[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/22506467/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/22541056/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   5 
 78 146 121  61   2 
  1   2   3   4 
 78 146 121  61 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
139 128  65  80 
  1   2   3   4 
139 128  65  80 
[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   4   5 
 72 137  38 104  57 
  1   2   3   4   5 
 72 137  38 104  57 
[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   4   5 
105  75 115  25  89 
  1   2   3   4   5 
105  75 115  25  89 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
269  84  56 
  1   2   3 
269  84  56 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
125  52 129  92 
  1   2   3   4 
125  52 129  92 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 88  61  42 133  74 
  1   2   3   4   5 
 88  61  42 133  74 
[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=216,	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 
239  47  76   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
239  47  76   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
239  47  76   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
239  47  76   8 
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 40 38
  subtype2 81 65
  subtype3 68 50
  subtype4 36 25
subtype1 subtype2 subtype3 subtype4 
      78      146      118       61 
subtype1 subtype2 subtype3 subtype4 
      38       65       50       25 
$subtype1
TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
       12.39        26.14        20.48        46.68        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA71 
       50.27        23.21        17.98        36.66       165.73        13.64 
TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TI 
       60.66        46.78        12.85        58.92        18.81         9.67 
TCGA-FT-A61P TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-KQ-A41O TCGA-SY-A9G0 
       11.08        21.40        19.82        20.28        50.56        33.14 
TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-AAN3 TCGA-XF-AAN7 
       86.83        97.45        97.12        15.35        86.30        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-4Z-AA81 
       13.64        21.11         3.48        57.90        24.13        41.75 
TCGA-BL-A3JM TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A3MG TCGA-CU-A5W6 TCGA-DK-A1AD 
        6.74         4.67        23.01        12.13         1.84       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW 
       17.95         7.79        43.59        22.16        24.03        13.68 
TCGA-E7-A85H TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FT-A3EE TCGA-GC-A3I6 
       12.95        20.91         5.36         7.10         3.25        20.71 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-AATQ TCGA-GV-A3JV 
       13.91         2.10         2.20        18.97         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41S 
       19.10        36.49        38.60        11.70         1.81         1.15 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A8OC TCGA-XF-A9SG TCGA-XF-A9SU TCGA-YF-AA3L 
       13.48        12.23         3.02        48.62         5.98        11.97 
TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 
       31.20        28.41         2.89        67.20        56.35        19.40 

$subtype2
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR 
      108.95        16.27         8.35        28.70         8.98        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV 
       18.48         2.14         8.22        21.30        66.05        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W 
       67.36        15.68        50.70        38.24       166.03        13.64 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ 
       11.18        15.35        25.58         0.92         1.22        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY 
       23.41        29.16        19.79        15.58        26.73         8.25 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-G2-A3VY 
       18.08         6.28         6.15         3.06         4.31        17.62 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A40E TCGA-GV-A40G 
       70.32        24.92        10.92        32.98         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P 
       22.72         9.01        25.02         2.76        52.73        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK 
       46.98        14.24         1.84        51.32         3.22        15.98 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMJ 
        4.21        11.90        26.27         2.24         2.10        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R 
       71.57        98.99        44.32        94.29        88.87        34.06 
TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W 
       19.69        11.97       104.65         8.35        17.16        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
        0.62        51.16        47.80         2.50        40.08         2.66 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HS 
       19.04         5.06        16.18        36.43         1.94        12.56 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.16        12.62        11.34        21.86        66.41        18.41 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 
        4.80        13.58         8.15        15.02        19.00        12.03 
TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
       38.83         0.56         4.24         8.09        16.77         8.94 
TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A62S TCGA-FD-A6TF TCGA-G2-A2EF TCGA-G2-A3IE 
       22.98        27.45        13.35         2.27        61.94        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OS 
       66.02        29.36        14.07         0.49        26.70        20.98 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OF 
        7.63         4.73        21.34         8.48        19.40        64.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-SY-A9G5 
       21.24         9.07        15.42        11.80        44.38        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       37.05        22.68        76.01       112.83        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SZ TCGA-XF-AAMW TCGA-XF-AAMX TCGA-ZF-A9R0 
        3.85         1.87        28.24         8.32         6.77        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA52 
       25.41        21.86        13.41        20.22        59.38        35.41 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$subtype3
TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A72E 
       33.83        14.89         9.96        18.58         4.90        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA74 TCGA-DK-AA77 
       19.00        16.70        53.29        76.60        56.15        20.32 
TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A6TA TCGA-G2-A2ES 
       17.98         3.62        53.88         5.69        62.86        33.01 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-K4-A3WU TCGA-XF-A8HE TCGA-XF-A9SV TCGA-XF-A9T2 
       32.78        27.35         3.45       125.49        12.76        18.90 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 
       13.74        11.31        91.73        30.94         3.88         9.63 
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       94.88        44.94        16.83        34.98        50.04        66.54 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
       17.42         7.33         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A27C 
       19.50        14.96         8.25        28.41        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WW 
       13.08        29.79        16.14        17.62        15.62        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 
       10.55       163.30        13.58        18.81        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        5.36         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B8 TCGA-FD-A3N6 
       24.66        14.07        15.32        14.37        12.62        27.98 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       14.96        19.33        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-GD-A3OQ TCGA-GU-A42Q TCGA-H4-A2HO TCGA-K4-A83P TCGA-LT-A8JT TCGA-S5-AA26 
        3.12        11.31         1.51        16.27        21.07        16.54 
TCGA-UY-A78P TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9T4 
       78.25        45.04        17.88        64.80        66.41        16.27 
TCGA-XF-AAME TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R5 
       92.98        27.06        75.39        18.84         0.66        35.84 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5N 
        8.61        60.16         8.52         5.52 

$subtype4
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A3IV 
       16.77        15.12        25.94        12.92       130.88         9.67 
TCGA-DK-AA6M TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A6TD 
       52.01        33.04         4.01        27.35        10.78        12.69 
TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3RB TCGA-GC-A3WC TCGA-K4-A4AC 
       12.36        31.07        17.23        19.13        17.75         9.14 
TCGA-K4-A54R TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-AAMF TCGA-XF-AAML 
       27.68        34.45        14.93        21.04        10.82         7.63 
TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-ZF-AA5P TCGA-4Z-AA86 TCGA-BT-A20R TCGA-BT-A42B 
       61.45        30.28        12.23        10.22         5.06        17.56 
TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP 
        5.19       142.78        32.02        22.52         5.52        25.74 
TCGA-FD-A62N TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GU-A764 TCGA-GU-A766 
        2.70        15.81        15.91         8.94        20.05        15.78 
TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-UY-A78K 
       12.16        17.72        15.32        15.58        16.67        17.62 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SX 
       69.34        35.24        29.56         6.58        79.66        23.64 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
      110.60         2.96        56.48        64.08        58.72        47.84 
TCGA-ZF-AA58 
       54.21 

subtype1 subtype2 subtype3 subtype4 
    1.15     0.49     0.66     2.70 
subtype1 subtype2 subtype3 subtype4 
  165.73   166.03   163.30   142.78 
subtype1 subtype2 subtype3 subtype4 
  19.250   18.245   16.045   17.620 
[1] "1.1 - 165.7 (19.2)" "0.5 - 166.0 (18.2)" "0.7 - 163.3 (16.0)"
[4] "2.7 - 142.8 (17.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       22        25       30
  subtype2       1       40        46       59
  subtype3       1       47        46       26
  subtype4       0       20        22       19
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        1        0
  STAGE II        22       40       47       20
  STAGE III       25       46       46       22
  STAGE IV        30       59       26       19
[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       23 39 13
  subtype2       38 72 22
  subtype3       42 50 18
  subtype4       20 32  5
D1V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       23       38       42       20
  T3             39       72       50       32
  T4             13       22       18        5
[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 34 14 14  3
  subtype2 76 17 36  3
  subtype3 88  9 12  2
  subtype4 37  6 13  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       34       76       88       37
  N1       14       17        9        6
  N2       14       36       12       13
  N3        3        3        2        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 33  0
  subtype2 66  5
  subtype3 73  5
  subtype4 19  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    0
  subtype2   66    5
  subtype3   73    5
  subtype4   19    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       33       66       73       19
  1        0        5        5        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"
D1V7, binary
          cls
clus         0   1
  subtype1  20  58
  subtype2  43 103
  subtype3  31  90
  subtype4  12  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   58
  subtype2   43  103
  subtype3   31   90
  subtype4   12   49
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       43       31       12
  MALE         58      103       90       49
[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  71   2
  subtype2 128   5
  subtype3 106  12
  subtype4  57   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71    2
  subtype2  128    5
  subtype3  106   12
  subtype4   57    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        71      128      106       57
  YES        2        5       12        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     5                         1    65
  subtype2     9                        11   120
  subtype3    26                         6    87
  subtype4     3                         4    53
D1V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            5        9       26        3
  BLACK OR AFRICAN AMERICAN        1       11        6        4
  WHITE                           65      120       87       53
[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   3  68
  subtype2   2 132
  subtype3   2 113
  subtype4   2  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   68
  subtype2    2  132
  subtype3    2  113
  subtype4    2   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        2        2
  NOT HISPANIC OR LATINO       68      132      113       54
[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 79 48
  subtype3 35 29
  subtype4 42 38
subtype1 subtype2 subtype3 subtype4 
     138      127       64       80 
subtype1 subtype2 subtype3 subtype4 
      65       48       29       38 
$subtype1
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        16.77        15.12        12.39        25.94         9.96 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
       12.92        18.48        87.32         8.22        17.72        23.21 
TCGA-DK-A6B5 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B6 
       50.70       165.73       166.03        56.15         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SM TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        4.01        17.98        15.58        53.88        10.78         5.69 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FT-A61P 
       58.92         6.28        18.81         6.15        12.69        11.08 
TCGA-GC-A3WC TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC TCGA-R3-A69X 
       17.75         8.58         9.01         3.45         9.14        14.24 
TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       33.14        97.45       125.49         3.22        15.98        34.45 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 
       11.90        21.04        18.90         2.24        66.64        13.74 
TCGA-XF-AAN8 TCGA-ZF-A9RC TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA7N 
        3.88        94.29        57.90        12.23        24.13        44.94 
TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX 
       27.62        51.16        10.22         7.33         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42E 
       19.04        12.16        14.96         5.06         8.25        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-DK-A1AF TCGA-DK-A2I2 
       28.41         1.94         2.93        12.56        17.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6T 
      142.78         8.15        20.81        10.55       163.30        18.81 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       15.35        43.59        14.07        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
        8.94        12.62         5.52        25.74        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A871 
       19.33         2.70        13.35         2.27        10.85         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3C TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q 
       61.94        48.00         6.94         8.94        20.98        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        7.63        20.05        15.78        12.16        21.24         9.07 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
       17.72        16.27        15.32        12.23        16.67        38.99 
TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL 
       37.05        78.25        29.56        48.62        79.66        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 
       23.64        28.24        92.98         2.96        27.06        75.39 
TCGA-YC-A9TC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
        0.66        13.41        64.08        58.72        20.22         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        35.41        19.40         8.52        54.21        29.49 

$subtype2
TCGA-4Z-AA7M TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-DK-A1AC 
       16.27         8.35        20.48         8.98        18.58       130.88 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 
       50.27        21.30        66.05        64.18        53.29        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-FD-A3NA 
       15.68        36.66        13.64        11.18        15.35        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A6TA TCGA-FD-A6TI TCGA-FJ-A3Z7 
       24.30        19.79        26.73        62.86         9.67        31.07 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       17.23        17.62        19.13        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-KQ-A41N TCGA-KQ-A41O 
       19.82        20.28        27.35        22.72        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG 
       35.97        46.98        86.83        51.32        97.12        15.35 
TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMY 
       14.93        26.27        10.82        11.31         7.63        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KP 
       30.94        18.58        30.28        88.87        19.69        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI 
       94.88         8.35        17.16         0.62        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       17.42        40.08         5.06        17.16        16.18         4.67 
TCGA-C4-A0F6 TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A3QU 
       23.01        12.16        12.62        12.10        11.87         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK 
       21.86        66.41        18.41       112.44        17.95         4.80 
TCGA-DK-A3IL TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       13.58        19.00        12.03        38.83        22.16         2.24 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A8O8 TCGA-E7-A97Q 
        0.56         4.24        24.03        13.68         0.43         8.09 
TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FJ-A3Z9 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE 
       22.98        27.45        12.66        15.95        26.93        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 
       66.02        29.36        14.07        13.91        26.70         2.20 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A6MB 
        8.48         1.51        19.40        38.60        64.01        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-UY-A78K 
       11.80        44.38        15.58        21.07        13.48        17.62 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       22.68        76.01       112.83        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-AAMG TCGA-XF-AAMX TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R3 
        1.87       110.60         6.77        18.84        22.36        31.20 
TCGA-ZF-AA51 
       56.35 

$subtype3
TCGA-4Z-AA89 TCGA-BT-A20T TCGA-C4-A0F7 TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AB 
       33.83        14.89         2.04         4.90        15.12        16.70 
TCGA-DK-A2HX TCGA-DK-A3IV TCGA-DK-A6B0 TCGA-DK-AA71 TCGA-E7-A7DU TCGA-FD-A3SL 
       46.68         9.67        76.60        13.64         0.92        23.41 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A5C0 TCGA-FD-A6TG TCGA-G2-AA3D TCGA-K4-A3WS 
       46.78        27.35        18.08         3.06        70.32        25.02 
TCGA-S5-A6DX TCGA-XF-A9ST TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-YC-A8S6 
        1.84         4.21        54.90        91.73        44.32         9.63 
TCGA-ZF-AA4R TCGA-2F-A9KR TCGA-BT-A20P TCGA-BT-A20Q TCGA-CF-A1HR TCGA-CF-A47S 
       34.06       104.65        17.88        19.50        12.79        10.95 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY 
       12.46        12.10        12.26        13.12        12.00        11.34 
TCGA-CF-A9FM TCGA-CU-A5W6 TCGA-DK-A1AG TCGA-DK-AA6P TCGA-E7-A3Y1 TCGA-E7-A519 
       13.08         1.84        15.62        15.02         5.36        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FJ-A3ZE 
        0.66        26.24        24.66        12.95        15.32        10.65 
TCGA-G2-A2EC TCGA-GC-A3OO TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JW 
       22.88        15.81         2.10        18.97         4.73        21.34 
TCGA-GV-A3QI TCGA-KQ-A41S TCGA-UY-A9PA TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH 
       36.49         1.15        35.24         6.58        17.88        64.80 
TCGA-XF-A9SU TCGA-XF-AAN0 TCGA-ZF-A9R5 TCGA-ZF-A9RM 
        5.98        56.48        35.84        47.84 

$subtype4
TCGA-BT-A20N TCGA-BT-A42C TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A3X2 
       26.14        28.70        13.58         2.14        19.00        17.98 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA77 TCGA-E7-A541 TCGA-FD-A3SN TCGA-FD-A3SS 
       38.24        52.01        20.32        25.58        29.16        12.85 
TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-A2ES TCGA-GC-A3BM 
        3.62         8.25        12.36         4.31        33.01        21.40 
TCGA-GC-A3YS TCGA-GV-A40G TCGA-K4-A4AB TCGA-K4-A54R TCGA-XF-A9SV TCGA-XF-A9T6 
       24.92        19.07         2.76        27.68        12.76         2.10 
TCGA-XF-AAMQ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       71.57        61.45        86.30        13.64        21.11         3.48 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-BL-A13J 
       16.83        34.98        50.04        41.75        66.54         2.66 
TCGA-BL-A3JM TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        6.74        17.56        13.97        12.59        12.13        13.08 
TCGA-CF-A47T TCGA-CF-A8HX TCGA-CU-A3YL TCGA-DK-A1AE TCGA-DK-AA6Q TCGA-E7-A3X6 
       12.66        11.34        29.79        16.14        13.58        29.72 
TCGA-E7-A677 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A5BV TCGA-FD-A62O TCGA-FT-A3EE 
       26.96        22.52        27.98         5.36         7.10         3.25 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GD-A3OQ 
       59.31         7.23        20.71        15.91         0.49         3.12 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-S5-AA26 
        7.00        14.27        19.10        11.70         1.81        16.54 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A8HB TCGA-XF-A9T4 TCGA-XF-AAMW TCGA-YF-AA3L 
       69.34         3.02        45.04        16.27         8.32        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       25.41        21.86        28.41         8.61        59.38        67.20 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

subtype1 subtype2 subtype3 subtype4 
    0.66     0.43     0.66     0.49 
subtype1 subtype2 subtype3 subtype4 
  166.03   130.88   104.65    86.30 
subtype1 subtype2 subtype3 subtype4 
  16.770   19.130   15.470   16.405 
[1] "0.7 - 166.0 (16.8)" "0.4 - 130.9 (19.1)" "0.7 - 104.7 (15.5)"
[4] "0.5 - 86.3 (16.4)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       31        64       44
  subtype2       1       43        37       45
  subtype3       1       24        16       24
  subtype4       0       33        24       23
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        1        0
  STAGE II        31       43       24       33
  STAGE III       64       37       16       24
  STAGE IV        44       45       24       23
[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       29 81 20
  subtype2       41 54 18
  subtype3       23 27 10
  subtype4       31 34 11
D2V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       29       41       23       31
  T3             81       54       27       34
  T4             20       18       10       11
[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 84 17 23  3
  subtype2 67 17 24  3
  subtype3 37  3 19  1
  subtype4 51 10 10  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       84       67       37       51
  N1       17       17        3       10
  N2       23       24       19       10
  N3        3        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 52  4
  subtype2 68  3
  subtype3 40  2
  subtype4 36  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    4
  subtype2   68    3
  subtype3   40    2
  subtype4   36    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       52       68       40       36
  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 42 97
  subtype2 36 92
  subtype3 12 53
  subtype4 18 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   97
  subtype2   36   92
  subtype3   12   53
  subtype4   18   62
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       36       12       18
  MALE         97       92       53       62
[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 115   3
  subtype3  55   6
  subtype4  70   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  126    5
  subtype2  115    3
  subtype3   55    6
  subtype4   70    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       126      115       55       70
  YES        5        3        6        6
[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    14                         7   100
  subtype3    18                         2    43
  subtype4     7                         6    63
D2V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            5       14       18        7
  BLACK OR AFRICAN AMERICAN        8        7        2        6
  WHITE                          121      100       43       63
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
          cls
clus         0   1
  subtype1   3 126
  subtype2   1 115
  subtype3   0  61
  subtype4   5  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  126
  subtype2    1  115
  subtype3    0   61
  subtype4    5   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        0        5
  NOT HISPANIC OR LATINO      126      115       61       69
[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 78 36
  subtype3 53 51
subtype1 subtype2 subtype3 
     123      114      104 
subtype1 subtype2 subtype3 
      68       36       51 
$subtype1
TCGA-4Z-AA7Q TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN 
       16.77         8.35        20.48         9.96         8.98        12.92 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-AA6L TCGA-DK-AA6M 
       46.68        17.72        21.30         9.67        38.24        52.01 
TCGA-DK-AA6S TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
      166.03        33.04         4.01        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BS 
       29.16        46.78        19.79        12.85        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TD 
       10.78         5.69        18.08        58.92        18.81        12.69 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-GV-A3QF TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WS 
       31.07        11.08        20.28         8.58         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-R3-A69X TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SP 
        3.45         2.76        14.24       125.49        15.98        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T6 
        4.21        12.76        11.90        21.04        26.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAN8 TCGA-YC-A8S6 
       13.74        10.82        54.90        98.99         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR TCGA-BL-A13I 
       13.64        19.69        12.23        24.13       104.65         7.33 
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A42B TCGA-C4-A0F0 TCGA-DK-A1A3 TCGA-DK-A1AD 
        6.58         5.06        17.56         1.94        21.86       112.44 
TCGA-DK-A1AF TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       17.62         4.80         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7XN TCGA-FD-A3B3 
       15.02        12.03        38.83        24.03        14.07        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A62N 
       16.77        12.62         5.52        25.74        14.96         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       13.35         2.27        10.85        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GD-A3OP TCGA-GD-A3OS 
       15.95        26.93         7.23         6.94         2.10        20.98 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-K4-A3WV TCGA-K4-A83P TCGA-KQ-A41S 
       15.78        14.27        21.34        21.24        16.27         1.15 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HH TCGA-XF-A9SI 
       15.32        12.23        76.01       112.83         1.87        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN0 
       66.41        23.64        28.24        92.98         2.96        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9RG TCGA-ZF-AA4N 
       27.06        75.39         0.66        22.36        58.72         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA58 
       60.16        35.41        54.21 

$subtype2
TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BT-A42C TCGA-CF-A9FL TCGA-DK-A1A5 TCGA-DK-A1AA 
       16.27        33.83        28.70        18.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       16.70        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-FD-A3NA TCGA-FD-A43X TCGA-FD-A6TA TCGA-FD-A6TI 
       11.18        20.32        60.66         3.62        62.86         9.67 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40G 
       17.23        17.62        21.40        32.78        27.35        19.07 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9T5 
       52.73        50.56         1.84        97.12        15.35        66.64 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMZ TCGA-2F-A9KQ TCGA-4Z-AA7O TCGA-4Z-AA7R 
        7.63        71.57        44.32        94.88        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-BL-A0C8 TCGA-BT-A0YX 
       34.98        50.04         0.62        66.54        40.08        13.15 
TCGA-BT-A20Q TCGA-BT-A2LB TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       19.50        16.18         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-A9FM TCGA-CU-A3QU TCGA-DK-A1AG TCGA-DK-A2I1 
       11.34        11.87        13.08         5.19        15.62        17.95 
TCGA-DK-A3IL TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       13.58         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-E7-A8O8 
       26.96        26.24        24.66        13.68        15.32         0.43 
TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A3IE 
        8.94        22.98        27.45        12.66        10.65        20.12 
TCGA-G2-AA3B TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-AATQ 
       66.02        26.70         3.12         2.20        18.97         7.00 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-K4-AAQO 
        8.48         1.51        19.40        64.01        15.42        11.80 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K 
       44.38        15.58        21.07        13.48        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       37.05        22.68        17.82        45.04         6.58        17.88 
TCGA-XF-A9SH TCGA-XF-A9T4 TCGA-XF-AAMX TCGA-YC-A89H TCGA-ZF-A9R9 TCGA-ZF-A9RM 
       64.80        16.27         6.77        18.84        28.41        47.84 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0F7 
      108.95        15.12        26.14        14.89        25.94         2.04 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X1 
       18.48        13.58       130.88         8.22        23.21        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E7-A541 TCGA-E7-A7DU 
       17.98        50.70       165.73        56.15        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A5BR TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-G2-A2ES 
        1.22        26.73        12.36         3.06         4.31        33.01 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A6ZA TCGA-K4-A4AC 
       17.75        24.92        32.98        19.82        22.72         9.14 
TCGA-K4-A54R TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A9SJ 
       27.68        35.97        46.98        86.83        97.45         3.22 
TCGA-XF-A9SM TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-AAMH TCGA-XF-AAN2 TCGA-XF-AAN3 
       34.45        18.90         2.24        11.31        61.45        86.30 
TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-AA53 TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 
       18.58        21.11        57.90        27.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J 
       10.22        47.80         2.50         2.66         6.74        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       12.16        17.88        14.96         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
        4.67        36.43        12.56        29.79         1.84        66.41 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E7-A3X6 
       16.14         7.79       142.78        13.58        43.59        29.72 
TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U 
        4.24        12.95        14.37        22.52        27.98        20.91 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-G2-A2EO TCGA-GC-A3I6 TCGA-GU-A762 TCGA-GU-A764 
        5.36         7.10        59.31        20.71         7.63        20.05 
TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       36.49        38.60        12.16         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A9SG TCGA-XF-AAMG TCGA-XF-AAMW 
        1.81        69.34         3.02        48.62       110.60         8.32 
TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 
       25.41        13.41        20.22        59.38        56.35        19.40 
TCGA-ZF-AA56 TCGA-GU-AATO 
        8.52        10.65 

subtype1 subtype2 subtype3 
    0.66     0.43     0.92 
subtype1 subtype2 subtype3 
  166.03    97.12   165.73 
subtype1 subtype2 subtype3 
   16.77    16.70    19.22 
[1] "0.7 - 166.0 (16.8)" "0.4 - 97.1 (16.7)"  "0.9 - 165.7 (19.2)"
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 56 15 22  5
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       66       79       56
  N1       13       11       15
  N2       30       14       22
  N3        1        1        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   9
  subtype3  99   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109    4
  subtype2   98    9
  subtype3   99    1
     clus
vv    subtype1 subtype2 subtype3
  NO       109       98       99
  YES        4        9        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 37 52
  subtype2 83 38
  subtype3 47 52
  subtype4 19 13
subtype1 subtype2 subtype3 subtype4 
      89      121       99       32 
subtype1 subtype2 subtype3 subtype4 
      52       38       52       13 
$subtype1
TCGA-4Z-AA7Q TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-DK-A1AA TCGA-DK-A1AB 
       16.77         8.35        20.48         8.98        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-AA6M TCGA-DK-AA6S TCGA-FD-A3B6 
       46.68        17.72        21.30        52.01       166.03        33.04 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y 
       24.30        23.41        46.78        19.79        12.85        15.58 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
       18.08        58.92        62.86        18.81        12.69         3.06 
TCGA-FT-A61P TCGA-GU-A763 TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       11.08        32.78         9.01        25.02         3.45         2.76 
TCGA-R3-A69X TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T6 
       14.24        15.35        14.93         4.21        12.76         2.10 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YC-A8S6 TCGA-YF-AA3M 
       10.82        54.90        98.99        44.32         9.63        13.64 
TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR TCGA-BL-A13I TCGA-BL-A13J 
       19.69        12.23        24.13       104.65         7.33         2.66 
TCGA-BT-A20R TCGA-BT-A2LB TCGA-BT-A42B TCGA-C4-A0F0 TCGA-CU-A5W6 TCGA-DK-A1A3 
        5.06        16.18        17.56         1.94         1.84        21.86 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3WY TCGA-E7-A6ME 
      112.44        17.62         7.79        13.58       163.30        24.03 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A5BZ 
       32.02        16.77        12.62         5.52        14.96        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-G2-A2EK TCGA-GD-A2C5 TCGA-GD-A3OP 
        2.70        13.35        10.85        15.95        26.70         2.10 
TCGA-GV-A3JV TCGA-K4-A3WV TCGA-K4-A83P TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-UY-A78O 
       14.27        21.24        16.27         1.15        12.23        76.01 
TCGA-UY-A8OD TCGA-XF-A8HH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-AAMT TCGA-XF-AAN0 
      112.83         1.87        66.41        23.64         2.96        56.48 
TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA52 
       27.06        22.36        28.41        58.72        35.41 

$subtype2
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A9FL 
       15.12        33.83        26.14        14.89        28.70        18.58 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       13.58         2.14        66.05        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       67.36        36.66        11.18        20.32        25.58         0.92 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       60.66        17.98         3.62         9.67        31.07        17.23 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40G 
       17.62        21.40        32.98        19.82        27.35        19.07 
TCGA-GV-A6ZA TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-UY-A78N 
       22.72        52.73        50.56        46.98         1.84        86.83 
TCGA-XF-A8HF TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R2 TCGA-2F-A9KQ TCGA-4Z-AA7O 
       97.12         7.63        71.57        21.11        94.88        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA87 
       17.16        34.98        50.04         0.62        66.54        47.80 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A3PH TCGA-C4-A0F6 
        2.50        40.08        17.88        19.50         4.67        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-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.00        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-E5-A2PC TCGA-E7-A3X6 
       29.79        66.41        15.62        17.95        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        5.36         2.24        16.70         0.56         0.66        26.24 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A43N 
       24.66        13.68        12.95        15.32         0.43        22.98 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B 
        5.36         7.10        12.66        59.31        20.12        66.02 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3QH TCGA-H4-A2HO TCGA-HQ-A2OE 
        3.12         2.20        18.97         8.48         1.51        38.60 
TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       64.01        15.42        11.80        44.38        15.58        21.07 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A9PD TCGA-XF-A8HB 
       13.48        16.54        17.62        22.68        17.82        45.04 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9RM 
        6.58        17.88        64.80         6.77        25.41        47.84 
TCGA-ZF-AA51 
       56.35 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A3PJ TCGA-C4-A0F7 TCGA-CU-A3KJ TCGA-DK-A1AC 
      108.95        16.27        25.94         2.04        18.48       130.88 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
        8.22        23.21         9.67        15.68        50.70        38.24 
TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SN TCGA-FD-A5BR 
      165.73        56.15         1.22         4.01        29.16        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-A2ES TCGA-GC-A3WC 
       53.88        10.78        12.36         4.31        33.01        17.75 
TCGA-GC-A3YS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P TCGA-XF-A8HD TCGA-XF-A9SJ 
       24.92         9.14        27.68        35.97        97.45         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       15.98        34.45        11.90        18.90         2.24        66.64 
TCGA-XF-AAMH TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-ZF-AA53 
       11.31        61.45        86.30        18.58         3.88        57.90 
TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A3JM TCGA-BT-A0S7 
       27.62        41.75        51.16        10.22         6.74         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-A42E TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-DK-A1AE TCGA-DK-A2I4 
       17.16        36.43         2.93        12.56        16.14       142.78 
TCGA-DK-A3IK TCGA-DK-AA6Q TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7XN TCGA-E7-A97P 
        4.80        13.58        26.96         4.24        14.07        14.37 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A6TF TCGA-G2-A2EL 
        8.94        22.52        27.98        20.91         2.27        26.93 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3QI 
        6.94        20.71         7.63        20.05         7.00        36.49 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-UY-A78L 
       12.16         9.07        11.70        17.72         1.81        37.05 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-A9T4 
       69.34         3.02        48.62        79.66        28.24        16.27 
TCGA-XF-AAMG TCGA-XF-AAMW TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
      110.60         8.32        13.41        20.22         2.89        59.38 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-GU-AATO 
       19.40         8.52        10.65 

$subtype4
TCGA-BT-A3PK TCGA-CU-A0YN TCGA-FD-A5BX TCGA-GV-A3QF TCGA-GV-A40E TCGA-XF-A8HE 
        9.96        12.92         5.69        20.28         8.58       125.49 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       21.04        26.27        13.74         8.15        20.81        10.55 
TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-FD-A3SP TCGA-FJ-A3ZE TCGA-G2-A2EC 
       15.02        12.03        38.83        25.74        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        15.78        21.34 
TCGA-H4-A2HQ TCGA-LC-A66R TCGA-XF-AAME TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       19.40        15.32        92.98        75.39        18.84         0.66 
TCGA-ZF-AA4W TCGA-ZF-AA58 
       60.16        54.21 

subtype1 subtype2 subtype3 subtype4 
    1.15     0.43     1.22     0.66 
subtype1 subtype2 subtype3 subtype4 
  166.03    97.12   165.73   125.49 
subtype1 subtype2 subtype3 subtype4 
   16.77    17.82    17.16    19.84 
[1] "1.1 - 166.0 (16.8)" "0.4 - 97.1 (17.8)"  "1.2 - 165.7 (17.2)"
[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 56 18 17  3
  subtype4 19  1  4  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       44       82       56       19
  N1       10       10       18        1
  N2       28       17       17        4
  N3        2        1        3        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   8
  subtype3  92   1
  subtype4  27   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79    2
  subtype2  108    8
  subtype3   92    1
  subtype4   27    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        79      108       92       27
  YES        2        8        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 32 39
  subtype2 92 43
  subtype3 23 15
  subtype4 53 51
  subtype5 27 30
subtype1 subtype2 subtype3 subtype4 subtype5 
      71      135       38      104       57 
subtype1 subtype2 subtype3 subtype4 subtype5 
      39       43       15       51       30 
$subtype1
TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-AA6S 
        2.14        46.68        17.72        21.30        23.21       166.03 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BS 
       23.41        17.98        46.78        19.79        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       10.78         5.69        18.08        18.81         6.15         3.06 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-GC-A3WC TCGA-K4-A3WS TCGA-K4-A3WU TCGA-R3-A69X 
        4.31        11.08        17.75        25.02         3.45        14.24 
TCGA-SY-A9G0 TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9T3 TCGA-XF-AAMJ 
       33.14        15.98        14.93        11.90         2.24        54.90 
TCGA-XF-AAMR TCGA-XF-AAN8 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-5N-A9KI 
       91.73         3.88        12.23        24.13        44.94         2.50 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A2LB TCGA-DK-A1A3 TCGA-DK-A1AF 
       12.16        19.50         5.06        16.18        21.86        17.62 
TCGA-DK-A2I4 TCGA-DK-A3WY TCGA-DK-AA6T TCGA-E7-A6MD TCGA-FD-A3B8 TCGA-FD-A3SP 
      142.78       163.30        18.81         4.24        12.62        25.74 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF TCGA-G2-A2EO 
       14.96        20.91        27.45         2.70         2.27        59.31 
TCGA-GC-A3OO TCGA-K4-A5RH TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-UY-A8OD 
       15.81         9.07        16.27        11.80         1.15       112.83 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAME TCGA-XF-AAN0 
       79.66        66.41         5.98        23.64        92.98        56.48 
TCGA-XF-AAN4 TCGA-ZF-A9R9 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-GU-AATO 
       27.06        28.41        35.41        54.21        10.65 

$subtype2
TCGA-BT-A20W TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YR TCGA-DK-A3IV TCGA-DK-A3X1 
        8.35        28.70        18.58        15.12         9.67        66.05 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A43X TCGA-FD-A6TA 
       13.64        20.32        25.58         0.92         3.62        62.86 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-G2-AA3D TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       12.36         9.67        70.32        32.78        32.98        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       27.35        19.07        22.72        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SV 
       46.98         1.84        51.32        97.12        15.35        12.76 
TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YC-A8S6 
       26.27         7.63        98.99        44.32        30.94         9.63 
TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7S 
       30.28        88.87        19.69        11.97        94.88        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A3PH 
        0.62        66.54        47.80        17.42        40.08         4.67 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI 
       23.01        12.79        13.97        12.59        12.13        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-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19        29.79         1.84        66.41        18.41       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       17.95         4.80        13.58         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 
        0.66        26.96        26.24        13.68        12.95        15.32 
TCGA-E7-A8O8 TCGA-E7-A97Q TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 
        0.43         8.09        22.98         5.36         7.10        12.66 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F 
        3.25        22.88        15.95        20.12        66.02        29.36 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A767 TCGA-GV-A3JV 
       14.07        13.91        26.70         2.10         4.73        14.27 
TCGA-GV-A3JW TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LT-A5Z6 
       21.34         1.51        38.60        15.42        44.38        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PD 
       21.07        13.48        17.62        22.68        76.01        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SZ 
        6.21         3.85         6.58         1.87        64.80        28.24 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        6.77        11.97        22.36        31.20        35.84        21.86 
TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        67.20        56.35 

$subtype3
TCGA-4Z-AA89 TCGA-BT-A20T TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
       33.83        14.89         4.90        13.58        19.00        16.70 
TCGA-DK-A3IS TCGA-GC-A3BM TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-XF-AAMQ TCGA-XF-AAN3 
       50.27        21.40         9.01         2.76        71.57        86.30 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7Y 
       13.64        21.11         3.48       104.65        16.83        50.04 
TCGA-CF-A3MH TCGA-CF-A8HY TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-AA6X TCGA-E5-A2PC 
       13.08        11.34        16.14        15.62        15.35        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A6MF TCGA-GU-A42R TCGA-GU-AATQ TCGA-K4-A5RI 
       29.72         5.36        24.66        18.97         7.00        11.70 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HI TCGA-ZF-A9R1 
       16.54        78.25        35.24        45.04        17.88        25.41 
TCGA-ZF-AA4U TCGA-ZF-AA56 
        8.61         8.52 

$subtype4
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD 
      108.95        16.77        15.12        12.39        26.14        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2I6 TCGA-DK-A3IN 
       25.94         9.96        12.92        18.48        87.32         8.22 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E5-A4TZ 
       50.70        38.24        52.01       165.73        56.15        15.35 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SS 
        1.22        33.04         4.01        60.66        29.16        12.85 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD TCGA-G2-A2ES 
       15.58         8.25        58.92         6.28        12.69        33.01 
TCGA-GC-A3YS TCGA-GV-A40E TCGA-K4-A4AC TCGA-K4-A54R TCGA-XF-A8HD TCGA-XF-A8HE 
       24.92         8.58         9.14        27.68        97.45       125.49 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAN2 
        3.22        34.45        21.04         2.10        13.74        61.45 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       34.06        57.90        27.62        41.75        51.16        10.22 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42E TCGA-BT-A42F 
        2.66        13.15        14.96         8.25        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW 
        1.94         2.93        12.56         7.79         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-AA6Q TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       10.55        13.58        14.07        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A5BU TCGA-FD-A62S 
        8.94        22.52        27.98         5.52        19.33        13.35 
TCGA-FD-A6TK TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC 
       10.85        61.94        48.00         7.23        20.71        15.91 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-HQ-A5NE 
        8.94         3.12         7.63        20.05        15.78        12.16 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78L 
        1.81        15.32        12.23        16.67        38.99        37.05 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-XF-AAMW 
       69.34         3.02        29.56        16.27         2.96         8.32 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       75.39        18.84        13.41         2.89        59.38        60.16 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

$subtype5
TCGA-4Z-AA7M TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-DK-A1AC TCGA-DK-A3X2 TCGA-DK-AA6W 
       16.27         8.98         2.04       130.88        17.98        13.64 
TCGA-DK-AA75 TCGA-FD-A3SJ TCGA-FD-A43P TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
       11.18        24.30        27.35        31.07        17.23        17.62 
TCGA-GC-A3RB TCGA-GU-A42P TCGA-GV-A3JZ TCGA-UY-A78N TCGA-XF-A9ST TCGA-XF-A9T2 
       19.13        10.92        19.82        86.83         4.21        18.90 
TCGA-XF-A9T5 TCGA-XF-AAMH TCGA-XF-AAN7 TCGA-ZF-A9RC TCGA-2F-A9KW TCGA-4Z-AA7R 
       66.64        11.31        18.58        94.29         8.35        17.16 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20V 
        7.33         6.74         6.58        19.04        17.88         5.06 
TCGA-BT-A2LA TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A4IJ 
       17.16        15.02        19.00        12.03        38.83        22.16 
TCGA-E7-A6ME TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-AA3C TCGA-GC-A4ZW 
       24.03        10.65         8.94        26.93         6.94         0.49 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       20.98         2.20        11.31        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-XF-AAMG TCGA-YC-A9TC 
       19.40        64.01        21.24        17.72       110.60         0.66 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA54 
       64.08        20.22        19.40 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.15     0.43     2.76     1.22     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 
  166.03   112.44   104.65   165.73   130.88 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.080   17.420   16.765   16.090   17.880 
[1] "1.1 - 166.0 (18.1)" "0.4 - 112.4 (17.4)" "2.8 - 104.7 (16.8)"
[4] "1.2 - 165.7 (16.1)" "0.5 - 130.9 (17.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0        9        30       33
  subtype2       2       60        34       39
  subtype3       0       16        11       11
  subtype4       0       29        41       34
  subtype5       0       16        24       17
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        2        0        0        0
  STAGE II         9       60       16       29       16
  STAGE III       30       34       11       41       24
  STAGE IV        33       39       11       34       17
[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        9 50 12
  subtype2       60 50 16
  subtype3       15 14  6
  subtype4       28 52 17
  subtype5       11 28  7
D5V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2        9       60       15       28       11
  T3             50       50       14       52       28
  T4             12       16        6       17        7
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 36  9 23  1
  subtype2 82  9 29  2
  subtype3 23  4  6  0
  subtype4 64 17 12  3
  subtype5 32  7  5  2
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       36       82       23       64       32
  N1        9        9        4       17        7
  N2       23       29        6       12        5
  N3        1        2        0        3        2
[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"
D5V6, binary
          cls
clus        0  1
  subtype1 24  3
  subtype2 82  2
  subtype3 21  0
  subtype4 41  2
  subtype5 28  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    3
  subtype2   82    2
  subtype3   21    0
  subtype4   41    2
  subtype5   28    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       24       82       21       41       28
  1        3        2        0        2        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1  21  51
  subtype2  34 103
  subtype3  10  28
  subtype4  29  75
  subtype5  13  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   51
  subtype2   34  103
  subtype3   10   28
  subtype4   29   75
  subtype5   13   44
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       21       34       10       29       13
  MALE         51      103       28       75       44
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1  62   4
  subtype2 118   9
  subtype3  35   3
  subtype4  97   1
  subtype5  50   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62    4
  subtype2  118    9
  subtype3   35    3
  subtype4   97    1
  subtype5   50    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        62      118       35       97       50
  YES        4        9        3        1        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
D5V10, continuous
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    68
  subtype2    32                         6    94
  subtype3     3                         2    29
  subtype4     3                        10    87
  subtype5     3                         4    46
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3       32        3        3        3
  BLACK OR AFRICAN AMERICAN        1        6        2       10        4
  WHITE                           68       94       29       87       46
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
          cls
clus         0   1
  subtype1   1  69
  subtype2   1 127
  subtype3   2  31
  subtype4   2  92
  subtype5   2  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   69
  subtype2    1  127
  subtype3    2   31
  subtype4    2   92
  subtype5    2   49
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        1        2        2        2
  NOT HISPANIC OR LATINO       69      127       31       92       49
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 58 60
  subtype2 84 27
  subtype3 85 91
subtype1 subtype2 subtype3 
     118      111      176 
subtype1 subtype2 subtype3 
      60       27       91 
$subtype1
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-CF-A9FL TCGA-CU-A0YO 
       16.27        26.14        14.89         8.35        18.58         4.90 
TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT 
       15.12         2.14       130.88        46.68        17.72        21.30 
TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       66.05        15.68        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A6TA 
       46.78        19.79        27.35        26.73        18.08        62.86 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GU-AATP TCGA-GV-A3JZ 
        6.15         3.06         9.67        31.07        32.98        19.82 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41P TCGA-KQ-A41Q 
       25.02         3.45         2.76        27.68        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF 
       14.24         1.84        33.14        86.83        51.32        97.12 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-AAMJ 
       15.98        14.93        12.76        11.90        26.27        54.90 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T 
       91.73        98.99        44.32        94.29        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       12.23        24.13         8.35        44.94        16.83        17.16 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13J TCGA-BT-A20Q TCGA-BT-A20R 
       47.80         2.50        17.42         2.66        19.50         5.06 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A1A6 
       16.18         4.67        23.01        12.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41       112.44        17.62        17.95         4.80        13.58 
TCGA-DK-AA6T TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A43N TCGA-FD-A43S 
       18.81         4.24        12.95         8.09        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BZ TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO TCGA-GC-A3OO 
       20.91        27.45        22.88        15.95        59.31        15.81 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A767 TCGA-K4-A6MB 
       14.07        13.91        26.70         2.10         4.73        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OD 
       16.27        11.80         1.15        17.62        22.68       112.83 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
       17.82         6.21         1.87        64.80        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMX TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       28.24       110.60         6.77        18.84        22.36        25.41 
TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-GU-AATO 
       28.41        56.35        35.41        10.65 

$subtype2
TCGA-4Z-AA89 TCGA-BT-A42C TCGA-DK-A1AA TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6AW 
       33.83        28.70        19.00        50.27        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 
       76.60        67.36        36.66        13.64        11.18        20.32 
TCGA-E7-A7DU TCGA-FD-A43X TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
        0.92         3.62        17.23        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G 
       19.13        10.92        32.78        20.28        27.35        19.07 
TCGA-GV-A6ZA TCGA-KQ-A41N TCGA-KQ-A41O TCGA-XF-A8HG TCGA-XF-AAML TCGA-XF-AAN1 
       22.72        52.73        50.56        15.35         7.63        30.94 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-2F-A9KP TCGA-2F-A9KQ 
        9.63        21.11        30.28        88.87        11.97        94.88 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-BL-A0C8 TCGA-BT-A20P 
       34.98        50.04         0.62        66.54        40.08        17.88 
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-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AG TCGA-DK-AA6P TCGA-DK-AA6U 
        5.19        29.79         1.84        15.62        15.02        19.00 
TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        38.83         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A7PW 
        0.56         0.66        26.96        26.24        24.03        13.68 
TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A5BV TCGA-FD-A62O TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       15.32         0.43         5.36         7.10        12.66        10.65 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JV 
       20.12        66.02        29.36         2.20        18.97        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34         8.48        36.49         1.51        19.40        38.60 
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-A8HI TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        3.85         6.58        17.88        11.97        31.20        35.84 
TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4X 
       47.84         8.61        67.20 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ 
      108.95        16.77        15.12        12.39        20.48        25.94 
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E 
        9.96         8.98         2.04        12.92        18.48        13.58 
TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       16.70        87.32         8.22        23.21         9.67        17.98 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       56.15        15.35        25.58         1.22        33.04         4.01 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       29.16        12.85        15.58        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        8.25        58.92         6.28        18.81        12.69        12.36 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A40E 
        4.31        11.08        33.01        17.75        24.92         8.58 
TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SM 
        9.01         9.14        97.45       125.49         3.22        34.45 
TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
        4.21        21.04        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       13.74        11.31        71.57        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-2F-A9KR TCGA-4Z-AA7W 
        3.88        13.64         3.48        57.90       104.65        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
       41.75        51.16        10.22         7.33         6.74         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-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A1HS 
       17.16        36.43        28.41         1.94         2.93        12.56 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       16.14         7.79       142.78         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A6MF 
      163.30        13.58        15.35        43.59        29.72        24.66 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.07        14.37        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A5BU TCGA-FD-A62N 
       22.52        27.98         5.52        25.74        19.33         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       13.35         2.27        10.85         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC 
       48.00        26.93         7.23         6.94        20.71        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 
        0.49         8.94         3.12        20.98        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-HQ-A2OF TCGA-HQ-A5NE 
       20.05        15.78         7.00        19.10        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R 
       21.24         9.07        11.70        17.72         1.81        15.32 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB 
       12.23        16.67        38.99        37.05        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A9SI TCGA-XF-A9SX 
        3.02        35.24        29.56        45.04        79.66        23.64 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       16.27        92.98         2.96         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN 
       75.39         0.66        21.86        13.41        64.08        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
        2.89        59.38        60.16        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

subtype1 subtype2 subtype3 
    1.15     0.43     0.49 
subtype1 subtype2 subtype3 
  130.88    94.88   166.03 
subtype1 subtype2 subtype3 
  18.695   16.700   16.205 
[1] "1.1 - 130.9 (18.7)" "0.4 - 94.9 (16.7)"  "0.5 - 166.0 (16.2)"
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 105  24  25   3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       52       80      105
  N1       17        5       24
  N2       40       10       25
  N3        4        1        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"
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  12
  subtype3 158   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104    3
  subtype2  100   12
  subtype3  158    5
     clus
vv    subtype1 subtype2 subtype3
  NO       104      100      158
  YES        3       12        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 55 50
  subtype2 39 35
  subtype3 82 32
  subtype4 10 15
  subtype5 42 46
subtype1 subtype2 subtype3 subtype4 subtype5 
     105       74      114       25       88 
subtype1 subtype2 subtype3 subtype4 subtype5 
      50       35       32       15       46 
$subtype1
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A3PJ TCGA-CU-A0YN 
      108.95        16.77        33.83        26.14        25.94        12.92 
TCGA-CU-A3KJ TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       18.48        66.05        17.98        50.70        36.66        52.01 
TCGA-DK-AA6R TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A6TD 
      165.73        33.04         4.01        27.35        15.58        12.69 
TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-UY-A9PH 
       33.01        19.13         8.58         9.01         9.14        51.32 
TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
      125.49        34.45        21.04        66.64         2.10        13.74 
TCGA-XF-AAN2 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-4Z-AA81 TCGA-4Z-AA86 
       61.45         3.48        57.90        24.13        41.75        10.22 
TCGA-BL-A13I TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20U TCGA-BT-A20X 
        7.33        19.04        12.16        17.88        14.96         8.25 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-DK-A1AE 
       17.56        36.43        28.41         1.94        12.56        16.14 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6Q 
       15.62         7.79         8.15        20.81        10.55        13.58 
TCGA-DK-AA6T TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 
       18.81        43.59        29.72        14.07        14.37         8.94 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43U TCGA-FJ-A871 TCGA-FT-A3EE 
       22.52        27.98         5.52        20.91         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC 
       61.94        48.00        59.31         7.23        20.71        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 
        0.49         8.94         3.12        20.98        11.31         7.63 
TCGA-GV-A3QI TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R 
       36.49        12.16         9.07        17.72         1.81        15.32 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       12.23        16.67        37.05        78.25         3.02        35.24 
TCGA-UY-A9PB TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAMW TCGA-XF-AAN5 
       29.56        48.62        23.64        16.27         8.32        75.39 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       13.41        64.08        58.72         2.89        59.38        60.16 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.52        54.21        29.49 

$subtype2
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A1A5 
        8.35        20.48         9.96        28.70        15.12         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-E7-A7DV 
      130.88        87.32        21.30        64.18        15.68         1.22 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TE 
       29.16        12.85        18.08        58.92         6.15        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF 
        4.31         9.67        31.07        24.92        10.92        20.28 
TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-S5-A6DX TCGA-XF-A9SJ 
       19.07         3.45         2.76        52.73         1.84         3.22 
TCGA-XF-A9SK TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YF-AA3M 
       15.98        11.31        54.90        98.99        44.32        13.64 
TCGA-ZF-AA4R TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 
       34.06        11.97        94.88         8.35        27.62        51.16 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-C4-A0F1 TCGA-CF-A3MG 
       17.42        40.08         2.66        13.15         2.93        12.13 
TCGA-CF-A47S TCGA-CU-A5W6 TCGA-DK-A3IK TCGA-E7-A677 TCGA-E7-A97Q TCGA-FD-A43N 
       10.95         1.84         4.80        26.96         8.09        22.98 
TCGA-FD-A62O TCGA-G2-AA3B TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.10        66.02        15.78        14.27         1.51        19.40 
TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A8OB TCGA-UY-A9PD 
       38.60        15.42        44.38        13.48        69.34        17.82 
TCGA-XF-A8HC TCGA-XF-A9SZ TCGA-XF-AAMX TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 
        6.58        28.24         6.77        21.86        28.41        56.35 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

$subtype3
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-DK-A1AA TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6AW 
        8.98        18.58        19.00        50.27         9.67        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 
       76.60        67.36        13.64        11.18        20.32        25.58 
TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A43X TCGA-FD-A6TA TCGA-FJ-A3ZF TCGA-G2-AA3D 
        0.92        60.66         3.62        62.86        17.23        70.32 
TCGA-GC-A3BM TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA 
       21.40        32.78        32.98        19.82        27.35        22.72 
TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF 
       27.68        50.56        46.98        86.83        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN1 
       15.35        12.76        26.27         7.63        71.57        30.94 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KR TCGA-4Z-AA7O 
       21.11        30.28        88.87        19.69       104.65        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-BT-A3PH TCGA-C4-A0F6 
       34.98        50.04        66.54        47.80         4.67        23.01 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V 
       13.97        12.59        13.08        12.16        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-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-AA6P TCGA-DK-AA6U 
       66.41        18.41       112.44        17.95        15.02        19.00 
TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        38.83         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 
        0.56         0.66        26.24        13.68        12.95        15.32 
TCGA-E7-A8O8 TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-A3IE 
        0.43         5.36        12.66        10.65        26.93        20.12 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QH 
       29.36        14.07        26.70        18.97        21.34         8.48 
TCGA-HQ-A2OF TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O 
       64.01        15.58        21.07        16.54        22.68        76.01 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH TCGA-YC-A89H TCGA-YF-AA3L 
        6.21        45.04        17.88        64.80        18.84        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4X 
       22.36        31.20        35.84        47.84         8.61        67.20 

$subtype4
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-DK-A3IN TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-FD-A3SM 
       16.27        15.12         8.22        13.64        15.35        17.98 
TCGA-G2-A3VY TCGA-KQ-A41P TCGA-XF-A9T2 TCGA-XF-AAN7 TCGA-4Z-AA7R TCGA-4Z-AA80 
       17.62        35.97        18.90        18.58        17.16         0.62 
TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LA TCGA-E7-A6MF TCGA-GD-A6C6 
        6.74         5.06         5.06        17.16        24.66         2.20 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-K4-A3WV TCGA-UY-A78K TCGA-XF-AAMG TCGA-YC-A9TC 
        7.00        19.10        21.24        17.62       110.60         0.66 
TCGA-ZF-A9RN 
       20.22 

$subtype5
TCGA-BT-A20T TCGA-C4-A0F7 TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A2HX 
       14.89         2.04         4.90        13.58        16.70        46.68 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA74 TCGA-FD-A3SJ 
       17.72        23.21        38.24       166.03        56.15        24.30 
TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       23.41        46.78        19.79        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FT-A61P 
        5.69         8.25         6.28        18.81         3.06        11.08 
TCGA-GC-A3WC TCGA-K4-A3WS TCGA-R3-A69X TCGA-SY-A9G0 TCGA-XF-A9SP TCGA-XF-A9SW 
       17.75        25.02        14.24        33.14        14.93        11.90 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 
        2.24        10.82        91.73        86.30         3.88         9.63 
TCGA-ZF-A9RC TCGA-ZF-AA5P TCGA-4Z-AA7N TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20Q 
       94.29        12.23        44.94         2.50         6.58        19.50 
TCGA-BT-A2LB TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A1AF TCGA-DK-A2I4 TCGA-DK-A3IL 
       16.18        12.79        21.86        17.62       142.78        13.58 
TCGA-DK-A3WY TCGA-DK-AA6X TCGA-E7-A6MD TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B4 
      163.30        15.35         4.24        24.03        32.02        16.77 
TCGA-FD-A3B8 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N 
       12.62        25.74        14.96        19.33        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO 
       13.35         2.27        10.85        22.88        15.95        15.81 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GU-A764 TCGA-GU-A767 TCGA-K4-A5RI TCGA-K4-A83P 
       13.91         2.10        20.05         4.73        11.70        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-SY-A9G5 TCGA-UY-A8OD TCGA-UY-A9PF TCGA-XF-A8HH 
       11.80         1.15        38.99       112.83         3.85         1.87 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN0 
       79.66        66.41         5.98        92.98         2.96        56.48 
TCGA-XF-AAN4 TCGA-ZF-A9R1 TCGA-ZF-AA52 TCGA-ZF-AA54 
       27.06        25.41        35.41        19.40 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.49     1.22     0.43     0.62     1.15 
subtype1 subtype2 subtype3 subtype4 subtype5 
  165.73   130.88   112.44   110.60   166.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.980   15.730   19.000   17.160   16.485 
[1] "0.5 - 165.7 (18.0)" "1.2 - 130.9 (15.7)" "0.4 - 112.4 (19.0)"
[4] "0.6 - 110.6 (17.2)" "1.1 - 166.0 (16.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       32        44       29
  subtype2       1       16        21       36
  subtype3       1       62        29       22
  subtype4       0        5        10       10
  subtype5       0       16        35       38
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        1        0        0
  STAGE II        32       16       62        5       16
  STAGE III       44       21       29       10       35
  STAGE IV        29       36       22       10       38
[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       26 56 13
  subtype2       20 38 14
  subtype3       59 31 11
  subtype4        4 13  5
  subtype5       15 56 15
D7V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       26       20       59        4       15
  T3             56       38       31       13       56
  T4             13       14       11        5       15
[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 66 15 11  1
  subtype2 34 13 18  4
  subtype3 78  6 14  2
  subtype4 13  2  5  1
  subtype5 46 10 28  0
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       66       34       78       13       46
  N1       15       13        6        2       10
  N2       11       18       14        5       28
  N3        1        4        2        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 47  0
  subtype2 29  2
  subtype3 77  3
  subtype4 11  4
  subtype5 31  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    0
  subtype2   29    2
  subtype3   77    3
  subtype4   11    4
  subtype5   31    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       47       29       77       11       31
  1        0        2        3        4        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 30 75
  subtype2 16 59
  subtype3 26 89
  subtype4  4 21
  subtype5 31 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   75
  subtype2   16   59
  subtype3   26   89
  subtype4    4   21
  subtype5   31   58
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       16       26        4       31
  MALE         75       59       89       21       58
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 94  3
  subtype2 71  2
  subtype3 99 11
  subtype4 22  2
  subtype5 77  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    3
  subtype2   71    2
  subtype3   99   11
  subtype4   22    2
  subtype5   77    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        94       71       99       22       77
  YES        3        2       11        2        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"
D7V9, continuous
D7V10, continuous
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    90
  subtype2     6                         4    62
  subtype3    29                         4    73
  subtype4     2                         2    21
  subtype5     4                         6    78
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        6       29        2        4
  BLACK OR AFRICAN AMERICAN        7        4        4        2        6
  WHITE                           90       62       73       21       78
[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"
D7V13, binary
          cls
clus         0   1
  subtype1   1  96
  subtype2   3  67
  subtype3   2 101
  subtype4   2  19
  subtype5   1  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   96
  subtype2    3   67
  subtype3    2  101
  subtype4    2   19
  subtype5    1   85
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        3        2        2        1
  NOT HISPANIC OR LATINO       96       67      101       19       85
[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(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 152 116
  subtype2  46  37
  subtype3  30  25
subtype1 subtype2 subtype3 
     268       83       55 
subtype1 subtype2 subtype3 
     116       37       25 
$subtype1
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        33.83        26.14 
TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN 
       14.89        25.94         8.98         2.04        18.58        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IS 
       18.48        13.58        19.00        16.70         8.22        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
        9.67        66.05        17.98        53.29        76.60        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        11.18        20.32        15.35        25.58         0.92 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A43X 
       33.04        60.66        17.98        29.16        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TD 
       15.58        53.88        10.78         5.69         8.25        12.69 
TCGA-FD-A6TE TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GU-A763 
       12.36        33.01        70.32        21.40        19.13        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       32.98        19.82        27.35         8.58        22.72         9.01 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N 
        9.14        27.68        50.56        35.97        46.98        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SM 
       51.32        97.45       125.49        97.12        15.35        34.45 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        21.04        26.27        18.90        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       13.74         7.63        71.57        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        30.28         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KR 
       88.87        34.06        19.69        57.90        24.13       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 
       44.94        16.83        17.16        34.98         0.62        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        10.22        47.80         2.50         7.33         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
        6.58        19.04        12.16        17.88        19.50        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        23.01        12.56        13.97        12.59 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.08        12.16        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       11.87        13.08        29.79        66.41        18.41        16.14 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62        17.95         7.79         8.15        20.81        10.55 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       16.70         0.56         0.66        26.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-E7-A97P 
       13.68        14.07        12.95        15.32         0.43        14.37 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43U 
        8.94        22.52        27.98         5.52        22.98        20.91 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        5.36         2.70        13.35        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        22.88        61.94        48.00        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        7.23        20.12        29.36        20.71        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        0.49         8.94         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
       18.97         7.63        20.05         7.00        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        8.48        36.49        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT 
       11.70        17.72         1.81         1.15        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        17.62        37.05        22.68 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       78.25         3.02        35.24        29.56         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SX 
       45.04         1.87        17.88        48.62        64.80        23.64 
TCGA-XF-A9T4 TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 
       16.27       110.60         2.96         8.32        56.48        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       35.84        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA54 
        2.89         8.61        59.38        60.16        67.20        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
        8.52        54.21        29.49         5.52 

$subtype2
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A1A5 
        8.35        20.48         9.96        28.70        15.12         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
      130.88        87.32        21.30        64.18        67.36        15.68 
TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A5C0 
       56.15         1.22         4.01        46.78        12.85        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       58.92        62.86         6.15         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A40G 
       17.23        17.62        24.92        10.92        20.28        19.07 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-S5-A6DX TCGA-XF-A9SJ 
       25.02         3.45         2.76        52.73         1.84         3.22 
TCGA-XF-A9SK TCGA-XF-A9SW TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ 
       15.98        11.90        11.31        54.90        98.99        44.32 
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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-C4-A0F1 TCGA-CF-A3MG 
       17.42        40.08         2.66        13.15         2.93        12.13 
TCGA-CF-A47S TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A3IK TCGA-E7-A677 TCGA-E7-A97Q 
       10.95         5.19         1.84         4.80        26.96         8.09 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-G2-AA3B TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO 
       27.45         7.10        66.02        15.78        14.27         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LC-A66R TCGA-MV-A51V 
       19.40        38.60        15.42        44.38        15.32        13.48 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A9SZ 
       38.99        76.01        69.34        17.82         6.58        28.24 
TCGA-XF-AAMX TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-GU-AATO 
        6.77        21.86        28.41        56.35        10.65 

$subtype3
TCGA-CU-A0YO TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.90        46.68        17.72        23.21        24.30        23.41 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FT-A61P 
       19.79        26.73         6.28        18.81         3.06        11.08 
TCGA-GC-A3WC TCGA-R3-A69X TCGA-SY-A9G0 TCGA-XF-A9SP TCGA-XF-A9T3 TCGA-XF-AAMF 
       17.75        14.24        33.14        14.93         2.24        10.82 
TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-ZF-A9RC TCGA-ZF-AA5P TCGA-BT-A20R TCGA-BT-A2LB 
       91.73        86.30        94.29        12.23         5.06        16.18 
TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I4 TCGA-DK-A3IL 
       12.79        21.86       112.44        17.62       142.78        13.58 
TCGA-DK-A3WY TCGA-E7-A6MD TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SP 
      163.30         4.24        32.02        16.77        12.62        25.74 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EK TCGA-GC-A3OO 
       14.96        19.33         2.27        10.85        15.95        15.81 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A767 TCGA-K4-A83P TCGA-K4-AAQO 
       13.91        26.70         2.10         4.73        16.27        11.80 
TCGA-UY-A8OD TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAN4 
      112.83        79.66        66.41         5.98        92.98        27.06 
TCGA-ZF-AA52 
       35.41 

subtype1 subtype2 subtype3 
    0.43     1.22     2.10 
subtype1 subtype2 subtype3 
  166.03   130.88   163.30 
subtype1 subtype2 subtype3 
   17.88    17.42    17.62 
[1] "0.4 - 166.0 (17.9)" "1.2 - 130.9 (17.4)" "2.1 - 163.3 (17.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1      101        96       70
  subtype2       1       19        24       39
  subtype3       0       11        19       26
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          1        1        0
  STAGE II       101       19       11
  STAGE III       96       24       19
  STAGE IV        70       39       26
[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       90 118  34
  subtype2       22  41  16
  subtype3       12  35   8
D8V4, multiclass
          clus
vv         subtype1 subtype2 subtype3
  T0+T1+T2       90       22       12
  T3            118       41       35
  T4             34       16        8
[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 168  26  35   4
  subtype2  40  14  21   4
  subtype3  29   6  20   0
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      168       40       29
  N1       26       14        6
  N2       35       21       20
  N3        4        4        0
[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"
D8V6, binary
          cls
clus         0   1
  subtype1 142   8
  subtype2  35   1
  subtype3  18   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  142    8
  subtype2   35    1
  subtype3   18    2
   clus
vv  subtype1 subtype2 subtype3
  0      142       35       18
  1        8        1        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  68 201
  subtype2  17  67
  subtype3  22  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68  201
  subtype2   17   67
  subtype3   22   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       68       17       22
  MALE        201       67       34
[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"
D8V8, binary
          cls
clus         0   1
  subtype1 235  18
  subtype2  80   2
  subtype3  48   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  235   18
  subtype2   80    2
  subtype3   48    0
     clus
vv    subtype1 subtype2 subtype3
  NO       235       80       48
  YES       18        2        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
D8V10, continuous
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    35                        14   204
  subtype2     7                         5    70
  subtype3     2                         4    50
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           35        7        2
  BLACK OR AFRICAN AMERICAN       14        5        4
  WHITE                          204       70       50
[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"
D8V13, binary
          cls
clus         0   1
  subtype1   7 237
  subtype2   1  77
  subtype3   1  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  237
  subtype2    1   77
  subtype3    1   54
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        1        1
  NOT HISPANIC OR LATINO      237       77       54
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 59 65
  subtype2 24 27
  subtype3 86 42
  subtype4 50 42
subtype1 subtype2 subtype3 subtype4 
     124       51      128       92 
subtype1 subtype2 subtype3 subtype4 
      65       27       42       42 
$subtype1
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20T TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A5 
      108.95        16.27        14.89         4.90        13.58         2.14 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 
       16.70        46.68         8.22        17.72        21.30        66.05 
TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA74 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
       38.24       166.03        56.15         4.01        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BS 
       17.98        29.16        46.78        19.79        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       10.78         6.28        62.86        18.81         6.15         3.06 
TCGA-FT-A61P TCGA-GC-A3WC TCGA-K4-A3WS TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       11.08        17.75        25.02        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T2 
       33.14        86.83        14.93        12.76        11.90        18.90 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN3 
        2.24        10.82        54.90        91.73        98.99        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.88         9.63        94.29        34.06        57.90        12.23 
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R 
       24.13        44.94         6.74         6.58        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42B TCGA-CF-A1HR TCGA-CF-A7I0 
       14.96         8.25        16.18        17.56        12.79        12.10 
TCGA-CF-A9FF TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I4 
       11.87        21.86       112.44        17.62        17.95       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WY TCGA-DK-AA6X TCGA-E7-A6MD TCGA-FD-A3B3 
        4.80        13.58       163.30        15.35         4.24        32.02 
TCGA-FD-A3B8 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62S 
       12.62        25.74        14.96        20.91        27.45        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2EO 
        2.27        10.85         8.94        22.88        15.95        59.31 
TCGA-GC-A3OO TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 
       15.81        13.91        26.70         2.10        20.98        20.05 
TCGA-GU-A767 TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        4.73        21.24        11.70        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A8OD 
        1.15        38.99        37.05        22.68         3.02       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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN0 
        5.98        23.64        28.24        92.98         2.96        56.48 
TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-AA52 
       27.06        22.36        25.41        35.41 

$subtype2
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2I6 
        8.35        20.48        28.70        15.12       130.88        87.32 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-FD-A3SS TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TH 
       64.18        15.68        12.85        18.08        58.92         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A40G 
        9.67        31.07        70.32        10.92        20.28        19.07 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-AAMH 
        3.45         2.76        52.73         3.22        15.98        11.31 
TCGA-XF-AAMZ TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA82 TCGA-5N-A9KM 
       44.32        11.97        94.88         8.35        51.16        17.42 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-C4-A0F1 TCGA-CF-A47S TCGA-CU-A5W6 
       40.08         2.66        13.15         2.93        10.95         1.84 
TCGA-E7-A677 TCGA-E7-A97Q TCGA-FD-A43N TCGA-FD-A62O TCGA-G2-AA3B TCGA-GV-A3JV 
       26.96         8.09        22.98         7.10        66.02        14.27 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-UY-A9PD TCGA-XF-AAMX TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        1.51        38.60        17.82         6.77        21.86        28.41 
TCGA-ZF-AA51 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35         5.52        10.65 

$subtype3
TCGA-4Z-AA89 TCGA-BT-A20N TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-DK-A1AA 
       33.83        26.14         8.98         2.04        18.58        19.00 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       50.27         9.67        17.98        53.29        76.60        67.36 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-FD-A43X 
       13.64        13.64        11.18        20.32        25.58         3.62 
TCGA-FD-A6TE TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GU-A763 
       12.36        17.23        17.62        21.40        19.13        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A54R TCGA-KQ-A41O 
       32.98        19.82        27.35        22.72        27.68        50.56 
TCGA-KQ-A41Q TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMQ 
       46.98        51.32        97.12        26.27         7.63        71.57 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T 
       30.94        18.58        21.11         3.48        88.87        19.69 
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-5N-A9KI TCGA-BT-A20P TCGA-BT-A2LA TCGA-BT-A3PH 
       66.54        47.80         2.50        17.88        17.16         4.67 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       23.01        13.97        12.59        12.13        13.08        12.16 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 
       11.34        11.34        13.08         5.19        29.79        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 
       18.41        16.14        15.62        15.02        19.00        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        38.83        29.72        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 
        0.56         0.66        24.03        13.68        12.95        15.32 
TCGA-E7-A8O8 TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-A3IE 
        0.43         5.36        12.66        10.65        26.93        20.12 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R 
       29.36        14.07         0.49         3.12         2.20        18.97 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ 
        7.00        21.34        19.10         8.48        36.49        19.40 
TCGA-HQ-A2OF TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 
       64.01        44.38        15.58        21.07        13.48        16.54 
TCGA-UY-A78K TCGA-UY-A78O TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-AAMG 
       17.62        76.01        45.04         6.58        17.88       110.60 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RM TCGA-ZF-A9RN 
        0.66        11.97        31.20        35.84        47.84        20.22 
TCGA-ZF-AA4U TCGA-ZF-AA4X 
        8.61        67.20 

$subtype4
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YN TCGA-DK-A3IU 
       16.77        15.12        25.94         9.96        12.92        23.21 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 
       50.70        52.01       165.73        15.35         1.22        33.04 
TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TD 
       60.66        27.35        15.58         5.69         8.25        12.69 
TCGA-G2-A2ES TCGA-GC-A3YS TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-XF-A8HD 
       33.01        24.92         8.58         9.01         9.14        97.45 
TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
      125.49        34.45        21.04        66.64         2.10        13.74 
TCGA-XF-AAN2 TCGA-YF-AA3M TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A13I 
       61.45        13.64        27.62        41.75        10.22         7.33 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       19.04        12.16         5.06        36.43        28.41         1.94 
TCGA-CF-A1HS TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-AA6Q 
       12.56         7.79         8.15        20.81        10.55        13.58 
TCGA-DK-AA6T TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 
       18.81        14.07        14.37        16.77         8.94        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A5BU TCGA-FD-A62N TCGA-FT-A3EE TCGA-G2-A2EF 
       27.98         5.52        19.33         2.70         3.25        61.94 
TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A762 
       48.00        20.71        15.91         8.94        11.31         7.63 
TCGA-GU-A766 TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-LC-A66R TCGA-PQ-A6FI 
       15.78        12.16         9.07         1.81        15.32        12.23 
TCGA-PQ-A6FN TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A9SG 
       16.67        78.25        69.34        35.24        29.56        48.62 
TCGA-XF-A9T4 TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9RD TCGA-ZF-A9RF 
       16.27         8.32        75.39        18.84        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 
       58.72         2.89        59.38        60.16        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       54.21        29.49 

subtype1 subtype2 subtype3 subtype4 
    1.15     1.51     0.43     1.22 
subtype1 subtype2 subtype3 subtype4 
  166.03   130.88   110.60   165.73 
subtype1 subtype2 subtype3 subtype4 
   17.85    15.98    17.93    16.47 
[1] "1.1 - 166.0 (17.9)" "1.5 - 130.9 (16.0)" "0.4 - 110.6 (17.9)"
[4] "1.2 - 165.7 (16.5)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       22        45       58
  subtype2       1        9        15       26
  subtype3       1       62        39       26
  subtype4       0       31        36       25
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          0        1        1        0
  STAGE II        22        9       62       31
  STAGE III       45       15       39       36
  STAGE IV        58       26       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       23 78 19
  subtype2       13 26 11
  subtype3       57 39 16
  subtype4       27 47 12
D9V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4
  T0+T1+T2       23       13       57       27
  T3             78       26       39       47
  T4             19       11       16       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 61 17 40  1
  subtype2 22  9 14  3
  subtype3 87  8 12  2
  subtype4 60 12 10  2
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       61       22       87       60
  N1       17        9        8       12
  N2       40       14       12       10
  N3        1        3        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 49  5
  subtype2 23  1
  subtype3 82  4
  subtype4 34  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    5
  subtype2   23    1
  subtype3   82    4
  subtype4   34    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       49       23       82       34
  1        5        1        4        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"
D9V7, binary
          cls
clus         0   1
  subtype1  38  87
  subtype2  13  39
  subtype3  28 101
  subtype4  28  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   87
  subtype2   13   39
  subtype3   28  101
  subtype4   28   64
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       38       13       28       28
  MALE         87       39      101       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"
D9V8, binary
          cls
clus         0   1
  subtype1 112   3
  subtype2  50   1
  subtype3 109  13
  subtype4  83   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  112    3
  subtype2   50    1
  subtype3  109   13
  subtype4   83    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       112       50      109       83
  YES        3        1       13        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"
D9V9, continuous
D9V10, continuous
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         5   113
  subtype2     3                         3    44
  subtype3    27                         6    85
  subtype4     4                         8    75
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            7        3       27        4
  BLACK OR AFRICAN AMERICAN        5        3        6        8
  WHITE                          113       44       85       75
[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   3 118
  subtype2   0  48
  subtype3   3 110
  subtype4   3  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  118
  subtype2    0   48
  subtype3    3  110
  subtype4    3   81
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        3        3
  NOT HISPANIC OR LATINO      118       48      110       81
[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 42 45
  subtype2 28 32
  subtype3 17 25
  subtype4 93 39
  subtype5 39 35
subtype1 subtype2 subtype3 subtype4 subtype5 
      87       60       42      132       74 
subtype1 subtype2 subtype3 subtype4 subtype5 
      45       32       25       39       35 
$subtype1
TCGA-BT-A20T TCGA-CU-A0YO TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT 
       14.89         4.90        16.70        46.68        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-AA74 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SQ 
       23.21        56.15         4.01        24.30        23.41        46.78 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FT-A61P TCGA-GC-A3WC 
       53.88        10.78        18.81         3.06        11.08        17.75 
TCGA-K4-A3WS TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A9SP TCGA-XF-A9SW 
       25.02        14.24        33.14        86.83        14.93        11.90 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-AA53 
        2.24        10.82        91.73         3.88         9.63        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A20Q 
       12.23        24.13        44.94        34.98         6.58        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CF-A7I0 
        5.06        14.96         8.25        16.18        12.79        12.10 
TCGA-CF-A9FF TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 
       11.87        29.79        21.86       112.44        17.62        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WY TCGA-DK-AA6X TCGA-E7-A6MD 
      142.78         4.80        13.58       163.30        15.35         4.24 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
       32.02        16.77        12.62        25.74        14.96        20.91 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EK TCGA-GC-A3OO 
        2.27        10.85         8.94        22.88        15.95        15.81 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-A767 TCGA-K4-A83P 
       26.70         2.10        20.98        20.05         4.73        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       11.80         1.15       112.83         6.21         3.85         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAME 
       64.80        79.66        66.41         5.98        23.64        92.98 
TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-AA52 
       27.06        22.36        35.41 

$subtype2
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A1A5 
        8.35        20.48         9.96        28.70        15.12         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-FD-A3SS TCGA-FD-A5C0 
      130.88        87.32        64.18        15.68        12.85        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-GU-A42P 
       58.92        62.86         6.15         4.31        31.07        10.92 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-S5-A6DX 
       20.28        19.07         3.45         2.76        52.73         1.84 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMY 
        3.22        15.98        12.76        11.31        54.90        98.99 
TCGA-XF-AAMZ TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 
       44.32        11.97        94.88         8.35        27.62        51.16 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-C4-A0F1 TCGA-CF-A47S 
       17.42        40.08         2.66        13.15         2.93        10.95 
TCGA-CU-A5W6 TCGA-E7-A97Q TCGA-FD-A5BZ TCGA-FD-A62O TCGA-GU-A766 TCGA-GV-A3JV 
        1.84         8.09        27.45         7.10        15.78        14.27 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD 
        1.51        38.60        38.99        76.01        69.34        17.82 
TCGA-XF-A9SZ TCGA-XF-AAMX TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-GU-AATO 
       28.24         6.77        21.86        28.41        56.35        10.65 

$subtype3
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-C4-A0EZ TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A72E 
      108.95        16.27         8.98         2.04        18.58        13.58 
TCGA-DK-A3X1 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-FD-A3SM TCGA-FD-A3SR 
       66.05        38.24       166.03        13.64        17.98        19.79 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A62P TCGA-GC-A3YS TCGA-KQ-A41P TCGA-XF-A9T2 
       15.58        26.73         6.28        24.92        35.97        18.90 
TCGA-XF-AAN3 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-2F-A9KR TCGA-5N-A9KI 
       86.30        94.29        34.06        19.69       104.65         2.50 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20V TCGA-DK-A1AE TCGA-E7-A6ME 
        6.74        19.04        17.88         5.06        16.14        24.03 
TCGA-E7-A85H TCGA-FD-A5BU TCGA-FD-A62S TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A6I3 
       12.95        19.33        13.35        26.93        59.31        13.91 
TCGA-GU-AATQ TCGA-K4-A3WV TCGA-K4-A5RI TCGA-UY-A78L TCGA-UY-A78M TCGA-ZF-A9R1 
        7.00        21.24        11.70        37.05        22.68        25.41 

$subtype4
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-CU-A0YN TCGA-DK-A1AA TCGA-DK-A3IS 
       15.12        33.83        26.14        12.92        19.00        50.27 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 
        9.67        17.98        53.29        76.60        67.36        50.70 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3NA 
       13.64        11.18        20.32        15.35        25.58        60.66 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A3VY 
       27.35         3.62        12.36         9.67        17.23        17.62 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       21.40        19.13        32.78        32.98        19.82        27.35 
TCGA-GV-A6ZA TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-UY-A9PH TCGA-XF-A8HD 
       22.72        27.68        50.56        46.98        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN1 
       97.12        26.27         2.10         7.63        71.57        30.94 
TCGA-XF-AAN2 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-4Z-AA7O TCGA-4Z-AA7R 
       61.45        21.11         3.48        88.87        16.83        17.16 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-BT-A3PH TCGA-C4-A0F6 
       50.04         0.62        66.54        47.80         4.67        23.01 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        12.16        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A8HX 
       12.46        12.10        12.62        12.26        12.00        11.34 
TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AG 
       11.34        13.08         5.19        66.41        18.41        15.62 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC 
        8.15        15.02        18.81        19.00        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-E7-A8O8 TCGA-FD-A43N 
        0.66        26.96        13.68        15.32         0.43        22.98 
TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B 
        5.36        12.66        10.65         3.25        20.12        66.02 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R 
       29.36        14.07         0.49         3.12         2.20        18.97 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OF 
       21.34        19.10         8.48        36.49        19.40        64.01 
TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 
       15.42        44.38        15.58        21.07        13.48        16.54 
TCGA-UY-A78K TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9T4 TCGA-XF-AAMG 
       17.62        45.04         6.58        17.88        16.27       110.60 
TCGA-XF-AAMW TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        8.32        18.84         0.66        11.97        31.20        35.84 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA5N 
       47.84        20.22         8.61        59.38        67.20         5.52 

$subtype5
TCGA-4Z-AA7Q TCGA-BT-A3PJ TCGA-DK-A3IN TCGA-DK-AA6M TCGA-DK-AA6R TCGA-E7-A7DV 
       16.77        25.94         8.22        52.01       165.73         1.22 
TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TD TCGA-G2-A2ES 
       33.04        29.16         5.69         8.25        12.69        33.01 
TCGA-G2-AA3D TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-XF-A8HE TCGA-XF-A9SM 
       70.32         8.58         9.01         9.14       125.49        34.45 
TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-4Z-AA81 
       21.04        66.64        13.74        18.58        13.64        41.75 
TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42E 
       10.22         7.33        12.16        17.16        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX 
       28.41         1.94        12.56         7.79        20.81        10.55 
TCGA-DK-AA6Q TCGA-E7-A7XN TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 
       13.58        14.07        14.37         8.94        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A62N TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC 
        5.52         2.70        61.94        48.00        20.71        15.91 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A762 TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A6FZ 
        8.94        11.31         7.63        12.16         9.07         1.81 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       15.32        12.23        16.67        78.25         3.02        35.24 
TCGA-UY-A9PB TCGA-XF-A9SG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9RD 
       29.56        48.62         2.96        56.48        75.39        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 
       64.08        58.72         2.89        60.16        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       54.21        29.49 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.15     1.51     2.04     0.43     1.22 
subtype1 subtype2 subtype3 subtype4 subtype5 
  163.30   130.88   166.03   110.60   165.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.770   16.700   19.185   17.930   16.290 
[1] "1.1 - 163.3 (16.8)" "1.5 - 130.9 (16.7)" "2.0 - 166.0 (19.2)"
[4] "0.4 - 110.6 (17.9)" "1.2 - 165.7 (16.3)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       0       18        33       37
  subtype2       1       12        18       29
  subtype3       0        9        17       16
  subtype4       1       65        36       30
  subtype5       0       20        31       23
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0        1        0        1        0
  STAGE II        18       12        9       65       20
  STAGE III       33       18       17       36       31
  STAGE IV        37       29       16       30       23
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1+T2 T3 T4
  subtype1       18 52 14
  subtype2       15 30 14
  subtype3        9 25  6
  subtype4       62 38 15
  subtype5       16 45  9
D10V4, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1+T2       18       15        9       62       16
  T3             52       30       25       38       45
  T4             14       14        6       15        9
[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 45  8 29  0
  subtype2 28 10 17  3
  subtype3 24  7  8  1
  subtype4 89  9 13  2
  subtype5 44 12  9  2
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       45       28       24       89       44
  N1        8       10        7        9       12
  N2       29       17        8       13        9
  N3        0        3        1        2        2
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 39  2
  subtype2 24  1
  subtype3 18  3
  subtype4 77  5
  subtype5 30  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    2
  subtype2   24    1
  subtype3   18    3
  subtype4   77    5
  subtype5   30    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       39       24       18       77       30
  1        2        1        3        5        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"
D10V7, binary
          cls
clus         0   1
  subtype1  30  58
  subtype2  14  47
  subtype3  12  30
  subtype4  29 104
  subtype5  22  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   58
  subtype2   14   47
  subtype3   12   30
  subtype4   29  104
  subtype5   22   52
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       14       12       29       22
  MALE         58       47       30      104       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"
D10V8, binary
          cls
clus         0   1
  subtype1  78   1
  subtype2  58   2
  subtype3  37   2
  subtype4 112  13
  subtype5  69   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78    1
  subtype2   58    2
  subtype3   37    2
  subtype4  112   13
  subtype5   69    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        78       58       37      112       69
  YES        1        2        2       13        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
D10V10, continuous
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         5    78
  subtype2     3                         3    53
  subtype3     4                         4    31
  subtype4    25                         6    94
  subtype5     4                         4    61
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        3        4       25        4
  BLACK OR AFRICAN AMERICAN        5        3        4        6        4
  WHITE                           78       53       31       94       61
[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"
D10V13, binary
          cls
clus         0   1
  subtype1   1  83
  subtype2   1  55
  subtype3   1  37
  subtype4   3 117
  subtype5   3  65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   83
  subtype2    1   55
  subtype3    1   37
  subtype4    3  117
  subtype5    3   65
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        1        1        3        3
  NOT HISPANIC OR LATINO       83       55       37      117       65
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
