53 51
subtype1 subtype2 subtype3 
     123      115      104 
subtype1 subtype2 subtype3 
      68       36       51 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20R 
       24.13       104.65        16.77         7.33         6.58         5.06 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.35        20.48         9.96        17.56         8.98         1.94 
TCGA-CU-A0YN TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A3IK 
       12.92        21.86       112.44        17.62        46.68         4.80 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.15        17.72        21.30         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA76 
      163.30        38.24        52.01        15.02       166.03        12.03 
TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       38.83        24.03        14.07        32.02        16.77        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        12.62        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S 
        5.52        25.74        46.78        19.79        12.85        14.96 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 
       15.58        53.88        11.01         5.69        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK 
        2.70        13.35        18.81        12.69         2.27        10.85 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       31.07        11.08        22.88        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A766 
       26.93         7.23         6.94         2.10        20.98         5.62 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WS 
       14.27        21.34        20.28         8.58         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A83P TCGA-KQ-A41S TCGA-LC-A66R 
        3.45        21.24         2.76        16.27         1.15        15.32 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HE TCGA-XF-A8HH 
       12.23        14.24        76.01       112.83       125.49         1.87 
TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       79.66        15.98        66.41        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T6 
       11.90        23.64        21.04        28.24        26.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMY 
       13.74        92.98        10.82        54.90         2.96        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       56.48        27.06        75.39         3.88         9.63         0.66 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W 
       13.64        22.36        58.72         2.89        19.69        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5P 
       35.41        54.21        12.23 

$subtype2
TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       94.88        16.27        16.83        17.16        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BT-A0YX TCGA-BT-A20Q 
        0.62        66.54        29.65        40.08        13.15        19.50 
TCGA-BT-A2LB TCGA-BT-A42C TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       16.18        28.70         2.93        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX 
       12.46        12.10        12.26        13.12        12.00        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A5 
       11.34        11.87        18.58        13.08         5.19         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A6AW 
       19.00        16.70        15.62        17.95        13.58        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA75 TCGA-DK-AA77 
       76.60        67.36        15.68        36.66        11.18        20.32 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A3B5 
       26.24        24.66        13.68        15.32         0.43         8.94 
TCGA-FD-A3NA TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BZ TCGA-FD-A6TA TCGA-FD-A6TI 
       60.66         7.56         3.62        27.45        62.86         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       12.66        10.65        17.23        20.12        17.62        66.02 
TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42R 
       21.40         7.73         3.12         2.20         7.36        18.97 
TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       32.78         7.00         8.48        27.35        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       19.40        64.01        15.42        11.80        52.73        50.56 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 
       44.38        15.58        21.07        13.48         1.84        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC 
       17.62        37.05        22.68        17.82        45.04         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9T4 TCGA-XF-A9T5 
       97.12        15.35        17.88        64.80        16.27        66.64 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-YC-A89H TCGA-ZF-A9R9 
        7.63        71.57         6.77        44.32        18.84        28.41 
TCGA-ZF-A9RM 
       47.84 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA86 
      108.95        27.62        41.75        51.16        15.12        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N 
       47.80         2.50         2.66         6.74        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        14.89        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0F7 TCGA-CF-A1HS 
       17.16         4.67        12.82        36.43         2.04        12.56 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AC 
       18.48        29.79         1.84        13.58        66.41       130.88 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X1 
       16.14         7.79       142.78         8.22        23.21        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E5-A2PC 
       17.98        50.70        13.58       165.73        56.15        43.59 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A85H 
       29.72        25.58         4.24         0.92         1.22        12.95 
TCGA-E7-A97P TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV 
       14.37        22.52        27.98        20.91        26.73         5.36 
TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-G2-A2EO TCGA-G2-A2ES 
        7.10        12.36         3.06         4.31        59.31        33.01 
TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATO 
       20.71        17.75        24.92         7.63        20.05        10.65 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5NE 
       32.98        19.82        36.49        22.72        38.60        12.16 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70        17.72         1.81 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A8HD 
       35.97        46.98        86.83        69.34         3.02        97.45 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-AAMG 
       48.62         3.22        34.45        18.90         2.24       110.60 
TCGA-XF-AAMH TCGA-XF-AAMW TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-ZF-A9R1 
       11.31         8.32        61.45        86.30        18.15        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 
       21.11        13.41        20.22        59.38        56.35        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 
       19.40         8.52 

subtype1 subtype2 subtype3 
    0.66     0.10     0.92 
subtype1 subtype2 subtype3 
  166.03    97.12   165.73 
subtype1 subtype2 subtype3 
   16.77    16.27    18.97 
[1] "0.7 - 166.0 (16.8)" "0.1 - 97.1 (16.3)"  "0.9 - 165.7 (19.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       30        48       45
  subtype2       2       53        31       29
  subtype3       0       22        40       42
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        2        0
  STAGE II        30       53       22
  STAGE III       48       31       40
  STAGE IV        45       29       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       20 73 17
  subtype2       52 39 11
  subtype3       28 57 20
D3V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       20       52       28
  T3             73       39       57
  T4             17       11       20
[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 66 13 30  1
  subtype2 79 11 14  1
  subtype3 55 15 22  6
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       66       79       55
  N1       13       11       15
  N2       30       14       22
  N3        1        1        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 41  6
  subtype2 72  2
  subtype3 50  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    6
  subtype2   72    2
  subtype3   50    2
   clus
vv  subtype1 subtype2 subtype3
  0       41       72       50
  1        6        2        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 38 85
  subtype2 27 89
  subtype3 20 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   85
  subtype2   27   89
  subtype3   20   85
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       27       20
  MALE         85       89       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1 109   4
  subtype2  98   8
  subtype3  99   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109    4
  subtype2   98    8
  subtype3   99    1
     clus
vv    subtype1 subtype2 subtype3
  NO       109       98       99
  YES        4        8        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, continuous
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         6   106
  subtype2    32                         8    71
  subtype3     3                         6    91
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5       32        3
  BLACK OR AFRICAN AMERICAN        6        8        6
  WHITE                          106       71       91
[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"
D3V13, binary
          cls
clus         0   1
  subtype1   4 112
  subtype2   1 103
  subtype3   3  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  112
  subtype2    1  103
  subtype3    3   90
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        3
  NOT HISPANIC OR LATINO      112      103       90
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 38 52
  subtype2 83 38
  subtype3 47 52
  subtype4 19 13
subtype1 subtype2 subtype3 subtype4 
      90      121       99       32 
subtype1 subtype2 subtype3 subtype4 
      52       38       52       13 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A20R 
       24.13       104.65        16.77         7.33         2.66         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.35        16.18        20.48        17.56         8.98         1.94 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF 
        1.84        21.86        19.00        16.70       112.44        17.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WY 
       46.68         7.79        13.58        17.72        21.30       163.30 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       52.01       166.03        24.03        32.02        16.77        33.04 
TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR 
       12.62        24.30        23.41         5.52        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.85        14.96        15.58        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
        2.70        13.35        62.86        18.81        12.69         3.06 
TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EK TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B 
       10.85        11.08        15.95         7.73         2.10         7.36 
TCGA-GU-A763 TCGA-GV-A3JV TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       32.78        14.27         9.01        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78O 
        2.76        16.27         1.15        12.23        14.24        76.01 
TCGA-UY-A8OD TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST 
      112.83        15.35         1.87        66.41        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT 
       12.76        23.64         2.10        10.82        54.90         2.96 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A8S6 TCGA-YF-AA3M 
       98.99        44.32        56.48        27.06         9.63        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA4T TCGA-ZF-AA52 TCGA-ZF-AA5P 
       22.36        28.41        58.72        19.69        35.41        12.23 

$subtype2
TCGA-2F-A9KQ TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       94.88        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 
       66.54        15.12        47.80        29.65         2.50        40.08 
TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A3PH TCGA-BT-A42C 
       26.14        17.88        19.50        14.89         4.67        28.70 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.16        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL 
       13.12        12.00        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
       13.08         5.19        29.79        13.58         2.14        66.41 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       15.62        17.95        66.05        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 
       67.36        36.66        11.18        20.32        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         2.24        16.70        25.58         0.56         0.66 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 
       26.24        24.66         0.92        13.68        12.95        15.32 
TCGA-E7-A8O8 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV 
        0.43        60.66        17.98         7.56         3.62         5.36 
TCGA-FD-A62O TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EO 
        7.10         9.67        31.07        12.66        17.23        59.31 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GD-A3OQ TCGA-GD-A6C6 
       20.12        17.62        66.02        21.40         3.12         2.20 
TCGA-GU-A42R TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
       18.97        32.98        19.82         8.48        27.35        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-K4-AAQO 
       22.72         1.51        38.60        64.01        15.42        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       52.73        50.56        46.98        44.38        15.58        21.07 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
       13.48         1.84        16.54        17.62        22.68        86.83 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH 
       17.82        45.04         6.58        97.12        17.88        64.80 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9RM 
        7.63        71.57         6.77        25.41        21.11        47.84 
TCGA-ZF-AA51 
       56.35 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
      108.95        16.27        27.62        41.75        51.16        10.22 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20U 
        6.74         6.58        13.15        19.04        12.16        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0F1 
        5.06         8.25        17.16        12.82        36.43         2.93 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2I4 
        2.04        12.56        18.48       130.88        16.14       142.78 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6B2 TCGA-DK-A6B5 
        4.80         8.22        23.21         9.67        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E7-A677 TCGA-E7-A6MD 
       38.24        13.58       165.73        56.15        26.96         4.24 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 
        1.22        14.07        14.37         8.94         4.01        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.98        29.16        20.91        26.73        53.88        11.01 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-AA3C 
       12.36         2.27         4.31        26.93        33.01         6.94 
TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATO 
       20.71        17.75        24.92         7.63        20.05        10.65 
TCGA-GU-AATQ TCGA-GV-A3QI TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        7.00        36.49        12.16         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41P TCGA-UY-A78L TCGA-UY-A8OB 
       11.70        17.72         1.81        35.97        37.05        69.34 
TCGA-UY-A8OC TCGA-XF-A8HD TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        3.02        97.45        48.62        79.66         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       34.45        11.90        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMW TCGA-XF-AAN2 TCGA-XF-AAN3 
       66.64       110.60        11.31         8.32        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       18.15         3.88        13.41        20.22         2.89        59.38 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       57.90        19.40         8.52 

$subtype4
TCGA-BT-A3PK TCGA-CU-A0YN TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6P 
        9.96        12.92         8.15        20.81        10.55        15.02 
TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-FD-A3SP TCGA-FD-A5BX TCGA-FJ-A3ZE TCGA-G2-A2EC 
       12.03        38.83        25.74         5.69        10.65        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-GD-A3OS TCGA-GU-A766 TCGA-GV-A3JW 
       61.94        48.00         7.23        20.98         5.62        21.34 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-H4-A2HQ TCGA-LC-A66R TCGA-XF-A8HE TCGA-XF-A9SY 
       20.28         8.58        19.40        15.32       125.49        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       26.27        13.74        92.98        75.39        18.84         0.66 
TCGA-ZF-AA4W TCGA-ZF-AA58 
       60.16        54.21 

subtype1 subtype2 subtype3 subtype4 
    1.15     0.10     1.22     0.66 
subtype1 subtype2 subtype3 subtype4 
  166.03    97.12   165.73   125.49 
subtype1 subtype2 subtype3 subtype4 
  16.735   17.620   16.270   19.840 
[1] "1.1 - 166.0 (16.7)" "0.1 - 97.1 (17.6)"  "1.2 - 165.7 (16.3)"
[4] "0.7 - 125.5 (19.8)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       14        36       40
  subtype2       2       55        34       29
  subtype3       0       22        39       39
  subtype4       0       14        10        8
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        2        0        0
  STAGE II        14       55       22       14
  STAGE III       36       34       39       10
  STAGE IV        40       29       39        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       15 56 18
  subtype2       58 40 14
  subtype3       22 59 15
  subtype4        5 14  1
D4V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       15       58       22        5
  T3             56       40       59       14
  T4             18       14       15        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 44 10 28  2
  subtype2 82 10 17  1
  subtype3 55 18 17  4
  subtype4 19  1  4  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       44       82       55       19
  N1       10       10       18        1
  N2       28       17       17        4
  N3        2        1        4        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"
D4V6, binary
          cls
clus        0  1
  subtype1 34  3
  subtype2 77  2
  subtype3 42  2
  subtype4 10  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    3
  subtype2   77    2
  subtype3   42    2
  subtype4   10    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       34       77       42       10
  1        3        2        2        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1  33  57
  subtype2  22 100
  subtype3  18  82
  subtype4  12  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   57
  subtype2   22  100
  subtype3   18   82
  subtype4   12   20
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       33       22       18       12
  MALE         57      100       82       20
[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, binary
          cls
clus         0   1
  subtype1  79   2
  subtype2 108   7
  subtype3  92   1
  subtype4  27   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79    2
  subtype2  108    7
  subtype3   92    1
  subtype4   27    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        79      108       92       27
  YES        2        7        1        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, continuous
D4V10, continuous
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    79
  subtype2    32                         7    77
  subtype3     5                         7    84
  subtype4     0                         3    28
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3       32        5        0
  BLACK OR AFRICAN AMERICAN        3        7        7        3
  WHITE                           79       77       84       28
[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"
D4V13, binary
          cls
clus         0   1
  subtype1   3  80
  subtype2   1 106
  subtype3   4  87
  subtype4   0  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   80
  subtype2    1  106
  subtype3    4   87
  subtype4    0   32
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        4        0
  NOT HISPANIC OR LATINO       80      106       87       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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  52  63
  subtype2 126  55
  subtype3  51  59
subtype1 subtype2 subtype3 
     115      181      110 
subtype1 subtype2 subtype3 
      63       55       59 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13I 
       24.13         8.35        44.94        10.22         2.50         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74        12.39         6.58        19.04        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-C4-A0EZ 
       19.50         5.06        17.16        16.18        20.48         8.98 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
       21.86         2.14       130.88        17.62        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY 
      142.78         8.22        17.72        21.30        23.21       163.30 
TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA74 TCGA-E7-A6MD TCGA-E7-A7DV 
       15.68       166.03        18.81        56.15         4.24         1.22 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
        4.01        12.62        23.41        17.98        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR 
       46.78        19.79        27.35        14.96        20.91        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       53.88        11.01         5.69        27.45        18.08         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
        6.28        13.35        18.81         6.15         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-AA3C 
        4.31        10.85         8.94        11.08        59.31         6.94 
TCGA-GC-A3OO TCGA-GD-A3OS TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATO TCGA-K4-A3WS 
       15.81        20.98         7.63        20.05        10.65        25.02 
TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO 
        3.45        27.68         9.07        17.72        16.27        11.80 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A8OD TCGA-UY-A9PB 
       14.24        12.43        38.99        17.62       112.83        29.56 
TCGA-XF-A8HD TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP 
       97.45        79.66         3.22        15.98        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21         5.98        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        18.15         3.88         0.66        28.41        94.29 
TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       64.08        34.06        35.41        19.40        54.21        19.17 
TCGA-ZF-AA5P 
       12.23 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       11.97        94.88        16.27        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM 
       50.04         0.62        66.54        47.80        29.65        17.42 
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F6 
       40.08        17.88         8.35         4.67        28.70        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        13.97        12.59        12.13        13.08        12.16 
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-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08         4.90        15.12         5.19        29.79 
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 
        4.80        13.58        50.27         9.67        66.05        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U 
       53.29        76.60        67.36        36.66        15.02        19.00 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 
       15.35        13.64        11.18        12.03        20.32        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24        24.03        24.66         0.92 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-E7-A97Q TCGA-FD-A3NA 
       13.68        12.95        15.32         0.43         8.09        60.66 
TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TA 
       24.30         7.56         3.62         5.36         7.10        62.86 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       12.36         9.67        31.07        12.66        10.65        17.23 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25        22.88        15.95        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW 
       70.32        29.36        21.40        19.13        14.07         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10         2.20         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97        32.78         4.73        32.98        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        36.49        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60        64.01 
TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       15.42        52.73        50.56        35.97        46.98        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 
        1.15        15.58        21.07        13.48         1.84        16.54 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       22.68        86.83        76.01        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       51.32         6.58        97.12        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ 
       64.80        12.76        26.27       110.60         7.63        71.57 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YC-A8S6 TCGA-YF-AA3L 
        6.77        98.99        44.32        30.94         9.63        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       21.86        88.87        47.84        19.69         8.61        63.02 
TCGA-ZF-AA51 
       56.35 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
      104.65       108.95        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        26.14        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        36.43        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        12.56        12.92        18.48        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         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q 
       10.55        17.98        50.70        38.24        52.01        13.58 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A7XN 
      165.73        13.64        43.59        15.35        29.72        14.07 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        33.04        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY 
       27.98         5.52        12.85        15.58        19.33         8.25 
TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES 
       58.92        12.69        61.94        48.00        26.93        33.01 
TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        7.23        20.71        15.91        17.75        24.92         8.94 
TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A40E TCGA-HQ-A5ND 
        3.12        11.31         5.62         7.00         8.58         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6FZ 
       12.16        21.24         2.76         9.14        11.70         1.81 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB 
       15.32        12.23        16.67        37.05        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9T4 
        3.02         3.91        45.04       125.49        34.45        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAMW 
       66.64         2.10        13.74        11.31         2.96         8.32 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9RD 
       61.45        86.30        75.39        18.84        13.64        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 
        3.48        20.22         2.89        59.38        60.16        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5N 
        8.52         5.52 

subtype1 subtype2 subtype3 
    0.66     0.10     1.81 
subtype1 subtype2 subtype3 
  166.03   112.44   165.73 
subtype1 subtype2 subtype3 
  17.950   17.420   15.465 
[1] "0.7 - 166.0 (17.9)" "0.1 - 112.4 (17.4)" "1.8 - 165.7 (15.5)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       18        49       49
  subtype2       2       79        50       49
  subtype3       0       33        41       36
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        2        0
  STAGE II        18       79       33
  STAGE III       49       50       41
  STAGE IV        49       49       36
[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 77 18
  subtype2       75 63 24
  subtype3       31 54 16
D5V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       17       75       31
  T3             77       63       54
  T4             18       24       16
[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  61  16  30   2
  subtype2 112  11  32   4
  subtype3  63  19  13   3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       61      112       63
  N1       16       11       19
  N2       30       32       13
  N3        2        4        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  39   5
  subtype2 109   4
  subtype3  48   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    5
  subtype2  109    4
  subtype3   48    2
   clus
vv  subtype1 subtype2 subtype3
  0       39      109       48
  1        5        4        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  29  87
  subtype2  41 141
  subtype3  37  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   87
  subtype2   41  141
  subtype3   37   73
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       29       41       37
  MALE         87      141       73
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1 102   5
  subtype2 160  11
  subtype3 100   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102    5
  subtype2  160   11
  subtype3  100    3
     clus
vv    subtype1 subtype2 subtype3
  NO       102      160      100
  YES        5       11        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
D5V10, continuous
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         5   107
  subtype2    38                        10   127
  subtype3     3                         8    90
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3       38        3
  BLACK OR AFRICAN AMERICAN        5       10        8
  WHITE                          107      127       90
[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"
D5V13, binary
          cls
clus         0   1
  subtype1   2 110
  subtype2   2 164
  subtype3   4  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  110
  subtype2    2  164
  subtype3    4   94
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        4
  NOT HISPANIC OR LATINO      110      164       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 59 59
  subtype2 85 27
  subtype3 85 91
subtype1 subtype2 subtype3 
     118      112      176 
subtype1 subtype2 subtype3 
      59       27       91 
$subtype1
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       24.13         8.35        16.27        44.94        16.83        17.16 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20Q 
       47.80         2.50        17.42         2.66        26.14        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F6 
        5.06        14.89         8.35        16.18         4.67        23.01 
TCGA-CF-A1HR TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.79        18.58         4.90        15.12        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
       66.41        18.41       130.88       112.44        17.62        46.68 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 
       17.95         4.80        13.58        17.72        21.30        66.05 
TCGA-DK-A6B2 TCGA-DK-AA6T TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3NA 
       15.68        18.81         4.24        12.95         8.09        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       24.30        23.41        17.98        46.78        19.79         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 
       27.35        14.96        20.91        26.73        27.45        18.08 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2EC 
       62.86         6.15         3.06         9.67        31.07        22.88 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.95        59.31        15.81        14.07        13.91         7.73 
TCGA-GD-A3OP TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JZ TCGA-K4-A3WS 
        2.10         4.73        10.65        32.98        19.82        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        3.45         2.76        27.68        15.42        16.27        11.80 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       35.97        46.98         1.15        14.24         1.84        12.43 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       17.62        22.68        86.83       112.83        17.82         6.21 
TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL 
       51.32        97.12         1.87        64.80        15.98        66.41 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 
       14.93         5.98        12.76        11.90        28.24        26.27 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
      110.60        54.90        91.73         6.77        98.99        44.32 
TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-AA4R 
       18.84        22.36        25.41        28.41        94.29        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5P 
       19.69        56.35        35.41        12.23 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 
       11.97        94.88        34.98        50.04         0.62        66.54 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A3MF 
       29.65        40.08        17.88        28.70        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        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-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6AW 
        1.84        19.00        15.62        50.27        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA71 
       76.60        67.36        36.66        15.02        19.00        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       11.18        12.03        20.32        38.83         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A43X 
       24.03         0.92        13.68        15.32         0.43         3.62 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3IE 
        5.36         7.10        12.66        10.65        17.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB 
       17.62        66.02        70.32        29.36        21.40        19.13 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JV 
        2.20         7.36        10.92        18.97        32.78        14.27 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       21.34        20.28         8.48        36.49        27.35        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-KQ-A41N TCGA-KQ-A41O 
       22.72         1.51        19.40        38.60        52.73        50.56 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78O 
       44.38        15.58        21.07        13.48        16.54        76.01 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-AAML TCGA-XF-AAN1 
        3.85         6.58        15.35        17.88         7.63        30.94 
TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        9.63        11.97        21.11        31.20        30.28        35.84 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4X 
       88.87        47.84         8.61        63.02 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
      104.65       108.95        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        36.43        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        12.56        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.48        13.58        16.70        16.14         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       87.32         8.15         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-AA6M 
       10.55       163.30        17.98        50.70        38.24        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 
       13.58       165.73       166.03        13.64        15.35        56.15 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A6MF TCGA-E7-A7DV 
       43.59        15.35        29.72        25.58        24.66         1.22 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.07        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SO 
        4.01        12.62        22.52        27.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       25.74        12.85        15.58        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        5.69         8.25        58.92         2.70         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK 
       18.81        12.69        12.36         2.27         4.31        10.85 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        8.94         3.25        11.08        61.94        48.00        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC 
       33.01         7.23         6.94        20.71        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
       24.92         0.49         8.94         3.12        20.98        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A40E 
        7.63        20.05         5.62         7.00        19.10         8.58 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH 
       64.01         9.01        12.16        21.24         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.70        17.72         1.81        15.32        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       38.99        37.05        78.25        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SI TCGA-XF-A9SJ 
       29.56        45.04        97.45       125.49        79.66         3.22 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
       34.45         4.21        23.64        21.04        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       16.27        66.64         2.10        13.74        92.98        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
       71.57         2.96         8.32        56.48        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3M 
       27.06        75.39        18.15         3.88         0.66        13.64 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        13.41         3.48        64.08        20.22         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        60.16        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.17         5.52 

subtype1 subtype2 subtype3 
    1.15     0.10     0.49 
subtype1 subtype2 subtype3 
  130.88    94.88   166.03 
subtype1 subtype2 subtype3 
  18.030   16.620   15.745 
[1] "1.1 - 130.9 (18.0)" "0.1 - 94.9 (16.6)"  "0.5 - 166.0 (15.7)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       17        40       62
  subtype2       2       65        27       17
  subtype3       0       48        73       55
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        2        0
  STAGE II        17       65       48
  STAGE III       40       27       73
  STAGE IV        62       17       55
[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 68 25
  subtype2       59 29 10
  subtype3       43 97 23
D6V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       21       59       43
  T3             68       29       97
  T4             25       10       23
[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  52  17  40   4
  subtype2  80   5  10   1
  subtype3 104  24  25   4
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       52       80      104
  N1       17        5       24
  N2       40       10       25
  N3        4        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 49  4
  subtype2 78  2
  subtype3 69  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    4
  subtype2   78    2
  subtype3   69    5
   clus
vv  subtype1 subtype2 subtype3
  0       49       78       69
  1        4        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  31  88
  subtype2  19  94
  subtype3  57 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   88
  subtype2   19   94
  subtype3   57  119
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       31       19       57
  MALE         88       94      119
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1 104   3
  subtype2 100  11
  subtype3 158   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104    3
  subtype2  100   11
  subtype3  158    5
     clus
vv    subtype1 subtype2 subtype3
  NO       104      100      158
  YES        3       11        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"
D6V9, continuous
D6V10, continuous
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         8   103
  subtype2    32                         4    72
  subtype3     6                        11   149
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6       32        6
  BLACK OR AFRICAN AMERICAN        8        4       11
  WHITE                          103       72      149
[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"
D6V13, binary
          cls
clus         0   1
  subtype1   1 107
  subtype2   1 105
  subtype3   6 156
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  107
  subtype2    1  105
  subtype3    6  156
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        6
  NOT HISPANIC OR LATINO      107      105      156
[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  59  62
  subtype2  57  39
  subtype3 114  76
subtype1 subtype2 subtype3 
     121       96      190 
subtype1 subtype2 subtype3 
      62       39       76 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BT-A0S7 
       24.13        44.94        16.77        10.22         2.50         6.58 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       19.04        12.16        19.50         5.06        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-C4-A0F0 TCGA-CF-A1HR 
        8.25        17.16        16.18        17.56         1.94        12.79 
TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AB TCGA-DK-A1AE 
       12.56         4.90        13.58        21.86        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IU 
       17.62        46.68       142.78        13.58        17.72        23.21 
TCGA-DK-A3WY TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X 
      163.30        38.24        13.58       166.03        18.81        15.35 
TCGA-DK-AA74 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 
       56.15         4.24        24.03        14.07        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ 
       16.77        12.62        24.30        23.41        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       19.79        14.96        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69         8.25         2.70         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P 
       18.81         2.27         3.06        10.85         8.94        11.08 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 
       22.88        15.95        15.81        17.75        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 
        2.10        20.98         7.36         7.63        20.05         4.73 
TCGA-GU-AATQ TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A83P TCGA-K4-AAQO 
        7.00         9.14         9.07        11.70        16.27        11.80 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78L TCGA-UY-A8OD TCGA-UY-A9PB 
       35.97        14.24        12.43        37.05       112.83        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SP 
        6.21         3.85         1.87        79.66        66.41        14.93 
TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T8 
        5.98        11.90        23.64        21.04         2.24        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN3 
       92.98        10.82        91.73         2.96        56.48        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9RC 
       27.06        75.39         3.88         9.63        25.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       13.41        60.16        35.41        57.90        19.40        54.21 
TCGA-ZF-AA5P 
       12.23 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       11.97        94.88         8.35        27.62        50.04        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        15.12        17.42        40.08         7.33         2.66 
TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F1 
       13.15         8.35        20.48         9.96        28.70         2.93 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47S TCGA-CF-A9FF TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.59        12.13        10.95        11.87        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 
        5.19         1.84         2.14       130.88        17.95        87.32 
TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A677 
        4.80        21.30        64.18        67.36        15.68        26.96 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SS 
       24.66         1.22         8.09         4.01        29.16        12.85 
TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA 
        7.56        27.45        18.08        58.92         7.10        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.69         4.31         9.67        31.07        17.23 
TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
       17.62        24.92        10.92         5.62        10.65        32.98 
TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       14.27        20.28        19.07         1.51        19.40        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41R 
       25.02         3.45         2.76        15.42        52.73        44.38 
TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB 
       15.32        13.48         1.84        38.99        76.01        69.34 
TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SZ TCGA-XF-A9T0 
       17.82         6.58         3.22        15.98        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        22.36        21.86        28.41        56.35         5.52 

$subtype3
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65       108.95        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        29.65         6.74        26.14 
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        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI 
        8.98        23.01         2.04        13.97        13.08        12.16 
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-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD 
       12.92        29.79        66.41        18.41        19.00       112.44 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV 
       15.62         7.79         8.15         8.22        50.27         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55        66.05        17.98        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6U 
       50.70        36.66        52.01        15.02       165.73        19.00 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        13.64        11.18        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DU 
       16.70        25.58         0.56         0.66        26.24         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        12.66        10.65 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        61.94        48.00        26.93        59.31        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        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        19.13        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        18.97        32.78        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        36.49        27.35         8.58 
TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A54R 
       22.72        64.01         9.01        12.16        21.24        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A5Z6 
       17.72         1.81        50.56        46.98         1.15        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M 
       21.07        12.23        16.67        16.54        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HB 
       86.83        78.25         3.02         3.91        51.32        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45       125.49        97.12        15.35        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       64.80        34.45        12.76        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMW TCGA-XF-AAN1 
        2.10       110.60         7.63        71.57         8.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       61.45        18.15        18.84         0.66        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       30.28        35.84         3.48        64.08        58.72        88.87 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
       59.38        63.02         8.52        19.17 

subtype1 subtype2 subtype3 
    1.87     1.22     0.10 
subtype1 subtype2 subtype3 
  166.03   130.88   165.73 
subtype1 subtype2 subtype3 
  15.810   16.605   18.710 
[1] "1.9 - 166.0 (15.8)" "1.2 - 130.9 (16.6)" "0.1 - 165.7 (18.7)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       23        47       51
  subtype2       1       24        31       40
  subtype3       1       84        61       44
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          0        1        1
  STAGE II        23       24       84
  STAGE III       47       31       61
  STAGE IV        51       40       44
[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 79 15
  subtype2       29 47 16
  subtype3       74 68 27
D7V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       21       29       74
  T3             79       47       68
  T4             15       16       27
[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  61  15  35   1
  subtype2  49  14  21   4
  subtype3 126  17  20   4
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       61       49      126
  N1       15       14       17
  N2       35       21       20
  N3        1        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  44   3
  subtype2  41   3
  subtype3 110   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    3
  subtype2   41    3
  subtype3  110    5
   clus
vv  subtype1 subtype2 subtype3
  0       44       41      110
  1        3        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  40  81
  subtype2  20  77
  subtype3  47 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   81
  subtype2   20   77
  subtype3   47  144
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       20       47
  MALE         81       77      144
[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, binary
          cls
clus         0   1
  subtype1 105   4
  subtype2  92   3
  subtype3 166  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105    4
  subtype2   92    3
  subtype3  166   12
     clus
vv    subtype1 subtype2 subtype3
  NO       105       92      166
  YES        4        3       12
[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"
D7V9, continuous
D7V10, continuous
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         7   106
  subtype2    10                         5    78
  subtype3    27                        11   140
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            7       10       27
  BLACK OR AFRICAN AMERICAN        7        5       11
  WHITE                          106       78      140
[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"
D7V13, binary
          cls
clus         0   1
  subtype1   1 116
  subtype2   4  85
  subtype3   4 167
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  116
  subtype2    4   85
  subtype3    4  167
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        4
  NOT HISPANIC OR LATINO      116       85      167
[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 41 48
  subtype2 56 43
  subtype3 60 34
  subtype4 43 28
  subtype5 30 24
subtype1 subtype2 subtype3 subtype4 subtype5 
      89       99       94       71       54 
subtype1 subtype2 subtype3 subtype4 subtype5 
      48       43       34       28       24 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20J 
       24.13        16.77        41.75         2.50         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA 
       12.16        19.50        14.89        14.96         5.06        17.16 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3KJ 
       12.82        17.56        28.41         1.94        12.56        18.48 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3WW 
       16.70        16.14         7.79         8.15         8.22        20.81 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       10.55        17.98        38.24        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A97P 
       18.81        43.59        15.35        24.66        14.07        14.37 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A5BS 
        8.94        33.04        22.52        27.98        20.91        53.88 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO 
        5.69         8.25         8.94        61.94        48.00        59.31 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-HQ-A2OF TCGA-HQ-A5ND 
       33.01        20.71        20.98        11.31        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.14         9.07        17.72         1.81 
TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P 
        1.15        12.23        16.67        17.62        37.05        78.25 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SY 
        3.02         3.91       125.49        48.62        34.45        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN7 
       18.90        66.64        13.74         2.96         8.32        18.15 
TCGA-XF-AAN8 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
        3.88        13.41         3.48        64.08        58.72        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H 
        2.89        60.16        19.40         8.52        19.17 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       11.97        94.88         8.35        27.62        50.04        51.16 
TCGA-4Z-AA86 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX 
       10.22        17.42        40.08         7.33         2.66        13.15 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F1 
        8.35        20.48         9.96        28.70        36.43         2.93 
TCGA-CF-A3MG TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
       12.13        10.95        15.12         5.19         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 
      130.88        87.32         4.80        21.30        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6M TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E7-A677 TCGA-E7-A7DV 
       15.68        52.01        15.35        56.15        26.96         1.22 
TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
        8.09         4.01        29.16         5.52        46.78        12.85 
TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TC 
       11.01        18.08        58.92         2.70         7.10         6.15 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
       12.69         4.31         9.67        31.07        17.23        17.62 
TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A42P TCGA-GU-A762 
       66.02        15.91        24.92         8.94        10.92         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QF 
       20.05         5.62        10.65        32.98        14.27        20.28 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51        19.40        38.60        25.02         3.45 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41R TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX 
        2.76        52.73        44.38        15.32        13.48         1.84 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC 
       38.99        76.01        69.34        29.56        17.82         6.58 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-AAMH TCGA-XF-AAMJ 
        3.22        15.98        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 
       56.35        57.90        54.21 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA83 TCGA-4Z-AA89 
      104.65        44.94        16.83        34.98        66.54        29.65 
TCGA-BT-A20P TCGA-C4-A0F7 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI 
       17.88         2.04        13.97        12.59        13.08        12.16 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IV 
       29.79        66.41        19.00        15.62        17.95         9.67 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF 
       53.29        76.60        29.72         0.10        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-FD-A3NA TCGA-FD-A43P 
       26.24         0.92        13.68        15.32        60.66        27.35 
TCGA-FD-A43X TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        3.62        62.86        12.36        12.66        10.65         3.25 
TCGA-G2-A2EC TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       22.88         7.23        20.12        70.32        29.36        21.40 
TCGA-GC-A3RB TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3QK 
       19.13         3.12        18.97        32.78        21.34        27.35 
TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PE 
       27.68        15.58        21.07        22.68        86.83         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        3.85        51.32        45.04        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAML 
       64.80        12.76        23.64        16.27         2.10         7.63 
TCGA-XF-AAMQ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-ZF-A9R0 
       71.57        56.48        61.45         9.63        11.97        22.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        31.20        30.28        35.84        88.87        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA5N 
        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 
      108.95        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        26.14         8.25         4.67         8.98        23.01 
TCGA-CF-A47X TCGA-CF-A9FL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3X1 
       12.62        18.58        13.58        18.41        50.27        66.05 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       50.70        36.66        15.02        19.00        13.64        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       11.18        12.03        20.32        38.83        22.16         2.24 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A8O8 TCGA-FD-A3SM 
       25.58         0.56        24.03        12.95         0.43        17.98 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S 
        7.56        15.58        26.73         5.36        27.45        13.35 
TCGA-G2-A2EL TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A6C6 TCGA-GU-AATQ 
       26.93        14.07         0.49        13.91         2.20         7.00 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA 
       19.10        19.82         8.48        36.49         8.58        22.72 
TCGA-K4-A5RI TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-S5-AA26 
       11.70        15.42        50.56        35.97        46.98        16.54 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAN1 TCGA-YC-A89H 
       97.45        97.12        26.27       110.60        30.94        18.84 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9RM TCGA-ZF-AA4T 
        0.66        13.64        25.41        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        12.79         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        46.68       142.78        13.58        17.72        23.21 
TCGA-DK-A3WY TCGA-E7-A6MD TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SJ 
      163.30         4.24        32.02        16.77        12.62        24.30 
TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62P 
       23.41        25.74        19.79        14.96        19.33         6.28 
TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EK 
       18.81         2.27         3.06        10.85        11.08        15.95 
TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A767 
       15.81        17.75         7.73         2.10         7.36         4.73 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A8OD TCGA-XF-A9SI 
       16.27        11.80        14.24        12.43       112.83        79.66 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9T3 TCGA-XF-AAME TCGA-XF-AAMF 
       66.41        14.93         5.98         2.24        92.98        10.82 
TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-ZF-A9RC TCGA-ZF-AA52 TCGA-ZF-AA5P 
       91.73        86.30        27.06        94.29        35.41        12.23 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.15     1.22     0.10     0.43     2.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  166.03   130.88   104.65   110.60   163.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.560   17.230   17.880   17.980   16.225 
[1] "1.1 - 166.0 (17.6)" "1.2 - 130.9 (17.2)" "0.1 - 104.7 (17.9)"
[4] "0.4 - 110.6 (18.0)" "2.1 - 163.3 (16.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       22        39       28
  subtype2       1       25        32       41
  subtype3       1       48        22       23
  subtype4       0       26        27       18
  subtype5       0       10        19       25
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        1        0        0
  STAGE II        22       25       48       26       10
  STAGE III       39       32       22       27       19
  STAGE IV        28       41       23       18       25
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       18 51 12
  subtype2       28 49 17
  subtype3       49 25 12
  subtype4       18 35  9
  subtype5       11 34  8
D8V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       18       28       49       18       11
  T3             51       49       25       35       34
  T4             12       17       12        9        8
[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 49 15 11  2
  subtype2 53 14 23  4
  subtype3 59  6 14  1
  subtype4 47  6  8  2
  subtype5 28  5 20  0
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       49       53       59       47       28
  N1       15       14        6        6        5
  N2       11       23       14        8       20
  N3        2        4        1        2        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 39  0
  subtype2 42  1
  subtype3 60  3
  subtype4 36  5
  subtype5 18  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    0
  subtype2   42    1
  subtype3   60    3
  subtype4   36    5
  subtype5   18    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       39       42       60       36       18
  1        0        1        3        5        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 30 59
  subtype2 21 79
  subtype3 20 75
  subtype4 15 56
  subtype5 21 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   59
  subtype2   21   79
  subtype3   20   75
  subtype4   15   56
  subtype5   21   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       21       20       15       21
  MALE         59       79       75       56       33
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 79  4
  subtype2 95  2
  subtype3 78 10
  subtype4 65  3
  subtype5 46  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79    4
  subtype2   95    2
  subtype3   78   10
  subtype4   65    3
  subtype5   46    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        79       95       78       65       46
  YES        4        2       10        3        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
D8V10, continuous
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         4    76
  subtype2     8                         6    84
  subtype3    22                         5    64
  subtype4     8                         5    51
  subtype5     2                         3    49
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            4        8       22        8        2
  BLACK OR AFRICAN AMERICAN        4        6        5        5        3
  WHITE                           76       84       64       51       49
[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"
D8V13, binary
          cls
clus        0  1
  subtype1  2 80
  subtype2  2 91
  subtype3  2 85
  subtype4  2 60
  subtype5  1 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    2   91
  subtype3    2   85
  subtype4    2   60
  subtype5    1   52
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        2        2        2        1
  NOT HISPANIC OR LATINO       80       91       85       60       52
[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 55 44
  subtype2 15 27
  subtype3 90 45
  subtype4 61 59
subtype1 subtype2 subtype3 subtype4 
      99       42      135      120 
subtype1 subtype2 subtype3 subtype4 
      44       27       45       59 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       24.13        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        36.43        28.41         1.94         2.93        12.56 
TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       12.92         7.79        87.32         8.15        20.81        10.55 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U 
       50.70        52.01        13.58       165.73        18.81        19.00 
TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.35         1.22        14.07        14.37         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43Y 
       22.52        27.98        60.66         5.52        27.35        15.58 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD 
       53.88        19.33         5.69         8.25        58.92        12.69 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS 
       61.94        48.00        33.01        20.71        15.91        24.92 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A40E TCGA-HQ-A5ND 
        8.94        11.31         7.63         5.62         8.58         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI 
       12.16         9.14         9.07         1.81        15.32        12.23 
TCGA-PQ-A6FN TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       16.67        78.25        69.34         3.02         3.91        29.56 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SX TCGA-XF-A9SY 
       97.45       125.49        48.62        34.45        23.64        21.04 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMW TCGA-XF-AAN2 
       16.27        66.64         2.10        13.74         8.32        61.45 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       75.39        18.84         0.66        13.64        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 
       64.08        58.72         2.89        59.38        60.16        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.52        54.21        19.17 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A0C8 
       11.97        94.88         8.35        51.16        17.42        40.08 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-CU-A0YR TCGA-CU-A5W6 
        2.66        13.15         8.35        20.48        15.12         1.84 
TCGA-DK-A1AC TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-E7-A97Q TCGA-FD-A3SS TCGA-FD-A43N 
      130.88        64.18        15.68         8.09        12.85         7.56 
TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GU-AATO 
       18.08         7.10         4.31        31.07        10.92        10.65 
TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU 
       14.27        20.28        19.07         1.51        38.60         3.45 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-S5-A6DX TCGA-UY-A9PD TCGA-XF-A9SJ TCGA-XF-A9SK 
        2.76        52.73         1.84        17.82         3.22        15.98 
TCGA-XF-AAMH TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-ZF-AA5N 
       11.31         6.77        44.32        28.41        56.35         5.52 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
      104.65        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BT-A20N TCGA-BT-A20P 
       66.54        47.80        29.65         2.50        26.14        17.88 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 
       17.16         4.67        28.70         8.98        23.01         2.04 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA 
       12.66        12.46        12.10        12.62        12.26        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        18.58        13.08         5.19        29.79 
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        53.29        76.60        67.36        15.02 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        13.64        11.18        12.03        20.32        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        29.72        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
        0.56         0.66        26.96        24.03        13.68        12.95 
TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A6TE 
       15.32         0.43        19.79         3.62         5.36        12.36 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EL 
        9.67        12.66        10.65        17.23         3.25        26.93 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62        66.02        70.32        29.36        21.40 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R 
       19.13        14.07         0.49         3.12         2.20        18.97 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.78        32.98         7.00        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        36.49        27.35        22.72        19.40        64.01 
TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       27.68        50.56        46.98        44.38        15.58        21.07 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A9PH TCGA-XF-A8HB 
       13.48        16.54        17.62        76.01        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-AAMG 
        6.58        97.12        17.88        26.27        18.90       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R2 
        7.63        71.57        30.94        18.15        11.97        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       31.20        35.84         3.48        88.87        47.84        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       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 
      108.95        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        12.79 
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        46.68        17.95       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        4.80        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 
      163.30        66.05        38.24       166.03        15.35        56.15 
TCGA-E7-A6MD TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ 
        4.24        32.02        16.77         4.01        12.62        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S 
       23.41        17.98        29.16        25.74        46.78        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62P 
       20.91        26.73        11.01        27.45         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81         6.15         2.27         3.06 
TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO 
       10.85         8.94        11.08        22.88        15.95        59.31 
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-A764 TCGA-GU-A767 TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI 
        7.36        20.05         4.73        25.02        21.24        11.70 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41P TCGA-KQ-A41S TCGA-R3-A69X 
       15.42        16.27        11.80        35.97         1.15        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OD 
       12.43        38.99        37.05        22.68        86.83       112.83 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        6.21         3.85         1.87        64.80        79.66        66.41 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T3 
       14.93         5.98        12.76        11.90        28.24         2.24 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMY 
       92.98        10.82        54.90        91.73         2.96        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R0 
       56.48        86.30        27.06         3.88         9.63        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA5P 
       25.41        94.29        34.06        35.41        57.90        12.23 

subtype1 subtype2 subtype3 subtype4 
    0.66     1.51     0.43     1.15 
subtype1 subtype2 subtype3 subtype4 
  165.73   130.88   110.60   166.03 
subtype1 subtype2 subtype3 subtype4 
  16.670   13.710   18.150   16.735 
[1] "0.7 - 165.7 (16.7)" "1.5 - 130.9 (13.7)" "0.4 - 110.6 (18.1)"
[4] "1.1 - 166.0 (16.7)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       32        36       31
  subtype2       1        4        13       24
  subtype3       1       65        41       28
  subtype4       0       23        45       52
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        1        0
  STAGE II        32        4       65       23
  STAGE III       36       13       41       45
  STAGE IV        31       24       28       52
[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 52 11
  subtype2        9 23 11
  subtype3       60 41 19
  subtype4       24 74 17
D9V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       27        9       60       24
  T3             52       23       41       74
  T4             11       11       19       17
[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 59 16 11  3
  subtype2 16  7 14  3
  subtype3 92  9 14  2
  subtype4 62 14 37  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       59       16       92       62
  N1       16        7        9       14
  N2       11       14       14       37
  N3        3        3        2        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"
D9V6, binary
          cls
clus        0  1
  subtype1 38  2
  subtype2 15  1
  subtype3 86  3
  subtype4 49  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    2
  subtype2   15    1
  subtype3   86    3
  subtype4   49    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       38       15       86       49
  1        2        1        3        5
[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  29  70
  subtype2  10  33
  subtype3  30 106
  subtype4  38  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   70
  subtype2   10   33
  subtype3   30  106
  subtype4   38   82
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       29       10       30       38
  MALE         70       33      106       82
[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, binary
          cls
clus         0   1
  subtype1  90   3
  subtype2  43   0
  subtype3 115  13
  subtype4 106   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90    3
  subtype2   43    0
  subtype3  115   13
  subtype4  106    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        90       43      115      106
  YES        3        0       13        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
D9V10, continuous
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    83
  subtype2     1                         3    38
  subtype3    29                         6    90
  subtype4     8                         6   106
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        1       29        8
  BLACK OR AFRICAN AMERICAN        7        3        6        6
  WHITE                           83       38       90      106
[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"
D9V13, binary
          cls
clus         0   1
  subtype1   3  87
  subtype2   0  40
  subtype3   3 117
  subtype4   3 113
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   87
  subtype2    0   40
  subtype3    3  117
  subtype4    3  113
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        3        3
  NOT HISPANIC OR LATINO       87       40      117      113
[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 34
  subtype2 21 25
  subtype3 65 30
  subtype4 26 40
  subtype5 24  6
  subtype6 44 40
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      75       46       95       66       30       84 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      34       25       30       40        6       40 
$subtype1
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R 
       24.13        44.94         2.50         6.58        19.50         5.06 
TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3YL 
       16.18        12.79        12.10        11.87         4.90        29.79 
TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
       21.86       112.44        17.62        17.95       142.78        13.58 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WY TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E7-A6MD 
       21.30        23.21       163.30        15.35        56.15         4.24 
TCGA-FD-A3B3 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP 
       32.02         4.01        12.62        24.30        23.41        25.74 
TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A6TF TCGA-FD-A6TG 
       19.79        14.96        53.88        11.01         2.27         3.06 
TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO 
       10.85         8.94        11.08        22.88        15.95        15.81 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A764 
       17.75         7.73         2.10        20.98         7.36        20.05 
TCGA-GU-A767 TCGA-K4-A3WS TCGA-K4-A83P TCGA-K4-AAQO TCGA-R3-A69X TCGA-SY-A9G0 
        4.73        25.02        16.27        11.80        14.24        12.43 
TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI 
      112.83         6.21         3.85         1.87        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9T3 TCGA-XF-AAME 
       66.41        14.93         5.98        11.90         2.24        92.98 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R0 
       10.82        91.73        27.06         3.88         9.63        22.36 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA5P 
       35.41        57.90        12.23 

$subtype2
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-5N-A9KM 
       11.97        94.88         8.35        27.62        51.16        17.42 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0F1 
       40.08         2.66        13.15         8.35        20.48         2.93 
TCGA-CF-A47S TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IK TCGA-DK-A6AV 
       10.95        15.12         1.84       130.88         4.80        64.18 
TCGA-E7-A677 TCGA-E7-A97Q TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TH 
       26.96         8.09        12.85        58.92         7.10         4.31 
TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A40G 
       31.07        10.92        10.65        14.27        20.28        19.07 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41R 
        1.51        38.60         3.45         2.76        52.73        44.38 
TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-AAMH TCGA-XF-AAMX 
       69.34        17.82         3.22        15.98        11.31         6.77 
TCGA-XF-AAMZ TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 
       44.32        21.86        28.41        56.35 

$subtype3
TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 
      104.65        17.16        34.98        50.04         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-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A6 
       12.59        12.13        12.16        12.62         5.19        66.41 
TCGA-DK-A1A7 TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B1 
       18.41        50.27         9.67        17.98        53.29        67.36 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA75 
       50.70        15.02        18.81        19.00        13.64        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       12.03        20.32        43.59        15.35        38.83        22.16 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
        2.24        25.58         0.56        24.03        13.68        12.95 
TCGA-E7-A8O8 TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A6TE TCGA-FJ-A3Z9 
        0.43         7.56        27.35         5.36        12.36        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
       10.65        17.23        20.12        17.62        66.02        29.36 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A6C6 TCGA-GU-A42R 
       19.13        14.07         0.49        13.91         2.20        18.97 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       32.98        21.34        19.10        19.82         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A54R TCGA-KQ-A41Q 
       27.35        22.72        19.40        64.01        27.68        46.98 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       15.58        13.48        17.62        51.32        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        31.20        35.84         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 
      108.95        16.27         6.74        19.04        26.14        17.88 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F6 TCGA-CF-A9FL 
       14.89        14.96         5.06         8.25        23.01        18.58 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A3IQ 
       13.58         2.14        16.70        16.14        46.68        17.72 
TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-FD-A3B4 
       66.05        15.68        38.24       166.03        13.64        16.77 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY 
       17.98        46.78        15.58        26.73        19.33         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       27.45        18.08         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TI TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GU-A42Q TCGA-GU-A766 
        6.15         9.67        26.93        59.31        11.31         5.62 
TCGA-GU-AATQ TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-KQ-A41P 
        7.00         9.01        21.24        11.70        15.42        35.97 
TCGA-KQ-A41S TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        1.15         1.84        38.99        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-AAMJ TCGA-XF-AAMT 
       76.01        12.76        28.24        18.90        54.90         2.96 
TCGA-XF-AAMY TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9RC TCGA-ZF-AA4R 
       98.99        86.30        13.64        25.41        94.29        34.06 

$subtype5
TCGA-4Z-AA7O TCGA-4Z-AA89 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47T TCGA-CF-A47V 
       16.83        29.65        13.97        13.08        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM 
       12.10        12.26        12.00        11.34        11.34        13.08 
TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A519 TCGA-E7-A5KF 
       19.00        15.62        76.60        29.72        16.70         0.66 
TCGA-E7-A8O7 TCGA-FD-A43X TCGA-GC-A3BM TCGA-GU-A763 TCGA-KQ-A41O TCGA-LT-A8JT 
       15.32         3.62        21.40        32.78        50.56        21.07 
TCGA-S5-AA26 TCGA-XF-A8HI TCGA-XF-AAN1 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4U 
       16.54        17.88        30.94        21.11        88.87         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        36.43        28.41         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN 
       12.56        12.92         7.79        87.32         8.15         8.22 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-E7-A7DV 
       20.81        10.55        52.01        13.58       165.73         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-A3SN TCGA-FD-A3SO TCGA-FD-A43U TCGA-FD-A5BX TCGA-FD-A62N 
       60.66        29.16         5.52        20.91         5.69         2.70 
TCGA-FD-A6TD TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-AA3D 
       12.69         3.25        61.94        48.00        33.01        70.32 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A762 
       20.71        15.91        24.92         8.94         3.12         7.63 
TCGA-GV-A40E TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-LC-A66R 
        8.58        12.16         9.14         9.07         1.81        15.32 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       12.23        16.67        78.25         3.02         3.91        29.56 
TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T4 
      125.49        48.62        34.45        23.64        21.04        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 
       66.64         2.10        13.74         8.32        56.48        61.45 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N 
       75.39        18.15        13.41        64.08        58.72         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        54.21        19.17 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.87     1.51     0.43     1.15     0.66     1.22 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  163.30   130.88   110.60   166.03    88.87   165.73 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   15.81    15.55    18.97    18.03    16.08    16.47 
[1] "1.9 - 163.3 (15.8)" "1.5 - 130.9 (15.6)" "0.4 - 110.6 (19.0)"
[4] "1.1 - 166.0 (18.0)" "0.7 - 88.9 (16.1)"  "1.2 - 165.7 (16.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       18        28       29
  subtype2       1        9        14       22
  subtype3       0       43        25       26
  subtype4       0       12        27       27
  subtype5       1       20         7        3
  subtype6       0       22        34       28
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          0        1        0        0        1        0
  STAGE II        18        9       43       12       20       22
  STAGE III       28       14       25       27        7       34
  STAGE IV        29       22       26       27        3       28
[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 44 10
  subtype2       12 24 10
  subtype3       36 30 11
  subtype4       13 40 11
  subtype5       21  5  4
  subtype6       21 47 12
D10V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T0+T1+T2       17       12       36       13       21       21
  T3             44       24       30       40        5       47
  T4             10       10       11       11        4       12
[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 40  6 23  0
  subtype2 21  7 13  3
  subtype3 56  6 14  2
  subtype4 37 11 15  1
  subtype5 25  1  1  0
  subtype6 50 15 10  3
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       40       21       56       37       25       50
  N1        6        7        6       11        1       15
  N2       23       13       14       15        1       10
  N3        0        3        2        1        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 31  2
  subtype2 20  0
  subtype3 52  6
  subtype4 27  3
  subtype5 26  0
  subtype6 32  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    2
  subtype2   20    0
  subtype3   52    6
  subtype4   27    3
  subtype5   26    0
  subtype6   32    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       31       20       52       27       26       32
  1        2        0        6        3        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 25 50
  subtype2 12 35
  subtype3 22 73
  subtype4 19 47
  subtype5  5 26
  subtype6 24 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   50
  subtype2   12   35
  subtype3   22   73
  subtype4   19   47
  subtype5    5   26
  subtype6   24   60
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       25       12       22       19        5       24
  MALE         50       35       73       47       26       60
[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, binary
          cls
clus        0  1
  subtype1 67  1
  subtype2 44  1
  subtype3 82  9
  subtype4 60  3
  subtype5 26  4
  subtype6 75  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    1
  subtype2   44    1
  subtype3   82    9
  subtype4   60    3
  subtype5   26    4
  subtype6   75    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        67       44       82       60       26       75
  YES        1        1        9        3        4        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
D10V10, continuous
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         3    67
  subtype2     3                         3    39
  subtype3    13                         6    69
  subtype4     3                         4    55
  subtype5    13                         2    14
  subtype6     4                         4    73
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        3       13        3       13
  BLACK OR AFRICAN AMERICAN        3        3        6        4        2
  WHITE                           67       39       69       55       14
                           clus
vv                          subtype6
  ASIAN                            4
  BLACK OR AFRICAN AMERICAN        4
  WHITE                           73
[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"
D10V13, binary
          cls
clus        0  1
  subtype1  1 72
  subtype2  1 41
  subtype3  3 80
  subtype4  2 59
  subtype5  0 28
  subtype6  2 77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   72
  subtype2    1   41
  subtype3    3   80
  subtype4    2   59
  subtype5    0   28
  subtype6    2   77
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        3        2        0        2
  NOT HISPANIC OR LATINO       72       41       80       59       28       77
[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"
