[1] "ofn"        "-oTSKCM-TM"
[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/SKCM-TM/22507034/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/22546664/SKCM-TM.mergedcluster.txt"

nPatients in clinical file=368, in cluster file=368, common to both=368
[1]  10 368
[1] "CN_CNMF"
[1] 3
  1   2   3 
154 110 103 
  1   2   3 
154 110 103 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
111 122  35  99 
  1   2   3   4 
111 122  35  99 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
39 78 43 69 33 
 1  2  3  4  5 
39 78 43 69 33 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
86 84 92 
 1  2  3 
86 84 92 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
117  73 105  73 
  1   2   3   4 
117  73 105  73 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
106 165  97 
  1   2   3 
106 165  97 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
 97 104  97  54 
  1   2   3   4 
 97 104  97  54 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
132  93  89  38 
  1   2   3   4 
132  93  89  38 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 85 119 134 
  1   2   3 
 85 119 134 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
36 24 51 64 38 17 64 29 15 
 1  2  3  4  5  6  7  8  9 
36 24 51 64 38 17 64 29 15 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"       
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 368 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=191,	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=164,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=288,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=110,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 368 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 41 73 81 68 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    73    81    68 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 73 81 68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    73    81    68 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
177  66  39  45 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
177  66  39  45 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
177  66  39  45 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
177  66  39  45 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=110, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
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 46 58
  subtype2 34 37
  subtype3 48 29
subtype1 subtype2 subtype3 
     104       71       77 
subtype1 subtype2 subtype3 
      58       37       29 
$subtype1
TCGA-D3-A2JF TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 
       62.07        13.41        31.96       166.75        52.90        19.04 
TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.73         7.40        60.46         8.42        31.89       110.93 
TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CE 
       25.64        86.30        64.83        66.08        43.53        59.70 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       23.67       173.85        31.76       177.86       124.08        78.21 
TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HY 
       23.61        69.53        70.62        16.90        69.21       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A95V 
      150.61        60.10        64.83        58.85       225.11        72.10 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29B 
       65.03        12.30         3.91        20.38         0.00        75.22 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 
       12.99        47.41        47.74       346.49       185.19        77.98 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
        0.76        71.31        81.99        89.26       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
       23.51       122.73        64.04        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
      111.85       135.98        10.49        53.29        39.81       184.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET 
       42.51        49.71       146.63         4.70        10.19        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 
       15.48        32.05        26.20        10.06       171.78       195.98 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A4EO 
        4.47         3.06        66.67        80.68        55.59        18.25 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
      117.93        17.06        42.48        34.49        46.92        43.23 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZQ 
       85.05         7.23         0.33        79.99        92.84        62.43 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

$subtype2
TCGA-D3-A2JE TCGA-EE-A2GD TCGA-FR-A729 TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q8 
        9.76       269.03       216.43        12.99        49.35        19.04 
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51J TCGA-D3-A51T 
      107.61        58.06        40.01         9.34       144.46        11.34 
TCGA-D3-A5GN TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 
       45.70       179.97       135.12        36.53        10.78        18.44 
TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A5UN 
       22.85        68.68       110.53         0.76        14.14        52.41 
TCGA-EE-A17Y TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
       24.89        27.16        30.02        26.14        12.95        68.65 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF 
       18.35        93.63         0.20       103.13        15.25       209.79 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19D 
        4.41        45.90         3.35       168.85         7.82        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
      150.12        99.06        59.84        22.36        16.87        28.67 
TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZM 
      173.29         4.50       174.21         4.14         8.35        78.61 
TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 
       35.28         5.29       173.19        11.54         1.91        53.29 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X TCGA-W3-A825 TCGA-WE-A8ZM 
        7.59       120.53        59.41       297.01         1.97        65.42 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-XV-AB01 
       21.90        10.95        48.39        24.99         6.61 

$subtype3
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-BF-AAP0 
       38.76        33.24       134.40        27.35        36.95        14.83 
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       15.72       133.25        76.41        62.60        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CF 
       15.75       168.00        36.30       171.58       140.98        24.53 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D9-A3Z1 
       90.21        30.67        62.70        42.05       120.00        15.02 
TCGA-DA-A1HV TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X 
       76.34        30.44         8.71        16.41        18.21        13.15 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       26.24        75.55        79.20        76.14         0.26        44.28 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 
       61.12       115.43       201.60        10.62        32.48         5.75 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       23.77        94.19       171.85        63.25       104.78       145.45 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19P 
       53.26       124.31        19.86        34.45         4.54       120.76 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A42L TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z4 
       47.18        73.05        74.47         5.65        49.74        27.62 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A3OT 
      136.27        23.21        30.90        13.28        19.30         9.90 
TCGA-GN-A265 TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
       96.92         0.20       174.12       120.07        44.05         8.09 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 
      185.13        47.54        12.69         1.94        37.32 

subtype1 subtype2 subtype3 
     0.0      0.2      0.2 
subtype1 subtype2 subtype3 
  346.49   297.01   201.60 
subtype1 subtype2 subtype3 
   57.22    28.67    44.05 
[1] "0.0 - 346.5 (57.2)" "0.2 - 297.0 (28.7)" "0.2 - 201.6 (44.0)"
D1V2, survival
          sevent
clus2       0  1
  subtype1 59 92
  subtype2 48 57
  subtype3 59 43
subtype1 subtype2 subtype3 
     151      105      102 
subtype1 subtype2 subtype3 
      92       57       43 
$subtype1
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       62.07        13.87        58.52        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 
        2.60       126.81        31.40        15.45        18.05        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       21.40        17.03        66.48        16.57       112.04       112.57 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       31.59        43.43        86.76        66.48        66.08        59.57 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N 
       46.98        60.23        39.75       174.84        32.94        22.62 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GL 
      178.32        18.18       125.19        79.59        23.61        89.13 
TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      107.15       151.53        54.67         3.65         7.10        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.90        25.18        77.56       144.89       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95V 
       88.87        65.92        68.09        10.49       225.96        72.10 
TCGA-DA-A95X TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20B 
       73.94        13.02        13.87        33.73        14.70       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
       13.55        63.35        85.08        13.97        64.64        56.84 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GP 
      369.93       195.02        17.92        39.29        86.14        13.91 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN 
       81.21        94.82        47.28        16.96       180.39        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      248.65       162.48        71.21       122.73        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI 
       13.81        41.59       172.18       127.20        53.19       152.81 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       13.94        98.40        48.89        13.02        26.37       302.07 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
        6.44        44.09        50.89         8.88       148.18        23.34 
TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A7U8 
       28.83        93.01        46.98        33.21        12.95        27.85 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       34.82        36.26       216.92       202.65        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4FD 
      133.55        26.56        27.02        50.14        66.67        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       17.46        55.59        19.43       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       48.00        39.35        10.42        48.89        22.13        50.10 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-AA1O TCGA-W3-AA1R 
       21.37       368.78         7.23         0.33         4.01       111.09 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
      105.04        24.03        63.22        37.94        14.43        96.99 
TCGA-Z2-AA3V 
       15.98 

$subtype2
TCGA-D3-A2JE TCGA-EB-A5SH TCGA-EE-A2GD TCGA-FR-A729 TCGA-3N-A9WD TCGA-D3-A1Q6 
       27.65        54.02       340.14       220.80        12.99        71.80 
TCGA-D3-A1Q8 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       28.08        11.87       113.52        12.10        58.06        86.93 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
        9.34        45.30       145.12        26.89       135.75       137.92 
TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1X3 
      241.38       161.00       152.75        29.06       129.63        18.12 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       18.44        22.95        36.03       222.51       135.02        53.92 
TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
       37.35        14.14        10.36        29.29        58.92        27.22 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        8.65         4.96        56.42        14.47        61.28        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       59.64        59.28       173.79        48.72       107.38        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MQ 
      102.12        42.77       129.27        28.83       268.73        43.23 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       28.77       138.81        36.95        64.08        34.32       201.80 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC 
        9.17        12.59       152.35       131.51        61.05        43.82 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A 
       20.15        48.99        41.56       247.04        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZM TCGA-FS-A1ZR 
       15.72        48.59        20.91         7.79       101.26        11.41 
TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3TV 
       53.16        27.09        28.73       174.84        26.73        13.51 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD 
        2.04       139.89        10.13        32.48       121.91        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-A825 TCGA-WE-A8K6 
        0.23        65.88       297.90         0.69        63.02        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      101.33        70.52        11.80        35.80        49.51        24.99 
TCGA-XV-AB01 TCGA-YD-A89C TCGA-YD-A9TA 
       13.25         6.90        49.18 

$subtype3
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FW-A3R5 
       46.32        68.25       134.40        27.35        50.76        36.95 
TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       14.93        16.67       133.25        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL 
       65.49        23.77       115.53       168.00        42.08       171.58 
TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
      130.72       166.52        24.53       103.59        55.73        56.35 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GS 
       63.81       125.79        30.84        26.43       170.20       117.17 
TCGA-D3-A8GV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 
      167.70        15.39        76.57        20.38        40.60        33.93 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 
       43.36        20.35         7.04        36.46        29.82        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N 
      151.27        91.56        78.97        63.78        72.07        18.61 
TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GK 
       66.74        46.82       115.96        67.43       220.24        54.74 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       79.66        44.88        21.67        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MU 
      103.20       204.66        96.23       216.66       167.90        53.26 
TCGA-EE-A3AA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19P 
      124.31        51.35       134.33        35.44        77.75       162.08 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A42L TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       49.48       105.07       149.03        18.77        38.27       104.42 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW 
      228.59        28.08        48.85        74.73       148.80        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 
       77.82        34.03        54.41        19.30         9.90        15.78 
TCGA-GN-A265 TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V 
       96.92         0.20       228.16       121.08        69.07        42.08 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
      219.16        49.05        58.98        12.16        40.41        27.58 

subtype1 subtype2 subtype3 
    0.33     0.23     0.20 
subtype1 subtype2 subtype3 
  369.93   340.14   228.59 
subtype1 subtype2 subtype3 
  50.100   48.590   62.645 
[1] "0.3 - 369.9 (50.1)" "0.2 - 340.1 (48.6)" "0.2 - 228.6 (62.6)"
D1V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        5       1       8       10       13        9         4
  subtype2        4       3       8        4        6       10         3
  subtype3        4       3      13        4        9        7         7
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         8         8        15          7         14         24
  subtype2         4         6        14          6         12         15
  subtype3         7         1        10          2          9         15
          vv
clus       STAGE IV
  subtype1       11
  subtype2        5
  subtype3        5
D1V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  I/II NOS          5        4        4
  STAGE 0           1        3        3
  STAGE I           8        8       13
  STAGE IA         10        4        4
  STAGE IB         13        6        9
  STAGE II          9       10        7
  STAGE IIA         4        3        7
  STAGE IIB         8        4        7
  STAGE IIC         8        6        1
  STAGE III        15       14       10
  STAGE IIIA        7        6        2
  STAGE IIIB       14       12        9
  STAGE IIIC       24       15       15
  STAGE IV         11        5        5
[1] 14  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    33 29 29 30
  subtype2    15 21 25 23
  subtype3    16 23 27 14
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       33       15       16
  T2          29       21       23
  T3          29       25       27
  T4          30       23       14
[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       N0 N1 N2 N3
  subtype1 72 22 19 24
  subtype2 46 30 11  8
  subtype3 59 13  9 13
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       72       46       59
  N1       22       30       13
  N2       19       11        9
  N3       24        8       13
[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"
D1V7, binary
          cls
clus         0   1
  subtype1 131  12
  subtype2  96   5
  subtype3  92   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  131   12
  subtype2   96    5
  subtype3   92    5
   clus
vv  subtype1 subtype2 subtype3
  0      131       96       92
  1       12        5        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"
D1V8, binary
          cls
clus        0  1
  subtype1 61 42
  subtype2 31 29
  subtype3 42 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   42
  subtype2   31   29
  subtype3   42   19
     clus
vv    subtype1 subtype2 subtype3
  NO        61       31       42
  YES       42       29       19
[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"
D1V9, binary
          cls
clus         0   1
  subtype1  23 131
  subtype2  11  99
  subtype3  13  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23  131
  subtype2   11   99
  subtype3   13   90
     clus
vv    subtype1 subtype2 subtype3
  NO        23       11       13
  YES      131       99       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"
D1V10, continuous
D1V11, binary
          cls
clus        0  1
  subtype1 63 91
  subtype2 47 63
  subtype3 28 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   91
  subtype2   47   63
  subtype3   28   75
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       63       47       28
  MALE         91       63       75
[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"
D1V12, binary
          cls
clus         0   1
  subtype1 136  18
  subtype2  94  16
  subtype3  89  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  136   18
  subtype2   94   16
  subtype3   89   13
     clus
vv    subtype1 subtype2 subtype3
  NO       136       94       89
  YES       18       16       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0   149
  subtype2     2                         0   105
  subtype3     2                         1    99
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        2
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                          149      105       99
[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"
D1V14, binary
          cls
clus         0   1
  subtype1   4 147
  subtype2   1 105
  subtype3   2 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  147
  subtype2    1  105
  subtype3    2  100
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        2
  NOT HISPANIC OR LATINO      147      105      100
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 32 46
  subtype2 53 35
  subtype3  9 17
  subtype4 33 27
subtype1 subtype2 subtype3 subtype4 
      78       88       26       60 
subtype1 subtype2 subtype3 subtype4 
      46       35       17       27 
$subtype1
TCGA-D3-A8GI TCGA-EE-A180 TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC 
       13.41        31.96        19.04        36.95        52.73        60.46 
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51J 
       15.72        76.41       107.61       171.58        23.67       144.46 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GM 
       11.34        42.05       124.08        78.21        69.53        70.62 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I2 
      135.12        36.53        10.78        69.21        22.85       150.61 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       64.83        58.85         0.76        65.03        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B 
        3.91        16.41        13.15         0.00        75.55        75.22 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GJ 
       12.99        47.41        27.16        30.02        77.98        68.65 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AC 
       18.35         0.20        81.99       104.78       145.45        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A2ND 
        4.41         6.28       111.85         3.35       135.98         4.70 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1ZE 
       16.87        32.05         4.50        10.06        49.74        43.92 
TCGA-FS-A1ZG TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GN-A264 
        7.82        30.90        66.67        13.28        55.59       117.93 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-RP-A693 TCGA-W3-A824 
       42.48       120.53        34.49        43.23         0.33       174.12 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-YG-AA3O 
       44.05        79.99        92.84        21.90        48.39        28.21 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-3N-A9WD 
       38.76        33.24       269.03       134.40        27.35        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 
       14.83        49.35       133.25        19.04        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JN 
       62.86        15.75       168.00        86.30        36.30        64.83 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A5GR 
       66.08       140.98        24.53        90.21        30.67       177.86 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I5 TCGA-DA-A3F2 
       23.61       179.97        15.02        16.90       110.53        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 
      225.11         8.71        52.41        18.21        20.38        26.24 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GH 
       44.28        47.74       346.49       115.43        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MJ 
       10.62        32.48         5.75        23.77        94.19        63.25 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       53.26       124.31       122.73        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        7.82         4.54        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A44A 
       47.18       146.63        73.05        28.67        74.47       174.21 
TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV 
        5.65        27.62        35.28        23.21       173.19        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 
       19.30         9.90        18.25        96.92         7.59        46.92 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
       59.41         7.23       120.07         8.09       185.13        47.54 
TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69         1.94        37.32        24.99 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A8GK 
        8.42        31.89       110.93        25.64        40.01       120.00 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19C 
       76.14         0.26       171.85       143.93        23.51        39.81 
TCGA-ER-A19L TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1ZD 
       99.06        10.19       173.29        15.48       195.98        32.78 
TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-GF-A6C8 TCGA-GN-A267 
       36.33       136.27         4.47        80.68         1.91        17.06 
TCGA-RP-A690 TCGA-WE-A8ZR 
        0.20         8.68 

$subtype4
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GO TCGA-FR-A729 TCGA-WE-AAA3 
        9.76        62.07       166.75        52.90       216.43         7.40 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51K 
       43.53        58.06        59.70         9.34       173.85        31.76 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       62.70        45.70        18.44        76.34       138.67        68.68 
TCGA-DA-A1I7 TCGA-DA-A95V TCGA-EE-A17Y TCGA-EE-A20F TCGA-EE-A29Q TCGA-EE-A29W 
       60.10        72.10        24.89        79.20        61.12       185.19 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       26.14        93.63         0.76        71.31       103.13        15.25 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      209.79        89.26       227.01        54.51        67.89        45.90 
TCGA-EE-A3JB TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A2NC 
      168.85        53.29        11.47       184.60       150.12        22.36 
TCGA-ER-A3ET TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       68.52         4.14        26.20       171.78         8.35       312.07 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-GN-A262 TCGA-LH-A9QB 
       78.61       130.95         5.29         3.06        53.29        85.05 
TCGA-OD-A75X TCGA-W3-A825 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-Z2-AA3S 
      297.01         1.97        65.42        62.43        10.95        91.23 

subtype1 subtype2 subtype3 subtype4 
    0.00     1.94     0.20     0.76 
subtype1 subtype2 subtype3 subtype4 
  174.12   346.49   195.98   312.07 
subtype1 subtype2 subtype3 subtype4 
  42.855   40.635   34.555   62.250 
[1] "0.0 - 174.1 (42.9)" "1.9 - 346.5 (40.6)" "0.2 - 196.0 (34.6)"
[4] "0.8 - 312.1 (62.2)"
D2V2, survival
          sevent
clus2       0  1
  subtype1 39 67
  subtype2 69 51
  subtype3 11 24
  subtype4 46 51
subtype1 subtype2 subtype3 subtype4 
     106      120       35       97 
subtype1 subtype2 subtype3 subtype4 
      67       51       24       51 
$subtype1
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L 
       13.87        58.52        54.02        94.98        68.15         2.60 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WB TCGA-3N-A9WC 
       31.40        50.76        36.95        61.15        17.03        66.48 
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51J 
       16.67        90.90       113.52       171.58        39.75       145.12 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GM 
       26.89       125.79       125.19        79.59        89.13       107.15 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      152.75       129.63       151.53        54.67         3.65        18.12 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC 
       25.18        77.56        22.95       176.55        65.92        68.09 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       37.35        73.94        14.14        13.02        13.87        20.35 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
       29.82        14.70         4.96       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X 
       85.08        13.97        64.64        56.42        61.28        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR 
       59.64        86.14        67.43       107.38        75.48        42.77 
TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       94.82        47.28       216.66       167.90        47.54        43.23 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       64.04        28.77        13.81       127.20        36.95        34.32 
TCGA-EE-A3JI TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A3YN 
      152.81         8.88        23.34        20.15        33.21        92.98 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A4F0 
       34.82        36.26       228.59        46.45         9.70        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3TU 
       50.14        66.67        28.73        34.03        54.41        55.59 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A8LK 
      117.93        62.79       121.91        39.35        10.42        50.10 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 
        0.33       228.16         4.01        69.07       111.09       105.04 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-A8RT 
       70.52        49.51        37.94        27.58 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-3N-A9WD 
       46.32        68.25       340.14       134.40        27.35        12.99 
TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 
       14.93        71.80       133.25        28.08        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CF 
       42.08        66.48        66.08       130.72       166.52        24.53 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A8GB 
      103.59        55.73        56.35        22.62       178.32        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A3Z1 
       23.61        26.43       241.38       161.00       117.17        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1IB 
       22.29         9.90        36.03        20.38       135.02        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       33.93       225.96        43.36        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N 
       36.46        33.73        26.89        72.07        56.84        18.61 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GH 
      369.93        25.87        46.82       115.96       173.79       220.24 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       54.74        79.66        44.88        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AA 
      103.27       103.20        16.96        96.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      122.73        51.35       134.33        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       77.75        61.05        44.09       162.08        50.89        49.48 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A44A 
      148.18       105.07        48.99        41.56       149.03       174.21 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZT 
       18.77        38.27       104.42        28.08        48.85        53.16 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.48       174.84        13.51        19.30         9.90        19.43 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD 
       15.78        96.92        10.13        32.48        48.89        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.23        65.88         7.23       121.08        42.08       219.16 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3V 
       49.05        58.98        12.16        40.41        24.99        15.98 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A8GK 
       16.57       112.04       112.57        43.43        86.93       170.20 
TCGA-DA-A1I4 TCGA-EB-A44R TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2MI TCGA-EE-A2MS 
       35.93        10.36        78.97        63.78       204.66       162.48 
TCGA-EE-A2MT TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV 
       71.21        48.89       131.51        28.83       247.04        46.98 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZR 
      202.65         7.79        53.52        47.38        23.93        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D 
      148.80        26.56        80.68         2.04        64.44        48.00 
TCGA-GN-A8LL TCGA-RP-A690 TCGA-WE-A8K6 TCGA-WE-A8ZR TCGA-YG-AA3P 
       21.37         0.20        17.95         9.01        14.43 

$subtype4
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GO TCGA-FR-A729 TCGA-FS-A1ZF 
       27.65        62.07       168.26       126.81       220.80        15.45 
TCGA-QB-AA9O TCGA-WE-AAA3 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 
       18.05        21.40        31.59        12.10        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K 
       46.98        60.23         9.34        45.30       174.84        32.94 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GQ TCGA-D3-A8GV 
       63.81       135.75       137.92        18.18        29.06       167.70 
TCGA-D9-A1JX TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 
        7.10        18.44        76.57       144.89       222.51        88.87 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A20B 
       53.92        10.49        72.10        27.22         8.65       133.81 
TCGA-EE-A20F TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GB 
       91.56        66.74        14.47       195.02        39.29        59.28 
TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       48.72       102.12        13.91        81.21       129.27        28.83 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      268.73       180.39       248.65        54.51        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19B TCGA-ER-A19D 
      172.18        64.08        53.19       201.80        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NC 
       13.02        26.37       302.07       152.35         6.44        43.82 
TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX 
       93.01        12.95        15.72        27.85       216.92        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP 
       20.91        27.72       357.37        32.75       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A262 
      133.55        27.09        27.02        26.73        17.46       139.89 
TCGA-GN-A4U9 TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-A825 TCGA-WE-A8JZ 
       22.13       368.78       297.90         0.69        63.02        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YD-A89C TCGA-YD-A9TA 
      101.33        63.22        11.80        35.80         6.90        49.18 
TCGA-Z2-AA3S 
       96.99 

subtype1 subtype2 subtype3 subtype4 
    0.33     0.23     0.20     0.69 
subtype1 subtype2 subtype3 subtype4 
  228.59   369.93   247.04   368.78 
subtype1 subtype2 subtype3 subtype4 
   54.54    49.48    48.00    54.51 
[1] "0.3 - 228.6 (54.5)" "0.2 - 369.9 (49.5)" "0.2 - 247.0 (48.0)"
[4] "0.7 - 368.8 (54.5)"
D2V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        3       3       5        7        9        6         6
  subtype2        4       2      12        5        8        8         3
  subtype3        1       0       3        1        2        3         2
  subtype4        5       2       9        5        9        8         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         8         7        13          8          5         14
  subtype2         3         1        15          5         13         24
  subtype3         4         4         1          1          4          6
  subtype4         4         3        10          1         13         11
          vv
clus       STAGE IV
  subtype1        7
  subtype2        7
  subtype3        0
  subtype4        7
D2V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  I/II NOS          3        4        1        5
  STAGE 0           3        2        0        2
  STAGE I           5       12        3        9
  STAGE IA          7        5        1        5
  STAGE IB          9        8        2        9
  STAGE II          6        8        3        8
  STAGE IIA         6        3        2        3
  STAGE IIB         8        3        4        4
  STAGE IIC         7        1        4        3
  STAGE III        13       15        1       10
  STAGE IIIA        8        5        1        1
  STAGE IIIB        5       13        4       13
  STAGE IIIC       14       24        6       11
  STAGE IV          7        7        0        7
[1] 14  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    16 20 26 26
  subtype2    27 23 28 18
  subtype3     2  9  7 11
  subtype4    19 21 19 13
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       16       27        2       19
  T2          20       23        9       21
  T3          26       28        7       19
  T4          26       18       11       13
[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       N0 N1 N2 N3
  subtype1 54 20 12 12
  subtype2 51 24 11 22
  subtype3 18  6  2  3
  subtype4 54 16 14  8
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       54       51       18       54
  N1       20       24        6       16
  N2       12       11        2       14
  N3       12       22        3        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"
D2V7, binary
          cls
clus         0   1
  subtype1  96   8
  subtype2 105   7
  subtype3  31   0
  subtype4  87   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96    8
  subtype2  105    7
  subtype3   31    0
  subtype4   87    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       96      105       31       87
  1        8        7        0        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1 51 33
  subtype2 47 23
  subtype3 11 12
  subtype4 25 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   33
  subtype2   47   23
  subtype3   11   12
  subtype4   25   23
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        51       47       11       25
  YES       33       23       12       23
[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, binary
          cls
clus         0   1
  subtype1  10 101
  subtype2  20 102
  subtype3   1  34
  subtype4  16  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  101
  subtype2   20  102
  subtype3    1   34
  subtype4   16   83
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        10       20        1       16
  YES      101      102       34       83
[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"
D2V10, continuous
D2V11, binary
          cls
clus        0  1
  subtype1 34 77
  subtype2 49 73
  subtype3 11 24
  subtype4 43 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   77
  subtype2   49   73
  subtype3   11   24
  subtype4   43   56
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       34       49       11       43
  MALE         77       73       24       56
[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"
D2V12, binary
          cls
clus         0   1
  subtype1  98  13
  subtype2 102  20
  subtype3  31   3
  subtype4  87  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98   13
  subtype2  102   20
  subtype3   31    3
  subtype4   87   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        98      102       31       87
  YES       13       20        3       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   107
  subtype2     1                         1   117
  subtype3     1                         0    33
  subtype4     1                         0    96
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                          107      117       33       96
[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"
D2V14, binary
          cls
clus         0   1
  subtype1   1 106
  subtype2   3 117
  subtype3   1  34
  subtype4   2  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  106
  subtype2    3  117
  subtype3    1   34
  subtype4    2   95
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        1        2
  NOT HISPANIC OR LATINO      106      117       34       95
[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 28  5
  subtype2 24 27
  subtype3 11 16
  subtype4 23 25
  subtype5  6 16
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       51       27       48       22 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       27       16       25       16 
$subtype1
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-3N-A9WC TCGA-BF-AAP0 
       33.24       134.40        27.35       216.43        60.46        14.83 
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-D3-A3CB TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A8GD 
      133.25        62.60       140.98       173.85        30.67        23.61 
TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A44Q TCGA-EE-A29T TCGA-EE-A2A6 
       76.34         8.71        65.03         3.91       346.49        77.98 
TCGA-EE-A2GK TCGA-EE-A2M8 TCGA-EE-A2MK TCGA-ER-A19A TCGA-ER-A19P TCGA-ER-A19S 
       10.62         5.75        89.26         4.54       120.76        47.18 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FW-A5DY 
       28.67        68.52        74.47         4.50       174.21        19.30 
TCGA-GF-A4EO TCGA-GN-A4U8 TCGA-Z2-AA3S 
       18.25        46.92        91.23 

$subtype2
TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 
        7.40        12.99         8.42        31.89        49.35        62.86 
TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51T TCGA-D9-A4Z6 
       66.08        59.70         9.34        90.21        11.34        18.44 
TCGA-DA-A1HY TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EE-A182 TCGA-EE-A20F 
      138.67        30.44       225.11        72.10         0.00        79.20 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP 
       76.14         0.26        44.28       185.19       201.60         0.76 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       81.99        23.77       171.85       104.78       227.01        53.26 
TCGA-EE-A3JH TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-FR-A69P 
       19.86        11.47        59.84       146.63        22.36         4.14 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1ZD TCGA-FS-A1ZZ TCGA-FS-A4F9 TCGA-GF-A3OT 
       10.06       171.78        32.78         3.06        13.28         9.90 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-RP-A693 TCGA-W3-AA1Q TCGA-WE-A8K1 
       96.92        17.06         7.59         0.33        44.05        47.54 
TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA4 
       21.90         1.94        24.99 

$subtype3
TCGA-ER-A193 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP 
       19.04       110.93        25.64        86.30        64.83        43.53 
TCGA-D9-A1X3 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29B 
       10.78       150.61       110.53        13.15        20.38        75.22 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2GR TCGA-EE-A3AA TCGA-EE-A3AB 
       47.41        47.74        27.16         0.20       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19L 
       64.04        54.51         6.28        34.45        10.49        99.06 
TCGA-ER-A19N TCGA-FS-A1ZJ TCGA-GN-A8LK 
       42.51        36.33        43.23 

$subtype4
TCGA-D3-A2JE TCGA-EE-A180 TCGA-WE-A8K5 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A51K 
        9.76        31.96        52.73        19.04        76.41        31.76 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D9-A6EC 
       45.70        78.21       120.00        70.62       135.12        69.21 
TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A20C TCGA-EE-A2A2 TCGA-EE-A2GL 
        0.76        12.30        16.41        75.55        30.02        32.48 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       71.31       103.13        63.25       145.45       143.93        23.51 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A1A1 
       67.89        45.90         7.82        53.29       184.60        73.05 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       16.87        10.19       173.29        32.05       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GF-A6C8 
       27.62       312.07         7.82        35.28         4.47         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-WE-A8ZQ 
       53.29       117.93        42.48        85.05         7.23        62.43 

$subtype5
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95Y TCGA-EB-A5UN 
       36.53        15.02        64.83        58.85        14.14        52.41 
TCGA-EB-A6L9 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND 
       18.21         4.41        39.81       150.12        49.71         4.70 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3TV TCGA-GN-A9SD TCGA-OD-A75X TCGA-WE-A8ZR 
       78.61       130.95        11.54        59.41       297.01         8.68 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3O 
       10.95        48.39         6.61        28.21 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.91     0.00     0.20     0.76     4.41 
subtype1 subtype2 subtype3 subtype4 subtype5 
  346.49   227.01   150.61   312.07   297.01 
subtype1 subtype2 subtype3 subtype4 subtype5 
  60.460   31.890   43.530   49.315   38.170 
[1] "3.9 - 346.5 (60.5)" "0.0 - 227.0 (31.9)" "0.2 - 150.6 (43.5)"
[4] "0.8 - 312.1 (49.3)" "4.4 - 297.0 (38.2)"
D3V2, survival
          sevent
clus2       0  1
  subtype1 33  6
  subtype2 34 41
  subtype3 13 28
  subtype4 32 36
  subtype5 10 22
subtype1 subtype2 subtype3 subtype4 subtype5 
      39       75       41       68       32 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       41       28       36       22 
$subtype1
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-3N-A9WC TCGA-BF-AAP0 
       68.25       134.40        27.35       220.80        66.48        14.93 
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-D3-A3CB TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      133.25        95.74       166.52       174.84        55.73        56.35 
TCGA-D3-A8GD TCGA-D3-A8GN TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A44Q 
       23.61       161.00        76.57        43.36        73.94        13.87 
TCGA-EB-A5VV TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2M8 
        7.04        18.61       369.93        86.14        54.74        19.76 
TCGA-EE-A2MK TCGA-ER-A19A TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3ET 
      180.39        77.75       162.08        49.48        48.99        93.01 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A8YE TCGA-FW-A5DY TCGA-GF-A4EO 
      149.03        92.98       174.21       104.42        19.30        19.43 
TCGA-GF-A6C9 TCGA-GN-A4U8 TCGA-Z2-AA3S 
       15.78        48.89        96.99 

$subtype2
TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 
       21.40        12.99        16.57       112.04        71.80        65.49 
TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A51T 
       66.08        60.23         9.34       103.59        22.62        26.89 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GS TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HY 
       30.84        26.43       117.17        18.44         9.90       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       20.38        35.93        53.92        33.93        10.49       225.96 
TCGA-DA-A95V TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       72.10        14.70        91.56        78.97        63.78        72.07 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH 
       14.47        61.28        25.87       195.02        46.82       220.24 
TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI 
       48.72        13.91        94.82        21.67        61.51       204.66 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19D TCGA-ER-A19E 
      216.66       248.65        53.26       134.33        12.59        13.02 
TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A69P TCGA-FR-A7U9 
       61.05       148.18        43.82        41.56        15.72        18.77 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZZ TCGA-FS-A4F9 
       34.82       216.92        27.72        53.52        27.02        34.03 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U9 
        9.90        96.92        10.13        64.44        32.48        22.13 
TCGA-HR-A2OG TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-AA1Q TCGA-WE-A8JZ TCGA-WE-A8K1 
        0.23         0.33         0.69        69.07        24.03        49.05 
TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA4 
       70.52        12.16        24.99 

$subtype3
TCGA-D3-A3ML TCGA-EE-A184 TCGA-EE-A29L TCGA-ER-A193 TCGA-ER-A198 TCGA-D3-A1Q5 
       13.87        68.15         2.60        31.40        50.76       112.57 
TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D9-A1X3 TCGA-DA-A1HW 
       43.43        86.76        66.48        59.57        18.12        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29B 
      176.55       135.02        40.60        29.82        33.73        85.08 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA 
       64.64        56.84        56.42        42.77        44.88       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A195 TCGA-ER-A197 
      122.73        64.04        54.51        13.81        35.44        13.94 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       26.37       131.51        44.09        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-WE-A8K6 
       74.73        10.42        50.10        21.37        17.95 

$subtype4
TCGA-D3-A2JE TCGA-EB-A5SH TCGA-EE-A180 TCGA-WE-A8K5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       27.65        54.02        94.98        61.15        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GK TCGA-D3-A8GM 
       90.90        32.94       135.75        79.59       170.20       107.15 
TCGA-D3-A8GP TCGA-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A6EA 
      152.75       167.70       151.53        54.67         7.10        25.18 
TCGA-D9-A6EC TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A20C TCGA-EE-A2A2 
       77.56        37.35        13.02        20.35       151.27        59.64 
TCGA-EE-A2GC TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ 
       67.43        79.66        81.21       129.27        47.28        96.23 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3J3 
      167.90        47.54       162.48        71.21        41.59       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
       64.08        53.19        51.35         9.17        98.40       302.07 
TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL 
        6.44       105.07        20.15        28.83       247.04        33.21 
TCGA-ER-A42K TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
       12.95        36.26       202.65        20.91        28.08       357.37 
TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 
        9.70        53.16        26.56        17.46         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-LH-A9QB TCGA-QB-A6FS TCGA-WE-A8ZQ 
      117.93        62.79        48.00       368.78         7.23        63.22 
TCGA-YD-A89C TCGA-YG-AA3P 
        6.90        14.43 

$subtype5
TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-DA-A1IA 
       11.87        45.30       129.63         3.65        15.39        65.92 
TCGA-DA-A1IC TCGA-DA-A95Y TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       68.09        14.14        10.36        29.29        58.92        36.46 
TCGA-EE-A185 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND 
        4.96        28.77        48.89       152.35        50.89        23.34 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4FC TCGA-FW-A3TV TCGA-GN-A9SD TCGA-HR-A2OH 
      101.26       133.55        54.41        13.51        59.41        65.88 
TCGA-OD-A75X TCGA-W3-AA1O TCGA-WE-A8ZR TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-XV-AB01 
      297.90         4.01         9.01        11.80        49.51        13.25 
TCGA-YG-AA3O TCGA-Z2-AA3V 
       37.94        15.98 

subtype1 subtype2 subtype3 subtype4 subtype5 
    7.04     0.23     2.60     2.04     3.65 
subtype1 subtype2 subtype3 subtype4 subtype5 
  369.93   248.65   176.55   368.78   297.90 
subtype1 subtype2 subtype3 subtype4 subtype5 
  73.940   41.560   44.880   57.155   37.200 
[1] "7.0 - 369.9 (73.9)" "0.2 - 248.7 (41.6)" "2.6 - 176.6 (44.9)"
[4] "2.0 - 368.8 (57.2)" "3.6 - 297.9 (37.2)"
D3V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        4       0       3        3        3        2         1
  subtype2        1       1       7        3        8        1         3
  subtype3        3       0       1        3        3        4         1
  subtype4        2       2       6        2        5        2         3
  subtype5        1       1       1        2        0        1         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0         5          1          4          6
  subtype2         3         2         6          5          9         19
  subtype3         3         2         6          1          3          5
  subtype4         5         3         7          1          5          9
  subtype5         0         2         4          0          6          6
          vv
clus       STAGE IV
  subtype1        2
  subtype2        5
  subtype3        2
  subtype4        7
  subtype5        2
D3V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  I/II NOS          4        1        3        2        1
  STAGE 0           0        1        0        2        1
  STAGE I           3        7        1        6        1
  STAGE IA          3        3        3        2        2
  STAGE IB          3        8        3        5        0
  STAGE II          2        1        4        2        1
  STAGE IIA         1        3        1        3        2
  STAGE IIB         0        3        3        5        0
  STAGE IIC         0        2        2        3        2
  STAGE III         5        6        6        7        4
  STAGE IIIA        1        5        1        1        0
  STAGE IIIB        4        9        3        5        6
  STAGE IIIC        6       19        5        9        6
  STAGE IV          2        5        2        7        2
[1] 14  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    10  7  7  4
  subtype2    12 18 19 15
  subtype3    13  5  8  8
  subtype4     9 11 12 14
  subtype5     6  5  6  5
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       10       12       13        9        6
  T2           7       18        5       11        5
  T3           7       19        8       12        6
  T4           4       15        8       14        5
[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       N0 N1 N2 N3
  subtype1 18  5  4  5
  subtype2 30 21  7 13
  subtype3 21  4  9  4
  subtype4 37  7  5 12
  subtype5  7  6  8  4
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       18       30       21       37        7
  N1        5       21        4        7        6
  N2        4        7        9        5        8
  N3        5       13        4       12        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 32  2
  subtype2 66  5
  subtype3 37  2
  subtype4 55  8
  subtype5 30  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32    2
  subtype2   66    5
  subtype3   37    2
  subtype4   55    8
  subtype5   30    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       32       66       37       55       30
  1        2        5        2        8        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"
D3V8, binary
          cls
clus        0  1
  subtype1 14  7
  subtype2 28 22
  subtype3 13 11
  subtype4 26 17
  subtype5 10  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    7
  subtype2   28   22
  subtype3   13   11
  subtype4   26   17
  subtype5   10    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        14       28       13       26       10
  YES        7       22       11       17        9
[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"
D3V9, binary
          cls
clus        0  1
  subtype1  8 31
  subtype2 11 67
  subtype3  8 35
  subtype4 10 59
  subtype5  2 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   31
  subtype2   11   67
  subtype3    8   35
  subtype4   10   59
  subtype5    2   31
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         8       11        8       10        2
  YES       31       67       35       59       31
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, binary
          cls
clus        0  1
  subtype1 22 17
  subtype2 29 49
  subtype3 17 26
  subtype4 25 44
  subtype5 13 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   17
  subtype2   29   49
  subtype3   17   26
  subtype4   25   44
  subtype5   13   20
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       29       17       25       13
  MALE         17       49       26       44       20
[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"
D3V12, binary
          cls
clus        0  1
  subtype1 31  8
  subtype2 69  9
  subtype3 38  5
  subtype4 60  9
  subtype5 30  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    8
  subtype2   69    9
  subtype3   38    5
  subtype4   60    9
  subtype5   30    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        31       69       38       60       30
  YES        8        9        5        9        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN WHITE
  subtype1     1    38
  subtype2     0    75
  subtype3     0    43
  subtype4     1    66
  subtype5     2    29
D3V13, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN        1        0        0        1        2
  WHITE       38       75       43       66       29
[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"
D3V14, binary
          cls
clus        0  1
  subtype1  0 39
  subtype2  2 74
  subtype3  0 42
  subtype4  2 66
  subtype5  1 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   39
  subtype2    2   74
  subtype3    0   42
  subtype4    2   66
  subtype5    1   31
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        0        2        1
  NOT HISPANIC OR LATINO       39       74       42       66       31
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 38 26
  subtype2 27 29
  subtype3 27 34
subtype1 subtype2 subtype3 
      64       56       61 
subtype1 subtype2 subtype3 
      26       29       34 
$subtype1
TCGA-D3-A2JE TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 TCGA-3N-A9WC 
        9.76        33.24       134.40        27.35       216.43        60.46 
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2JC TCGA-D3-A2JO 
        8.42       133.25        19.04        76.41        86.30        66.08 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A5GN 
      140.98        59.70       173.85        30.67        31.76        45.70 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A95X 
       78.21        23.61        70.62        69.21        76.34        65.03 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL 
       27.16       346.49       185.19        30.02        10.62        32.48 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
       81.99       103.13       171.85        89.26       145.45       143.93 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19B 
      124.31       122.73         6.28        45.90         7.82        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       11.47       184.60        42.51        73.05        22.36        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
       10.19       173.29       174.21       195.98        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A4EO 
       32.78        35.28         4.47        13.28        19.30        18.25 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U8 
      117.93        17.06        42.48        46.92 

$subtype2
TCGA-ER-A193 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1QB 
       19.04         7.40        12.99        14.83        49.35        62.60 
TCGA-D3-A2J8 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A51T TCGA-D3-A8GP TCGA-D9-A1X3 
       62.86        64.83        43.53        11.34       135.12        10.78 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F5 
       15.02        18.44       138.67       150.61        30.44       225.11 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       20.38         0.00        79.20        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M8 
       44.28        47.41        47.74         0.76         0.20         5.75 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19H 
       23.77        53.26        19.86        34.45         4.54       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A3YN 
       99.06        59.84       146.63        28.67        74.47         4.50 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1ZZ TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A26A 
        4.14        10.06         3.06         9.90        96.92         7.59 
TCGA-GN-A9SD TCGA-RP-A693 TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA4 
       59.41         0.33        47.54        21.90         1.94        24.99 
TCGA-XV-AB01 TCGA-Z2-AA3S 
        6.61        91.23 

$subtype3
TCGA-EE-A180 TCGA-WE-A8K5 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3MO 
       31.96        52.73        31.89       110.93        25.64         9.34 
TCGA-D3-A3MR TCGA-D3-A8GK TCGA-D3-A8GR TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
       90.21       120.00        36.53       110.53        64.83        58.85 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
        8.71        72.10         0.76        14.14        12.30         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A2A6 
       16.41        52.41        18.21        13.15        75.55        77.98 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT 
      201.60        71.31        63.25       104.78       227.01        23.51 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A19C 
       64.04         4.41        54.51        67.89        10.49        39.81 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
      120.76        49.71        47.18         4.70        68.52        32.05 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      171.78         8.35         7.82        36.33        78.61       130.95 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
       11.54         1.91        53.29        43.23        85.05       297.01 
TCGA-QB-A6FS TCGA-W3-AA1Q TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-A8ZT TCGA-WE-A8ZY 
        7.23        44.05        62.43         8.68        10.95        48.39 
TCGA-YG-AA3O 
       28.21 

subtype1 subtype2 subtype3 
    4.47     0.00     0.76 
subtype1 subtype2 subtype3 
  346.49   225.11   297.01 
subtype1 subtype2 subtype3 
  56.495   26.830   47.180 
[1] "4.5 - 346.5 (56.5)" "0.0 - 225.1 (26.8)" "0.8 - 297.0 (47.2)"
D4V2, survival
          sevent
clus2       0  1
  subtype1 44 40
  subtype2 37 43
  subtype3 41 50
subtype1 subtype2 subtype3 
      84       80       91 
subtype1 subtype2 subtype3 
      40       43       50 
$subtype1
TCGA-D3-A2JE TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FR-A729 
       27.65        68.25        54.02       134.40        27.35       220.80 
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2JC 
       66.48        16.57       133.25        28.08        90.90        86.76 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       66.08       166.52        60.23       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       32.94        22.62       135.75        79.59        23.61        26.43 
TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I8 
      107.15       117.17       167.70        77.56        76.57        53.92 
TCGA-DA-A95X TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GK 
       73.94        56.42       369.93       195.02        59.64        54.74 
TCGA-EE-A2GL TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       79.66        94.82       129.27       204.66       180.39       167.90 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AG 
       47.54       162.48       124.31       122.73        13.81        41.59 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       64.08        53.19         9.17        98.40        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      302.07         6.44        44.09       105.07        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A8YD TCGA-FS-A1Z0 
       28.83       247.04        12.95       174.21        36.26       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU 
       28.08        27.72       357.37        53.52        53.16        26.56 
TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 
       34.03        19.30        19.43        15.78       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-YD-A89C 
       64.44        62.79        48.00        48.89        22.13         6.90 

$subtype2
TCGA-ER-A193 TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1QB 
       31.40        21.40        12.99        14.93        71.80        95.74 
TCGA-D3-A2J8 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A51T TCGA-D3-A8GB TCGA-D3-A8GN 
       65.49        66.48        59.57        26.89        30.84       161.00 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW 
      152.75        18.12        15.39        18.44         9.90        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 
      144.89        20.38       176.55        35.93        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5VV TCGA-EE-A181 TCGA-EE-A182 
       10.49       225.96        10.36         7.04        33.73        14.70 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       91.56        85.08        78.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2GP 
       56.84        18.61        14.47        25.87        46.82        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MU 
       42.77        44.88        21.67        19.76        61.51        53.26 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
      134.33        35.44        77.75       152.35       131.51        61.05 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U9 
      148.18        48.99       149.03        92.98        15.72        18.77 
TCGA-FR-A8YC TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-GF-A3OT 
       34.82        32.75        74.73        27.02        54.41         9.90 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A9SD TCGA-HR-A2OG TCGA-RP-A693 TCGA-RP-A694 
       96.92        32.48        59.41         0.23         0.33         0.69 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA4 
       24.03        49.05        17.95        70.52        12.16        24.99 
TCGA-XV-AB01 TCGA-Z2-AA3S 
       13.25        96.99 

$subtype3
TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L TCGA-ER-A198 TCGA-WE-A8K5 
       13.87        94.98        68.15         2.60        50.76        61.15 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MO 
      112.04       112.57        31.59        43.43        11.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 
      103.59        45.30       170.20       129.63       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A6EA TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
        3.65         7.10        25.18       135.02        65.92        68.09 
TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       43.36        72.10        37.35        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A185 
       20.35        29.29        58.92        36.46        29.82         4.96 
TCGA-EE-A20C TCGA-EE-A29S TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
      151.27        61.28        86.14        67.43       220.24        48.72 
TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT 
       81.21        47.28        96.23       216.66       248.65        71.21 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JE TCGA-ER-A197 
       64.04        28.77        54.51       172.18        51.35        13.94 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND 
       48.89        26.37       162.08        50.89        49.48        23.34 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1Z3 
       41.56        93.01        33.21       104.42       216.92        20.91 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 
        9.70        47.38        23.93       101.26       133.55        17.46 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL 
       13.51         2.04       139.89        10.42        50.10        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-AA1O TCGA-W3-AA1Q 
       65.88       368.78       297.90         7.23         4.01        69.07 
TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       63.22         9.01        11.80        49.51        37.94        14.43 
TCGA-Z2-AA3V 
       15.98 

subtype1 subtype2 subtype3 
    6.44     0.23     2.04 
subtype1 subtype2 subtype3 
  369.93   225.96   368.78 
subtype1 subtype2 subtype3 
   58.03    35.98    49.48 
[1] "6.4 - 369.9 (58.0)" "0.2 - 226.0 (36.0)" "2.0 - 368.8 (49.5)"
D4V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        5       2      10        3        7        2         3
  subtype2        4       0       4        4        6        5         3
  subtype3        2       2       4        6        6        3         4
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         3         5        10          2          5         15
  subtype2         4         0         7          4         12         17
  subtype3         4         4        11          2         10         13
          vv
clus       STAGE IV
  subtype1        4
  subtype2        6
  subtype3        8
D4V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  I/II NOS          5        4        2
  STAGE 0           2        0        2
  STAGE I          10        4        4
  STAGE IA          3        4        6
  STAGE IB          7        6        6
  STAGE II          2        5        3
  STAGE IIA         3        3        4
  STAGE IIB         3        4        4
  STAGE IIC         5        0        4
  STAGE III        10        7       11
  STAGE IIIA        2        4        2
  STAGE IIIB        5       12       10
  STAGE IIIC       15       17       13
  STAGE IV          4        6        8
[1] 14  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    22 16  7 17
  subtype2    11 15 28 13
  subtype3    17 15 17 16
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       22       11       17
  T2          16       15       15
  T3           7       28       17
  T4          17       13       16
[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       N0 N1 N2 N3
  subtype1 43  7  8 17
  subtype2 31 21 12 10
  subtype3 39 15 13 11
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       31       39
  N1        7       21       15
  N2        8       12       13
  N3       17       10       11
[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"
D4V7, binary
          cls
clus        0  1
  subtype1 72  4
  subtype2 71  6
  subtype3 77  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    4
  subtype2   71    6
  subtype3   77    9
   clus
vv  subtype1 subtype2 subtype3
  0       72       71       77
  1        4        6        9
[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"
D4V8, binary
          cls
clus        0  1
  subtype1 27 21
  subtype2 28 21
  subtype3 36 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   21
  subtype2   28   21
  subtype3   36   24
     clus
vv    subtype1 subtype2 subtype3
  NO        27       28       36
  YES       21       21       24
[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"
D4V9, binary
          cls
clus        0  1
  subtype1 18 68
  subtype2 10 74
  subtype3 11 81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   68
  subtype2   10   74
  subtype3   11   81
     clus
vv    subtype1 subtype2 subtype3
  NO        18       10       11
  YES       68       74       81
[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"
D4V10, continuous
D4V11, binary
          cls
clus        0  1
  subtype1 40 46
  subtype2 33 51
  subtype3 33 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   46
  subtype2   33   51
  subtype3   33   59
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       33       33
  MALE         46       51       59
[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"
D4V12, binary
          cls
clus        0  1
  subtype1 67 19
  subtype2 76  8
  subtype3 85  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   19
  subtype2   76    8
  subtype3   85    7
     clus
vv    subtype1 subtype2 subtype3
  NO        67       76       85
  YES       19        8        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN WHITE
  subtype1     0    86
  subtype2     1    80
  subtype3     3    85
D4V13, multiclass
       clus
vv      subtype1 subtype2 subtype3
  ASIAN        0        1        3
  WHITE       86       80       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"
D4V14, binary
          cls
clus        0  1
  subtype1  2 84
  subtype2  1 81
  subtype3  2 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   84
  subtype2    1   81
  subtype3    2   87
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        2
  NOT HISPANIC OR LATINO       84       81       87
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 34 47
  subtype2 38 18
  subtype3 31 37
  subtype4 25 23
subtype1 subtype2 subtype3 subtype4 
      81       56       68       48 
subtype1 subtype2 subtype3 subtype4 
      47       18       37       23 
$subtype1
TCGA-D3-A8GI TCGA-EE-A180 TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       13.41        31.96        36.95        76.41        62.60        25.64 
TCGA-D3-A2JG TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A8GK 
      107.61        40.01        23.67       173.85        42.05       120.00 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       69.53        70.62        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95V 
       18.44        69.21        22.85        64.83        58.85        72.10 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A182 
       14.14         3.91        16.41        52.41        13.15         0.00 
TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       26.24        75.22        76.14        12.99         0.26        47.41 
TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MT TCGA-EE-A2MU 
       47.74        26.14         0.20        81.99        23.51        53.26 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-ER-A197 TCGA-ER-A19C 
       64.04         4.41         6.28       111.85        10.49        39.81 
TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3EV 
       49.71         4.70        16.87        10.19        28.67        15.48 
TCGA-FR-A3YN TCGA-FS-A1YY TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
        4.50        49.74        43.92         7.82       130.95         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 
       30.90        66.67        13.28        55.59        11.54       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-QB-A6FS TCGA-RP-A690 
       17.06        42.48       120.53        43.23         7.23         0.20 
TCGA-W3-A824 TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZR TCGA-WE-A8ZY 
      174.12        79.99        47.54        12.69         8.68        48.39 
TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O 
       24.99         6.61        28.21 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-ER-A193 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
       38.76        33.24        19.04        60.46        14.83        15.72 
TCGA-D3-A1Q7 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CF 
      133.25       168.00       171.58        66.08       140.98        24.53 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A8GD TCGA-DA-A1HV TCGA-DA-A1I1 
       90.21        30.67       144.46        23.61        76.34        68.68 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29P 
       30.44         8.71        18.21        20.38        79.20        27.16 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
      115.43        30.02        77.98       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA 
       32.48         5.75        94.19        63.25       104.78       124.31 
TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A199 TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
       54.51        19.86         7.82        42.51       120.76        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1Z4 
      146.63        73.05        74.47       174.21         5.65        27.62 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A9SD TCGA-RP-A693 
       23.21       173.19        19.30        18.25        59.41         0.33 
TCGA-W3-AA1W TCGA-WE-AAA0 
      185.13        37.32 

$subtype3
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07       166.75       269.03        52.90       134.40        27.35 
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       12.99        31.89       110.93        49.35        19.04        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       62.86        15.75        86.30        64.83        43.53        58.06 
TCGA-D3-A3MO TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-DA-A1HY 
        9.34        62.70        45.70       177.86        78.21       138.67 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A20C 
      110.53        60.10       225.11        65.03        24.89        75.55 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GE TCGA-EE-A2GP 
       44.28        61.12       346.49       185.19        12.95         0.76 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
      103.13        15.25        23.77       171.85        89.26       145.45 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
      122.73         3.35       168.85        34.45         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A69P 
       11.47        99.06        22.36        68.52        32.05         4.14 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GF-A3OT 
        8.35       312.07        32.78        78.61       136.27         9.90 
TCGA-GN-A265 TCGA-GN-A26A TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
       96.92         7.59        85.05         1.97       120.07         8.09 
TCGA-WE-A8ZM TCGA-WE-AA9Y 
       65.42         1.94 

$subtype4
TCGA-D3-A2JE TCGA-FR-A729 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A2JH 
        9.76       216.43        52.73         7.40         8.42        36.30 
TCGA-D3-A3CE TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GP 
       59.70        31.76        11.34       124.08       179.97       135.12 
TCGA-DA-A1I2 TCGA-DA-A95W TCGA-DA-A95Z TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
      150.61         0.76        12.30        18.35        93.63        71.31 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JI 
      209.79       227.01       143.93        67.89        45.90       135.98 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A3ES TCGA-FR-A7U8 TCGA-FR-A8YC 
      184.60       150.12        59.84       173.29        26.20        10.06 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
      171.78       195.98        36.33        35.28         4.47         5.29 
TCGA-FS-A4FD TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       80.68         1.91        53.29        34.49        46.92       297.01 
TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-Z2-AA3S 
       44.05        92.84        21.90        62.43        10.95        91.23 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.33     0.76     0.76 
subtype1 subtype2 subtype3 subtype4 
  174.12   201.60   346.49   297.01 
subtype1 subtype2 subtype3 subtype4 
  30.900   50.845   60.610   56.495 
[1] "0.0 - 174.1 (30.9)" "0.3 - 201.6 (50.8)" "0.8 - 346.5 (60.6)"
[4] "0.8 - 297.0 (56.5)"
D5V2, survival
          sevent
clus2       0  1
  subtype1 43 71
  subtype2 44 28
  subtype3 44 57
  subtype4 35 37
subtype1 subtype2 subtype3 subtype4 
     114       72      101       72 
subtype1 subtype2 subtype3 subtype4 
      71       28       57       37 
$subtype1
TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L 
       13.87        58.52        54.02        94.98        68.15         2.60 
TCGA-ER-A198 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-3N-A9WB TCGA-D3-A1Q9 TCGA-D3-A1QA 
       50.76        36.95        18.05        17.03        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ 
       95.74        43.43        11.87       113.52        12.10       130.72 
TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A8GK TCGA-D3-A8GL 
       86.93        39.75       174.84       125.79       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      107.15       129.63       151.53        54.67         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       15.39        22.29        18.44         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95V 
       22.95        20.38        35.93        65.92        68.09        72.10 
TCGA-DA-A95Y TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       14.14        13.87        20.35        29.29        58.92        29.82 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
       14.70        26.89         4.96        13.55        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X 
       13.97        63.78        64.64        56.84        25.87        17.92 
TCGA-EE-A2GB TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MT TCGA-EE-A2MU 
       59.28        42.77        94.82        47.28        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-ER-A197 TCGA-ER-A19C 
       64.04        28.77        13.81       127.20        13.94        48.89 
TCGA-ER-A19F TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       26.37        50.89        23.34        20.15        28.83        48.99 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZE 
       46.98        92.98        36.26       228.59        48.85        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        9.70        23.93       133.55        27.02        77.82        66.67 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       34.03        55.59        13.51       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-QB-A6FS 
       48.00       121.91        10.42        50.10        21.37         7.23 
TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZN 
        0.20       228.16         4.01       111.09        49.05        58.98 
TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3V 
        9.01        49.51        24.99        13.25        37.94        15.98 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-ER-A193 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
       46.32        68.25        31.40        66.48        14.93        16.67 
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB 
      133.25        23.77       168.00       171.58        66.08       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A8GB 
       24.53       103.59        55.73        56.35       145.12        30.84 
TCGA-D3-A8GD TCGA-D3-A8GS TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
       23.61       117.17        76.57       222.51        40.60        33.93 
TCGA-DA-A3F8 TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N 
       43.36         7.04        36.46        33.73        91.56        18.61 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GH 
       56.42        46.82       115.96        59.64        86.14       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME 
      107.38        54.74        79.66        44.88        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA TCGA-EE-A3AE 
      103.20        16.96        96.23       216.66       124.31        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A199 TCGA-ER-A19N TCGA-ER-A19P 
       36.95        51.35       134.33         9.17        44.09       162.08 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A44A 
       49.48       148.18       105.07        41.56       149.03       174.21 
TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO 
       38.27        28.08        49.48       174.84        19.30        19.43 
TCGA-GF-A6C9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-W3-AA1W TCGA-WE-AAA0 
       15.78        59.41        65.88         0.33       219.16        40.41 

$subtype3
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07       168.26       340.14       126.81       134.40        27.35 
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       12.99       112.04       112.57        71.80        28.08       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       65.49       115.53        86.76        66.48        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       46.98         9.34        45.30        22.62        63.81       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-D3-A8GV 
      137.92       178.32        79.59        26.43        29.06       167.70 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A95X 
      144.89       135.02        88.87        53.92       225.96        73.94 
TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29Q 
       27.22       133.81       151.27        63.35        72.07        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GE TCGA-EE-A2GP 
       14.47        61.28       369.93       195.02       173.79        13.91 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK 
       21.67       129.27        28.83        61.51       204.66       180.39 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JB 
      167.90        43.23       122.73        41.59        34.32       201.80 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L 
       35.44        77.75        98.40        12.59        13.02       131.51 
TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U9 
       43.82        93.01        33.21        12.95        15.72        18.77 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      104.42        48.59        20.91         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F2 
       53.52        32.75       101.26        11.41       148.80        50.14 
TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       28.73        54.41         9.90        96.92        10.13        32.48 
TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
       22.13         0.23       368.78        63.02       121.08        42.08 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-YD-A9TA 
       24.03        17.95       101.33        12.16        49.18 

$subtype4
TCGA-D3-A2JE TCGA-FR-A729 TCGA-FS-A1ZF TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q1 
       27.65       220.80        15.45        61.15        21.40        16.57 
TCGA-D3-A2JH TCGA-D3-A3CE TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU 
       42.08        60.23        32.94        26.89        18.18       125.19 
TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I2 
      241.38       161.00       152.75         7.10        36.03       176.55 
TCGA-DA-A3F3 TCGA-DA-A95W TCGA-DA-A95Z TCGA-EB-A44R TCGA-EE-A17Z TCGA-EE-A2A5 
       10.49        37.35        13.02        10.36         8.65        39.29 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2MF 
       67.43        48.72        75.48       102.12        81.21       268.73 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       47.54       248.65       162.48       138.81       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       53.19       152.81       302.07       152.35         6.44        61.05 
TCGA-ER-A19T TCGA-ER-A3ES TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 
        8.88       247.04        27.85        34.82       216.92       202.65 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB 
       47.38        74.73        53.16        26.56        27.09        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U4 TCGA-GN-A4U8 
       80.68        17.46         2.04       139.89        39.35        48.89 
TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      297.90         0.69        69.07       105.04        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       11.80        35.80         6.90        14.43        27.58        96.99 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.33     0.23     0.69 
subtype1 subtype2 subtype3 subtype4 
  228.59   222.51   369.93   302.07 
subtype1 subtype2 subtype3 subtype4 
  46.715   56.040   62.070   51.025 
[1] "0.2 - 228.6 (46.7)" "0.3 - 222.5 (56.0)" "0.2 - 369.9 (62.1)"
[4] "0.7 - 302.1 (51.0)"
D5V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        3       3       2        7        9        8         3
  subtype2        3       1       8        5        4        5         4
  subtype3        6       3      11        2        7        9         4
  subtype4        1       0       8        4        8        4         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         8         8        11          7         10         23
  subtype2         1         2         9          0         10         14
  subtype3         3         2        13          8          8         12
  subtype4         7         3         6          0          7          6
          vv
clus       STAGE IV
  subtype1        3
  subtype2        2
  subtype3        8
  subtype4        8
D5V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  I/II NOS          3        3        6        1
  STAGE 0           3        1        3        0
  STAGE I           2        8       11        8
  STAGE IA          7        5        2        4
  STAGE IB          9        4        7        8
  STAGE II          8        5        9        4
  STAGE IIA         3        4        4        3
  STAGE IIB         8        1        3        7
  STAGE IIC         8        2        2        3
  STAGE III        11        9       13        6
  STAGE IIIA        7        0        8        0
  STAGE IIIB       10       10        8        7
  STAGE IIIC       23       14       12        6
  STAGE IV          3        2        8        8
[1] 14  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    17 17 29 32
  subtype2    18 11 17 13
  subtype3    16 26 23 14
  subtype4    13 19 12  9
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       17       18       16       13
  T2          17       11       26       19
  T3          29       17       23       12
  T4          32       13       14        9
[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       N0 N1 N2 N3
  subtype1 49 22 14 17
  subtype2 34 12  7 11
  subtype3 55 21 12 10
  subtype4 39 11  6  7
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       49       34       55       39
  N1       22       12       21       11
  N2       14        7       12        6
  N3       17       11       10        7
[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"
D5V7, binary
          cls
clus         0   1
  subtype1 104   4
  subtype2  65   2
  subtype3  90   8
  subtype4  61   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104    4
  subtype2   65    2
  subtype3   90    8
  subtype4   61    8
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      104       65       90       61
  1        4        2        8        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 46 39
  subtype2 28 17
  subtype3 30 20
  subtype4 30 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   39
  subtype2   28   17
  subtype3   30   20
  subtype4   30   15
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        46       28       30       30
  YES       39       17       20       15
[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"
D5V9, binary
          cls
clus         0   1
  subtype1   8 109
  subtype2  11  62
  subtype3  17  88
  subtype4  11  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  109
  subtype2   11   62
  subtype3   17   88
  subtype4   11   62
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8       11       17       11
  YES      109       62       88       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"
D5V10, continuous
D5V11, binary
          cls
clus        0  1
  subtype1 40 77
  subtype2 29 44
  subtype3 41 64
  subtype4 28 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   77
  subtype2   29   44
  subtype3   41   64
  subtype4   28   45
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       40       29       41       28
  MALE         77       44       64       45
[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"
D5V12, binary
          cls
clus         0   1
  subtype1 102  14
  subtype2  60  13
  subtype3  93  12
  subtype4  64   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102   14
  subtype2   60   13
  subtype3   93   12
  subtype4   64    9
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       102       60       93       64
  YES       14       13       12        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   113
  subtype2     1                         1    70
  subtype3     1                         0   102
  subtype4     1                         0    69
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                          113       70      102       69
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   3 112
  subtype2   0  72
  subtype3   2  99
  subtype4   2  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  112
  subtype2    0   72
  subtype3    2   99
  subtype4    2   70
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        2        2
  NOT HISPANIC OR LATINO      112       72       99       70
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 24 51
  subtype2 74 42
  subtype3 30 32
subtype1 subtype2 subtype3 
      75      116       62 
subtype1 subtype2 subtype3 
      51       42       32 
$subtype1
TCGA-D3-A2JE TCGA-D3-A8GI TCGA-EE-A180 TCGA-WE-AAA3 TCGA-D3-A1Q1 TCGA-D3-A2J6 
        9.76        13.41        31.96         7.40         8.42        25.64 
TCGA-D3-A2JG TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU 
      107.61        40.01        23.67        31.76        42.05       124.08 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 
      120.00        69.53       135.12        36.53        10.78        18.44 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95Y 
       69.21        22.85        64.83        58.85         0.76        14.14 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29B 
       12.30        16.41        52.41        13.15         0.00        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2GM 
       76.14        12.99         0.26        44.28        61.12        18.35 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 
       93.63         0.20        23.51         4.41         6.28        45.90 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       10.49        39.81         4.70        16.87        10.19       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE 
       68.52        15.48        26.20        49.74         8.35        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        7.82        36.33       130.95         4.47         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A267 
       30.90        13.28        80.68        55.59       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 TCGA-WE-A8ZR 
       42.48       120.53        43.23       297.01         0.20         8.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-XV-AB01 
       48.39         1.94         6.61 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       38.76        33.24       269.03       134.40        27.35        19.04 
TCGA-FR-A729 TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 
      216.43        36.95        52.73        60.46        14.83        15.72 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC 
      133.25        76.41        62.60        45.99       168.00        86.30 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       36.30       171.58        66.08       140.98        24.53        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51T TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
      173.85        30.67        11.34        78.21        23.61       179.97 
TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       70.62        15.02        16.90        68.68       150.61       110.53 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A6L9 
       30.44         8.71        72.10        65.03         3.91        18.21 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       20.38        26.24        79.20        47.41        47.74        27.16 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MF 
       10.62        32.48         0.76        81.99         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       94.19        63.25        89.26       104.78       227.01        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JH 
      124.31        64.04        54.51        67.89       111.85        19.86 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N 
      135.98         7.82         4.54       184.60        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG 
      120.76        49.71        47.18       146.63        73.05        28.67 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       32.05         4.50       174.21         5.65        10.06       171.78 
TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.62        78.61        35.28        23.21        66.67       173.19 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       11.54        19.30        18.25        34.49        46.92        59.41 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        7.23         0.33       174.12        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-WE-AAA4 
       92.84        47.54        12.69        21.90        37.32        24.99 
TCGA-YG-AA3O TCGA-Z2-AA3S 
       28.21        91.23 

$subtype3
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GO TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       62.07       166.75        52.90        12.99        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JP 
       49.35        19.04        62.86        15.75        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN 
       58.06        59.70         9.34       144.46        62.70        45.70 
TCGA-D3-A5GR TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y 
      177.86        76.34       138.67        60.10       225.11        24.89 
TCGA-EE-A20C TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M6 
       75.55       346.49       185.19        12.95        71.31       103.13 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AB 
       15.25        23.77       171.85       145.45       143.93       122.73 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H 
        3.35       168.85        34.45        53.29        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1ZC 
       99.06        22.36        74.47         4.14       195.98       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
       32.78       136.27         9.90         1.91        53.29        96.92 
TCGA-GN-A26A TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZM 
        7.59        85.05         1.97       120.07         8.09        65.42 
TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       62.43        10.95 

subtype1 subtype2 subtype3 
    0.00     0.33     1.91 
subtype1 subtype2 subtype3 
  297.01   269.03   346.49 
subtype1 subtype2 subtype3 
   25.64    51.22    62.25 
[1] "0.0 - 297.0 (25.6)" "0.3 - 269.0 (51.2)" "1.9 - 346.5 (62.2)"
D6V2, survival
          sevent
clus2       0  1
  subtype1 29 74
  subtype2 94 69
  subtype3 43 50
subtype1 subtype2 subtype3 
     103      163       93 
subtype1 subtype2 subtype3 
      74       69       50 
$subtype1
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-D3-A8GI TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L 
       27.65        13.87        58.52        54.02        94.98         2.60 
TCGA-WE-AAA3 TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK 
       21.40        17.03        16.57        43.43       113.52        12.10 
TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GK 
       86.93        39.75        32.94       125.79       125.19       170.20 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
       89.13       152.75       129.63        18.12        18.44        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95W 
       77.56        22.95        35.93        65.92        68.09        37.35 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X 
       14.14        13.02        10.36        20.35        58.92        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        8.65        14.70         4.96        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A2GM TCGA-EE-A2GN 
       63.78        72.07        66.74        25.87        75.48       102.12 
TCGA-EE-A2GR TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A197 
       42.77        71.21        28.77        13.81        64.08        13.94 
TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       48.89         6.44         8.88        23.34        20.15        28.83 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YY 
      247.04        93.01        46.98        27.85        36.26       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.91        48.85        46.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       133.55        11.41        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        50.14        28.73        34.03        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       17.46        55.59       117.93        64.44        62.79        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 
      121.91        10.42        50.10        21.37       297.90         0.20 
TCGA-W3-AA1O TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-XV-AB01 TCGA-YG-AA3P 
        4.01         9.01        49.51        12.16        13.25        14.43 
TCGA-Z2-AA3V 
       15.98 

$subtype2
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       46.32        68.25        68.15       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FR-A729 TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 
       31.40        50.76       220.80        36.95        18.05        61.15 
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       66.48        14.93        16.67       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       95.74       103.10        23.77       168.00        86.76        11.87 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CB TCGA-D3-A3CF 
       42.08       171.58        66.08       130.72       166.52        24.53 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51T TCGA-D3-A5GO 
      103.59       174.84        55.73        56.35        26.89       137.92 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
       18.18        30.84        79.59        23.61       241.38       107.15 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00       117.17       151.53        54.67         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       15.39        22.29         9.90        36.03        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
      176.55       135.02        40.60        33.93        10.49        43.36 
TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 
       72.10        73.94        13.87        29.29         7.04        36.46 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29H TCGA-EE-A29M 
       33.73        26.89        91.56        13.55        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       18.61        56.42        61.28        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
       59.64        86.14        59.28        67.43       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU 
      107.38        54.74        79.66        13.91        44.88        94.82 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       180.39       216.66        47.54       248.65        43.23 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 
       53.26       124.31        64.04        54.51       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       36.95        53.19        51.35       134.33       152.81         9.17 
TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       77.75        26.37       302.07        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A3PL 
       50.89        49.48       148.18       105.07        48.99        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z4 
       92.98       174.21        38.27        34.82       216.92        28.08 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3TV 
      101.26        53.16        49.48        66.67       174.84        13.51 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       19.30        19.43        15.78        39.35        48.89        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q 
       65.88         7.23         0.33         0.69       228.16        69.07 
TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZN 
      111.09       219.16       105.04        24.03        49.05        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
       70.52        35.80        40.41        24.99        37.94        27.58 
TCGA-Z2-AA3S 
       96.99 

$subtype3
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GO TCGA-FS-A1ZF TCGA-3N-A9WD TCGA-D3-A1Q4 
       62.07       168.26       126.81        15.45        12.99       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JN 
      112.57        71.80        28.08        65.49       115.53        66.48 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV 
       59.57        58.06        46.98        60.23         9.34        45.30 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GE 
      145.12        22.62        63.81       135.75       178.32        26.43 
TCGA-D3-A8GQ TCGA-D3-A8GV TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 
       29.06       167.70        76.57       144.89        88.87        53.92 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29R 
      225.96        27.22       133.81       151.27        63.35        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M5 
      369.93       195.02        39.29       173.79        81.21        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MS 
      129.27        28.83        61.51       204.66       167.90       162.48 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 
      122.73        41.59       138.81        34.32       201.80        35.44 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A2NC 
       98.40        12.59        13.02       152.35       131.51        43.82 
TCGA-ER-A2NH TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE 
       41.56        12.95       149.03        15.72        18.77       104.42 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59       202.65         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZS TCGA-FS-A4FB TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       32.75       148.80        26.73         9.90         2.04       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB 
       96.92        10.13        32.48        22.13         0.23       368.78 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       63.02       121.08        42.08        17.95       101.33        63.22 
TCGA-WE-A8ZT TCGA-YD-A89C TCGA-YD-A9TA 
       11.80         6.90        49.18 

subtype1 subtype2 subtype3 
    0.20     0.33     0.23 
subtype1 subtype2 subtype3 
  297.90   340.14   369.93 
subtype1 subtype2 subtype3 
   36.26    55.73    62.07 
[1] "0.2 - 297.9 (36.3)" "0.3 - 340.1 (55.7)" "0.2 - 369.9 (62.1)"
D6V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        2       2       3        4        6        6         5
  subtype2        5       2      16       10       15       10         6
  subtype3        6       3      10        4        7       10         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9        10         8          8          9         21
  subtype2         8         3        19          2         19         24
  subtype3         2         2        12          5          7         10
          vv
clus       STAGE IV
  subtype1        6
  subtype2       10
  subtype3        5
D6V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  I/II NOS          2        5        6
  STAGE 0           2        2        3
  STAGE I           3       16       10
  STAGE IA          4       10        4
  STAGE IB          6       15        7
  STAGE II          6       10       10
  STAGE IIA         5        6        3
  STAGE IIB         9        8        2
  STAGE IIC        10        3        2
  STAGE III         8       19       12
  STAGE IIIA        8        2        5
  STAGE IIIB        9       19        7
  STAGE IIIC       21       24       10
  STAGE IV          6       10        5
[1] 14  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    11 16 25 34
  subtype2    34 34 33 26
  subtype3    19 23 23  8
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       11       34       19
  T2          16       34       23
  T3          25       33       23
  T4          34       26        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 46 18 13 15
  subtype2 82 27 18 21
  subtype3 49 21  8  9
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       46       82       49
  N1       18       27       21
  N2       13       18        8
  N3       15       21        9
[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"
D6V7, binary
          cls
clus         0   1
  subtype1  92   6
  subtype2 144  11
  subtype3  84   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    6
  subtype2  144   11
  subtype3   84    5
   clus
vv  subtype1 subtype2 subtype3
  0       92      144       84
  1        6       11        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 40 33
  subtype2 65 42
  subtype3 29 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   33
  subtype2   65   42
  subtype3   29   16
     clus
vv    subtype1 subtype2 subtype3
  NO        40       65       29
  YES       33       42       16
[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, binary
          cls
clus         0   1
  subtype1  10  96
  subtype2  22 143
  subtype3  15  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   96
  subtype2   22  143
  subtype3   15   82
     clus
vv    subtype1 subtype2 subtype3
  NO        10       22       15
  YES       96      143       82
[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"
D6V10, continuous
D6V11, binary
          cls
clus         0   1
  subtype1  39  67
  subtype2  59 106
  subtype3  40  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   67
  subtype2   59  106
  subtype3   40   57
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39       59       40
  MALE         67      106       57
[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"
D6V12, binary
          cls
clus         0   1
  subtype1  93  12
  subtype2 139  26
  subtype3  87  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93   12
  subtype2  139   26
  subtype3   87   10
     clus
vv    subtype1 subtype2 subtype3
  NO        93      139       87
  YES       12       26       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   103
  subtype2     2                         1   157
  subtype3     1                         0    94
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          103      157       94
[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"
D6V14, binary
          cls
clus         0   1
  subtype1   3 101
  subtype2   2 160
  subtype3   2  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  101
  subtype2    2  160
  subtype3    2   92
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        2
  NOT HISPANIC OR LATINO      101      160       92
[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 35 34
  subtype2 32 42
  subtype3 34 35
  subtype4 20 12
subtype1 subtype2 subtype3 subtype4 
      69       74       69       32 
subtype1 subtype2 subtype3 subtype4 
      34       42       35       12 
$subtype1
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-3N-A9WC 
       62.07        33.24        52.90       134.40        27.35        60.46 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99        14.83         8.42       110.93        62.60        25.64 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A51J TCGA-D3-A8GD 
      168.00        86.30       140.98        24.53       144.46        23.61 
TCGA-D9-A3Z1 TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       15.02         8.71        72.10        12.30         3.91        16.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29Q TCGA-EE-A29T 
       18.21        13.15        26.24        75.55        61.12       346.49 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MG 
       77.98        10.62        18.35        81.99       103.13        94.19 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-ER-A199 
      145.45       143.93        23.51        64.04        54.51         7.82 
TCGA-ER-A19B TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       53.29        99.06        42.51        73.05        16.87        10.19 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F8 
      195.98        27.62        43.92       130.95         4.47       173.19 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-OD-A75X 
       55.59        18.25        53.29       120.53        59.41       297.01 
TCGA-RP-A690 TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-A8ZY 
        0.20        79.99         8.09       185.13        65.42        48.39 
TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O 
       37.32         6.61        28.21 

$subtype2
TCGA-D3-A2JE TCGA-EE-A180 TCGA-WE-A8K5 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG 
        9.76        31.96        52.73        15.72        76.41       107.61 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL 
      171.58        43.53        58.06       173.85        31.76        42.05 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      124.08        78.21       179.97        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       10.78        16.90        18.44        69.21        76.34        68.68 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95Y TCGA-EE-A181 
      150.61        64.83        58.85         0.76        14.14        20.38 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       79.20        75.22        12.99         0.26        47.41        47.74 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MJ 
       68.65        32.48        93.63         0.20       209.79        63.25 
TCGA-EE-A2MK TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI 
       89.26       124.31         4.41         6.28       111.85       135.98 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES 
       10.49        39.81        49.71        47.18         4.70       173.29 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZY 
       32.05         4.50       171.78         7.82        36.33         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK 
        3.06        30.90       117.93        17.06        42.48        43.23 
TCGA-QB-A6FS TCGA-W3-A824 TCGA-W3-AA1Q TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZR 
        7.23       174.12        44.05        47.54        21.90         8.68 
TCGA-WE-A8ZT TCGA-Z2-AA3S 
       10.95        91.23 

$subtype3
TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-WE-AAA3 
       38.76       166.75       269.03        19.04        36.95         7.40 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       31.89        49.35       133.25        45.99        62.86        15.75 
TCGA-D3-A2JN TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A8GL TCGA-DA-A1HY 
       64.83        40.01         9.34        30.67        69.53       138.67 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A29C 
      110.53        60.10        30.44        52.41        24.89        76.14 
TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP 
       44.28       185.19       115.43        12.95       201.60         0.76 
TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 
       71.31         5.75        23.77       171.85        53.26        67.89 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D 
       45.90       168.85        19.86        34.45         4.54        11.47 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG 
      150.12        59.84       120.76       146.63        22.36        28.67 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM 
       15.48        74.47         4.14        49.74        32.78        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT 
      136.27        35.28        66.67        80.68        11.54         9.90 
TCGA-GN-A26A TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZN 
        7.59        85.05         0.33         1.97       120.07        12.69 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA4 
       62.43         1.94        24.99 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       19.04        36.30        66.08        59.70        90.21        23.67 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EE-A182 
       62.70        11.34        45.70       225.11        65.03         0.00 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A2MP 
       27.16        30.02        26.14        15.25       104.78       227.01 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7UA 
      122.73         3.35       184.60        68.52        26.20         5.65 
TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZW TCGA-GN-A265 TCGA-GN-A4U4 
       10.06         8.35       312.07        23.21        96.92        34.49 
TCGA-GN-A4U8 TCGA-W3-AA21 
       46.92        92.84 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.20     0.33     0.00 
subtype1 subtype2 subtype3 subtype4 
  346.49   209.79   269.03   312.07 
subtype1 subtype2 subtype3 subtype4 
  53.290   45.615   45.900   41.000 
[1] "0.2 - 346.5 (53.3)" "0.2 - 209.8 (45.6)" "0.3 - 269.0 (45.9)"
[4] "0.0 - 312.1 (41.0)"
D7V2, survival
          sevent
clus2       0  1
  subtype1 44 49
  subtype2 43 60
  subtype3 43 51
  subtype4 26 27
subtype1 subtype2 subtype3 subtype4 
      93      103       94       53 
subtype1 subtype2 subtype3 subtype4 
      49       60       51       27 
$subtype1
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-3N-A9WC 
       62.07        68.25       126.81       134.40        27.35        66.48 
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99        14.93        16.57       112.57        95.74        43.43 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A3C7 TCGA-D3-A3CB 
       23.77       168.00        86.76        11.87        46.98       166.52 
TCGA-D3-A3CF TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GD TCGA-D3-A8GS 
       24.53        56.35       145.12        22.62        23.61       117.17 
TCGA-D3-A8GV TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I8 TCGA-DA-A3F8 
      167.70        15.39         9.90        25.18        53.92        43.36 
TCGA-DA-A95V TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 
       72.10        13.02        13.87        20.35         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       29.82        26.89       151.27        18.61        66.74       369.93 
TCGA-EE-A29X TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 
       17.92        86.14        54.74        75.48        94.82       129.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT 
      103.20        16.96       167.90        47.54       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E 
       64.04        54.51        36.95         9.17        98.40        13.02 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
      131.51        44.09       105.07        20.15        28.83        41.56 
TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK 
      104.42       202.65        28.08        27.72        46.45        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 
      133.55        26.56       174.84        55.59        19.43       139.89 
TCGA-GN-A266 TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A690 
       10.13       121.91        10.42        59.41       297.90         0.20 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA0 
      111.09        42.08       219.16       101.33        49.51        40.41 
TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3V 
       13.25        37.94        15.98 

$subtype2
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L 
       27.65        13.87        54.02        94.98        68.15         2.60 
TCGA-ER-A198 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG 
       50.76        18.05        61.15        16.67        90.90       113.52 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL 
      171.58        59.57        58.06       174.84        32.94       125.79 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP 
       18.18       125.19        79.59       241.38       107.15       152.75 
TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z3 
      129.63       151.53        54.67         3.65        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       18.44        77.56        76.57        36.03       222.51       176.55 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A5UL 
       65.92        40.60        68.09        37.35        14.14        29.29 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
        8.65        33.73         4.96        91.56        13.55        85.08 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GC TCGA-EE-A2GJ 
       13.97        63.78        64.64        56.84        67.43       107.38 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MF TCGA-EE-A2MJ 
       79.66       102.12        42.77        44.88       268.73        96.23 
TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      180.39        43.23       124.31        28.77        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A19S 
      127.20       152.81        13.94        48.89        50.89        49.48 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YD TCGA-FS-A1YW 
       23.34       247.04        33.21        92.98        36.26       216.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        9.70        47.38        74.73        11.41        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       77.82        28.73        26.73       117.93        64.44        62.79 
TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q 
       50.10        65.88         7.23         0.69       228.16        69.07 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZT TCGA-YG-AA3P TCGA-Z2-A8RT 
       49.05        70.52         9.01        11.80        14.43        27.58 
TCGA-Z2-AA3S 
       96.99 

$subtype3
TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GD TCGA-ER-A193 TCGA-FS-A1ZF TCGA-FW-A3R5 
       46.32       168.26       340.14        31.40        15.45        36.95 
TCGA-WE-AAA3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
       21.40       112.04        71.80       133.25       103.10        65.49 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F 
      115.53        66.48       130.72        86.93         9.34        55.73 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN TCGA-DA-A1HY TCGA-DA-A1I4 
       30.84        26.43        89.13       161.00       144.89        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A29A 
      135.02        88.87        33.93        58.92        27.22        63.35 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 
       78.97        72.07        61.28        25.87       195.02       115.96 
TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 
       39.29       173.79       220.24        13.91        81.21        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 
       19.76        61.51       103.27       204.66        53.26       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D 
       64.08       201.80       134.33        35.44        77.75        12.59 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2NC 
      152.35         6.44        61.05       162.08       148.18        43.82 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX 
       48.99        46.98       149.03        15.72        18.77        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
      228.59         7.79        48.85        53.52       101.26       148.80 
TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A26A 
       53.16        66.67        80.68        13.51         9.90        32.48 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A825 
       22.13        21.37         0.23       368.78         0.33        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
      121.08         4.01        24.03        17.95        58.98        63.22 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        24.99         6.90        49.18 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3CE 
       28.08        31.59        42.08        12.10        66.08        60.23 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      103.59        39.75        45.30        63.81        26.89       135.75 
TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95X 
       29.06         7.10        20.38        10.49       225.96        73.94 
TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A0 
       10.36        14.70       133.81        56.42        14.47        46.82 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML 
       59.64        59.28        48.72        28.83        47.28       216.66 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      248.65       122.73        41.59        34.32        53.19        51.35 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7UA 
       26.37       302.07        93.01        12.95        27.85        38.27 
TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZW TCGA-FW-A3I3 
       34.82        20.91       357.37        32.75        49.48        17.46 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-W3-AA21 
       96.92        48.00        39.35        48.89       105.04 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.69     0.23     7.10 
subtype1 subtype2 subtype3 subtype4 
  369.93   268.73   368.78   357.37 
subtype1 subtype2 subtype3 subtype4 
  47.540   56.840   60.015   46.820 
[1] "0.2 - 369.9 (47.5)" "0.7 - 268.7 (56.8)" "0.2 - 368.8 (60.0)"
[4] "7.1 - 357.4 (46.8)"
D7V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        6       5       9       10        3        7         2
  subtype2        2       1       6        3       10        7         3
  subtype3        3       1       9        2       11        5         4
  subtype4        2       0       4        1        4        5         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         2         5        10          2          6         15
  subtype2        10         3        12          5         11         15
  subtype3         5         4        11          4          9         16
  subtype4         1         2         4          3          7          8
          vv
clus       STAGE IV
  subtype1        3
  subtype2        7
  subtype3        5
  subtype4        5
D7V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  I/II NOS          6        2        3        2
  STAGE 0           5        1        1        0
  STAGE I           9        6        9        4
  STAGE IA         10        3        2        1
  STAGE IB          3       10       11        4
  STAGE II          7        7        5        5
  STAGE IIA         2        3        4        3
  STAGE IIB         2       10        5        1
  STAGE IIC         5        3        4        2
  STAGE III        10       12       11        4
  STAGE IIIA        2        5        4        3
  STAGE IIIB        6       11        9        7
  STAGE IIIC       15       15       16        8
  STAGE IV          3        7        5        5
[1] 14  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    25 13 15 16
  subtype2    18 20 27 20
  subtype3     7 30 21 17
  subtype4    10 10 13 10
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       25       18        7       10
  T2          13       20       30       10
  T3          15       27       21       13
  T4          16       20       17       10
[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       N0 N1 N2 N3
  subtype1 48 11  6 16
  subtype2 50 20 14 12
  subtype3 47 20 10 10
  subtype4 25 11  9  5
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       48       50       47       25
  N1       11       20       20       11
  N2        6       14       10        9
  N3       16       12       10        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 84  3
  subtype2 91  8
  subtype3 86  5
  subtype4 46  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84    3
  subtype2   91    8
  subtype3   86    5
  subtype4   46    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       84       91       86       46
  1        3        8        5        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 33 19
  subtype2 45 27
  subtype3 36 22
  subtype4 13 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   19
  subtype2   45   27
  subtype3   36   22
  subtype4   13   19
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        33       45       36       13
  YES       19       27       22       19
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 13 84
  subtype2 13 91
  subtype3  9 88
  subtype4 10 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   84
  subtype2   13   91
  subtype3    9   88
  subtype4   10   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        13       13        9       10
  YES       84       91       88       44
[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"
D7V10, continuous
D7V11, binary
          cls
clus        0  1
  subtype1 39 58
  subtype2 39 65
  subtype3 32 65
  subtype4 21 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   58
  subtype2   39   65
  subtype3   32   65
  subtype4   21   33
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       39       39       32       21
  MALE         58       65       65       33
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
          cls
clus        0  1
  subtype1 84 12
  subtype2 91 13
  subtype3 90  7
  subtype4 43 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84   12
  subtype2   91   13
  subtype3   90    7
  subtype4   43   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        84       91       90       43
  YES       12       13        7       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    92
  subtype2     0                         0   101
  subtype3     1                         0    92
  subtype4     1                         0    53
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        1        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                           92      101       92       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"
D7V14, binary
          cls
clus        0  1
  subtype1  1 95
  subtype2  3 99
  subtype3  2 90
  subtype4  1 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   95
  subtype2    3   99
  subtype3    2   90
  subtype4    1   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        2        1
  NOT HISPANIC OR LATINO       95       99       90       53
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 50 42
  subtype2 30 33
  subtype3 26 38
  subtype4 15 10
subtype1 subtype2 subtype3 subtype4 
      92       63       64       25 
subtype1 subtype2 subtype3 subtype4 
      42       33       38       10 
$subtype1
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2GD TCGA-WE-A8K5 TCGA-WE-AAA3 
        9.76        62.07        33.24       269.03        52.73         7.40 
TCGA-3N-A9WC TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JP 
       60.46        76.41        45.99       107.61       171.58        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       58.06       140.98        23.67       173.85       144.46        31.76 
TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL 
       11.34       124.08        78.21        23.61       179.97        69.53 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
      135.12        10.78        15.02        69.21        76.34        68.68 
TCGA-DA-A1I5 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EE-A181 
      110.53        72.10         0.76        65.03         3.91        20.38 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       79.20        12.99        47.41        12.95       201.60        68.65 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM 
       93.63         0.76        71.31       209.79        89.26       145.45 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JH 
      227.01        53.26         4.41        54.51        67.89        19.86 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      135.98        10.49        59.84       120.76        49.71        47.18 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW 
       68.52        15.48         4.50        26.20         5.65       171.78 
TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU 
        8.35         7.82        36.33        78.61       130.95         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-GN-A262 TCGA-GN-A264 
       23.21         5.29         3.06        30.90        53.29       117.93 
TCGA-GN-A268 TCGA-GN-A9SD TCGA-OD-A75X TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 
       42.48        59.41       297.01        44.05        79.99        92.84 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
       47.54        21.90        62.43        10.95        48.39        37.32 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       24.99        91.23 

$subtype2
TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 
       38.76       166.75        52.90       134.40        19.04        36.95 
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 
       12.99        31.89       110.93        49.35        62.60        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51F 
       15.75        86.30        64.83        59.70         9.34        30.67 
TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A20C 
      138.67        60.10        12.30        16.41        13.15        75.55 
TCGA-EE-A29C TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK 
       76.14        61.12       346.49       185.19       115.43        10.62 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A3JB 
       18.35       103.13        23.77        94.19       171.85       168.85 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H 
       34.45         7.82         4.54        53.29        11.47       150.12 
TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A69P 
       42.51       146.63        73.05        22.36        74.47         4.14 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT 
       27.62        32.78        43.92       136.27       173.19         9.90 
TCGA-GF-A4EO TCGA-GN-A26A TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
       18.25         7.59        85.05         1.97       120.07         8.09 
TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-AA9Y 
      185.13        65.42         1.94 

$subtype3
TCGA-EE-A180 TCGA-EE-A3JD TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 
       31.96        27.35        14.83         8.42        15.72       133.25 
TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A5GL TCGA-D3-A8GM 
       25.64       168.00        40.01        24.53        42.05        70.62 
TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC 
       36.53        16.90        18.44       150.61        64.83        58.85 
TCGA-DA-A95Y TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E 
       14.14        52.41        18.21        26.24        75.22         0.26 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2M8 
       44.28        47.74        77.98        32.48         0.20         5.75 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       63.25       143.93        23.51       124.31        64.04         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE 
      111.85        45.90        39.81        99.06         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 
       10.19        28.67       173.29        32.05        49.74       195.98 
TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A267 
       35.28        66.67        80.68        55.59        11.54        17.06 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 
      120.53        43.23         7.23         0.20         0.33       174.12 
TCGA-WE-A8ZN TCGA-WE-A8ZR TCGA-XV-AB01 TCGA-YG-AA3O 
       12.69         8.68         6.61        28.21 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51R TCGA-D3-A5GN 
       19.04        36.30        66.08        90.21        62.70        45.70 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A29P 
       30.44       225.11         8.71        24.89         0.00        27.16 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AB 
       30.02        26.14        81.99        15.25       104.78       122.73 
TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-GN-A265 TCGA-GN-A4U4 
        3.35       184.60        10.06       312.07        96.92        34.49 
TCGA-GN-A4U8 
       46.92 

subtype1 subtype2 subtype3 subtype4 
    0.76     1.94     0.20     0.00 
subtype1 subtype2 subtype3 subtype4 
  297.01   346.49   195.98   312.07 
subtype1 subtype2 subtype3 subtype4 
   53.90    52.90    33.88    36.30 
[1] "0.8 - 297.0 (53.9)" "1.9 - 346.5 (52.9)" "0.2 - 196.0 (33.9)"
[4] "0.0 - 312.1 (36.3)"
D8V2, survival
          sevent
clus2       0  1
  subtype1 59 67
  subtype2 45 46
  subtype3 33 56
  subtype4 19 18
subtype1 subtype2 subtype3 subtype4 
     126       91       89       37 
subtype1 subtype2 subtype3 subtype4 
      67       46       56       18 
$subtype1
TCGA-D3-A2JE TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A29L 
       27.65        62.07        68.25        54.02        68.15         2.60 
TCGA-EE-A2GD TCGA-FS-A1ZF TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-3N-A9WC 
      340.14        15.45        18.05        61.15        21.40        66.48 
TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       90.90       103.10       113.52        12.10       171.58        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       58.06       166.52        39.75       174.84       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       22.62        26.89        18.18       125.19        79.59        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA 
      241.38        89.13       152.75        18.12        15.39        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-DA-A95V 
       77.56        76.57       222.51       135.02        10.49        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 
       37.35        73.94        13.87         8.65        33.73         4.96 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29S 
       91.56        13.55        13.97        64.64        14.47        61.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GN 
       67.43       173.79       220.24        48.72       107.38       102.12 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       13.91        81.21        47.28       103.27       268.73        16.96 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE 
      180.39       167.90       248.65        53.26        28.77        54.51 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
      138.81       172.18        53.19       134.33       152.81        13.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       26.37         6.44        61.05       162.08        50.89        49.48 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       93.01        46.98        12.95        92.98        27.85        38.27 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       36.26       216.92        48.59        20.91         9.70        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26        74.73       133.55        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A262 TCGA-GN-A264 
       27.02        77.82        28.73        26.73       139.89       117.93 
TCGA-GN-A268 TCGA-GN-A4U7 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-OD-A75X TCGA-RP-A694 
       62.79        10.42        21.37        59.41       297.90         0.69 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       69.07       111.09       105.04        49.05        70.52        63.22 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       11.80        49.51        40.41        24.99        27.58        96.99 

$subtype2
TCGA-D3-A3C8 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 
       46.32       168.26       126.81       134.40        31.40        36.95 
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 
       12.99       112.04       112.57        71.80        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3BZ 
       23.77       115.53        86.76        11.87        66.48       130.72 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A8GE 
       46.98        60.23         9.34        55.73        56.35        26.43 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D3-A8GV TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 
      161.00       117.17       167.70       144.89        88.87        53.92 
TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29A 
       13.02        20.35         7.04        29.82       151.27        63.35 
TCGA-EE-A29C TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK 
       78.97        66.74       369.93       195.02       115.96        54.74 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
       75.48        21.67       129.27        61.51       103.20       204.66 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
      201.80        35.44         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       13.02       152.35        44.09       148.18       105.07        43.82 
TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 
       41.56       149.03        15.72        18.77       104.42        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS 
        7.79        27.72        48.85        53.52        46.45       148.80 
TCGA-FS-A4F8 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
      174.84         9.90        19.43        10.13        32.48        22.13 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.23       368.78        63.02       121.08        42.08       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YD-A9TA 
       24.03        17.95       101.33        12.16         6.90        49.18 
TCGA-Z2-AA3V 
       15.98 

$subtype3
TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A3JD TCGA-ER-A198 TCGA-BF-AAP0 TCGA-D3-A1Q1 
       13.87        94.98        27.35        50.76        14.93        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A3CC TCGA-D3-A3CF 
       16.67       133.25        43.43       168.00        86.93        24.53 
TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 
      125.79        30.84       107.15       129.63       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I2 
        3.65        22.29        18.44         9.90        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A95Y TCGA-EB-A5UL 
       35.93        65.92        40.60        68.09        14.14        29.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       58.92        36.46        26.89        85.08        63.78        72.07 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 
       56.84        18.61        25.87        17.92        39.29        86.14 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MN 
       79.66        42.77        44.88        19.76        96.23        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       162.48        71.21       124.31        64.04        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND 
      127.20        36.95        64.08        48.89       131.51        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YY 
       20.15        28.83        48.99       247.04        33.21       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD 
      202.65        23.93        11.41        53.16        66.67        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK 
       55.59        13.51        64.44        48.00       121.91        50.10 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1O 
       65.88         7.23         0.20         0.33       228.16         4.01 
TCGA-WE-A8ZN TCGA-WE-A8ZR TCGA-XV-AB01 TCGA-YG-AA3O TCGA-YG-AA3P 
       58.98         9.01        13.25        37.94        14.43 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        31.59        42.08        66.08       103.59        45.30 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 
       63.81       135.75        29.06         7.10        20.38        33.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B 
      225.96        43.36        10.36        27.22        14.70       133.81 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       56.42        46.82        59.64        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G 
      216.66       122.73        41.59        34.32        51.35       302.07 
TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U4 
       34.82       357.37        32.75        17.46        96.92        39.35 
TCGA-GN-A4U8 
       48.89 

subtype1 subtype2 subtype3 subtype4 
    0.69     0.23     0.20     7.10 
subtype1 subtype2 subtype3 subtype4 
  340.14   369.93   247.04   357.37 
subtype1 subtype2 subtype3 subtype4 
  58.735   56.350   47.540   45.300 
[1] "0.7 - 340.1 (58.7)" "0.2 - 369.9 (56.4)" "0.2 - 247.0 (47.5)"
[4] "7.1 - 357.4 (45.3)"
D8V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        8       0      11        9       14        6         5
  subtype2        3       3      11        4        6        7         1
  subtype3        1       4       4        2        7        7         3
  subtype4        1       0       2        1        1        4         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         8         5        11          4          9         22
  subtype2         4         3        11          4          6         16
  subtype3         5         5        12          5          9         13
  subtype4         1         1         3          1          9          3
          vv
clus       STAGE IV
  subtype1       10
  subtype2        3
  subtype3        3
  subtype4        4
D8V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  I/II NOS          8        3        1        1
  STAGE 0           0        3        4        0
  STAGE I          11       11        4        2
  STAGE IA          9        4        2        1
  STAGE IB         14        6        7        1
  STAGE II          6        7        7        4
  STAGE IIA         5        1        3        3
  STAGE IIB         8        4        5        1
  STAGE IIC         5        3        5        1
  STAGE III        11       11       12        3
  STAGE IIIA        4        4        5        1
  STAGE IIIB        9        6        9        9
  STAGE IIIC       22       16       13        3
  STAGE IV         10        3        3        4
[1] 14  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    21 36 23 25
  subtype2    18 19 16 13
  subtype3    13 14 26 18
  subtype4     8  4 11  7
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       21       18       13        8
  T2          36       19       14        4
  T3          23       16       26       11
  T4          25       13       18        7
[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       N0 N1 N2 N3
  subtype1 72 19 11 18
  subtype2 47 19  6 12
  subtype3 36 16 14 10
  subtype4 15  8  8  3
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       72       47       36       15
  N1       19       19       16        8
  N2       11        6       14        8
  N3       18       12       10        3
[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"
D8V7, binary
          cls
clus         0   1
  subtype1 115  10
  subtype2  82   3
  subtype3  78   4
  subtype4  32   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115   10
  subtype2   82    3
  subtype3   78    4
  subtype4   32    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      115       82       78       32
  1       10        3        4        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 50 33
  subtype2 29 18
  subtype3 38 23
  subtype4 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   33
  subtype2   29   18
  subtype3   38   23
  subtype4   10   13
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        50       29       38       10
  YES       33       18       23       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1  16 116
  subtype2  15  78
  subtype3   8  81
  subtype4   6  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16  116
  subtype2   15   78
  subtype3    8   81
  subtype4    6   32
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        16       15        8        6
  YES      116       78       81       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"
D8V10, continuous
D8V11, binary
          cls
clus        0  1
  subtype1 57 75
  subtype2 32 61
  subtype3 30 59
  subtype4 12 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   75
  subtype2   32   61
  subtype3   30   59
  subtype4   12   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       57       32       30       12
  MALE         75       61       59       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus         0   1
  subtype1 118  14
  subtype2  81  12
  subtype3  78  10
  subtype4  31   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   14
  subtype2   81   12
  subtype3   78   10
  subtype4   31    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       118       81       78       31
  YES       14       12       10        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0   129
  subtype2     1                         0    90
  subtype3     1                         1    83
  subtype4     2                         0    36
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        2
  BLACK OR AFRICAN AMERICAN        0        0        1        0
  WHITE                          129       90       83       36
[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"
D8V14, binary
          cls
clus         0   1
  subtype1   3 128
  subtype2   2  87
  subtype3   2  85
  subtype4   0  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  128
  subtype2    2   87
  subtype3    2   85
  subtype4    0   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        2        0
  NOT HISPANIC OR LATINO      128       87       85       37
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 34 25
  subtype2 37 45
  subtype3 44 49
subtype1 subtype2 subtype3 
      59       82       93 
subtype1 subtype2 subtype3 
      25       45       49 
$subtype1
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-3N-A9WC 
       62.07        38.76       134.40        27.35        36.95        60.46 
TCGA-BF-AAP0 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB 
       14.83       168.00        86.30        64.83        43.53       140.98 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       24.53        90.21        23.61        70.62        15.02        16.90 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-EB-A6L9 TCGA-EE-A17X 
       76.34        68.68       150.61         8.71        18.21        13.15 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.24        79.20        77.98        68.65        10.62        32.48 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AA 
       81.99        15.25         5.75        63.25        23.51       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19P 
       54.51         6.28        19.86         4.54       184.60       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7UA 
       49.71        47.18        73.05         4.70        28.67         5.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A9SD TCGA-W3-AA1R 
       27.62       130.95        35.28        55.59        59.41        79.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
        8.09       185.13        37.32        24.99        28.21 

$subtype2
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-WE-A8K5 TCGA-WE-AAA3 
      166.75       269.03        52.90        19.04        52.73         7.40 
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       12.99        31.89        49.35       133.25        19.04        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3C6 
       62.86        15.75       107.61        36.30        66.08        58.06 
TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       40.01         9.34        30.67        62.70        42.05        45.70 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UN 
      138.67       110.53        60.10        58.85       225.11        52.41 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2A1 
       24.89         0.00        76.14        44.28       185.19       115.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MG 
       12.95       201.60         0.76        71.31        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-ER-A195 
      171.85        53.26       122.73        67.89       168.85        34.45 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W 
       53.29        11.47       150.12        99.06        59.84       146.63 
TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A69P TCGA-FS-A1YY 
       22.36        68.52        15.48        74.47         4.14        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZS 
        8.35       312.07        32.78        43.92        78.61       136.27 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 
      173.19        80.68        11.54         9.90       117.93        96.92 
TCGA-GN-A26A TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8K1 
        7.59        85.05         0.33         1.97       120.07        47.54 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y 
       65.42        12.69        62.43         1.94 

$subtype3
TCGA-D3-A2JE TCGA-EE-A180 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1QA 
        9.76        31.96         8.42        15.72       110.93        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51J 
       62.60        25.64       171.58        59.70       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP 
       31.76        11.34       124.08       179.97        69.53       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A95V 
       36.53        10.78        18.44        69.21        64.83        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
        0.76        65.03        14.14        12.30         3.91        16.41 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       20.38        75.55        75.22        12.99         0.26        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB 
       47.74        27.16        61.12       346.49        30.02        26.14 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2MK 
       18.35        93.63         0.20       103.13       209.79        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD 
      104.78       145.45       227.01       143.93        64.04         4.41 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
      111.85        45.90         3.35       135.98        10.49         7.82 
TCGA-ER-A19C TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       39.81        16.87        10.19       173.29        32.05         4.50 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZU 
       26.20        10.06       171.78       195.98        36.33         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-GN-A262 TCGA-GN-A267 
       23.21         5.29         3.06        66.67        53.29        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-OD-A75X 
       42.48       120.53        34.49        46.92        43.23       297.01 
TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZR 
        0.20       174.12        44.05        92.84        21.90         8.68 
TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-Z2-AA3S 
       48.39         6.61        91.23 

subtype1 subtype2 subtype3 
    4.54     0.00     0.20 
subtype1 subtype2 subtype3 
  185.13   312.07   346.49 
subtype1 subtype2 subtype3 
  43.530   53.275   43.230 
[1] "4.5 - 185.1 (43.5)" "0.0 - 312.1 (53.3)" "0.2 - 346.5 (43.2)"
D9V2, survival
          sevent
clus2       0  1
  subtype1 43 36
  subtype2 50 67
  subtype3 57 76
subtype1 subtype2 subtype3 
      79      117      133 
subtype1 subtype2 subtype3 
      36       67       76 
$subtype1
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-QB-AA9O 
       62.07        46.32       134.40        27.35        36.95        18.05 
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       66.48        14.93        23.77       168.00        86.76        11.87 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       66.48        59.57        46.98       166.52        24.53       103.59 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GS 
       56.35        22.62        30.84        23.61       107.15       117.17 
TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
      151.53        15.39        22.29        76.57        36.03       222.51 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
      176.55        40.60        43.36         7.04        36.46        29.82 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GJ 
       26.89        91.56        13.55        18.61        86.14       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       54.74        79.66        44.88        94.82        28.83        19.76 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
       16.96        96.23        71.21       124.31        54.51        13.81 
TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q 
       36.95       134.33        77.75       302.07       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A7UA 
       49.48       105.07        23.34        48.99        41.56        38.27 
TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A9SD 
      104.42        28.08       133.55        53.16        55.59        59.41 
TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
      111.09        42.08       219.16        40.41        24.99        37.94 
TCGA-Z2-AA3V 
       15.98 

$subtype2
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-FS-A1ZF TCGA-WE-A8K5 
      168.26       340.14       126.81        31.40        15.45        61.15 
TCGA-WE-AAA3 TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       21.40        12.99       112.04        71.80       133.25        28.08 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10        65.49       115.53       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV 
       66.08       130.72        58.06        86.93         9.34        45.30 
TCGA-D3-A51F TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GE TCGA-D3-A8GN 
       55.73        63.81       125.79       135.75        26.43       161.00 
TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
       29.06       144.89        35.93       135.02        88.87        68.09 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B 
      225.96        10.36        58.92        27.22        14.70       133.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       63.35        78.97        72.07        14.47        61.28        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82       115.96        39.29       173.79       220.24 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       13.91        81.21        21.67        61.51       103.27       103.20 
TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE 
      204.66        53.26       122.73       172.18       201.80        51.35 
TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J 
       35.44        98.40        12.59        13.02       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3EV 
      131.51        61.05       148.18        43.82        93.01        46.98 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
      149.03        15.72        18.77        48.59       228.59        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH 
        7.79        48.85       357.37        53.52        46.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV 
      101.26        11.41       148.80       174.84        80.68        13.51 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
        9.90       117.93        96.92        10.13        32.48        22.13 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.23       368.78         0.33        63.02       121.08         4.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       24.03        49.05        17.95       101.33        58.98        63.22 
TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YD-A9TA 
       12.16         6.90        49.18 

$subtype3
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L 
       27.65        13.87        54.02        94.98        68.15         2.60 
TCGA-ER-A198 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       50.76        16.57        16.67       112.57        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51J 
       95.74        43.43       171.58        60.23       174.84       145.12 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL 
       32.94        26.89        18.18       125.19       241.38        89.13 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GV TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      152.75       129.63       167.70        54.67         3.65         7.10 
TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I8 
       18.12        18.44         9.90        25.18        77.56        53.92 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y 
       65.92        10.49        72.10        37.35        73.94        14.14 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A181 
       13.02        13.87        20.35        29.29         8.65        33.73 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.96       151.27        85.08        13.97        63.78        64.64 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB 
       56.84        56.42        66.74       369.93        59.64        59.28 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 
       67.43        48.72        75.48       102.12        42.77       129.27 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       47.28       268.73       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
      248.65        43.23       162.48        64.04        28.77        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI 
      138.81       127.20        64.08        34.32        53.19       152.81 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A2NE TCGA-ER-A2NF 
       13.94         9.17        48.89        26.37        20.15        28.83 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD 
      247.04        33.21        92.98        27.85        34.82        36.26 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      216.92       202.65        27.72        47.38        23.93        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        66.67        28.73 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       26.73        17.46       139.89        64.44        62.79        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
      121.91        39.35        10.42        48.89        50.10        21.37 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 
      297.90         0.20         0.69       228.16        69.07       105.04 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-XV-AB01 TCGA-YG-AA3P TCGA-Z2-A8RT 
       70.52         9.01        49.51        13.25        14.43        27.58 
TCGA-Z2-AA3S 
       96.99 

subtype1 subtype2 subtype3 
    7.04     0.23     0.20 
subtype1 subtype2 subtype3 
  302.07   368.78   369.93 
subtype1 subtype2 subtype3 
   49.48    61.15    49.51 
[1] "7.0 - 302.1 (49.5)" "0.2 - 368.8 (61.1)" "0.2 - 369.9 (49.5)"
D9V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        7       2       5       10        3        4         3
  subtype2        2       2      12        2       14        8         6
  subtype3        4       3      11        4       10       12         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         0        14          0          7         17
  subtype2         5         4         8          7         11         18
  subtype3        11        10        15          6         13         14
          vv
clus       STAGE IV
  subtype1        4
  subtype2        8
  subtype3        6
D9V4, multiclass
            clus
vv           subtype1 subtype2 subtype3
  I/II NOS          7        2        4
  STAGE 0           2        2        3
  STAGE I           5       12       11
  STAGE IA         10        2        4
  STAGE IB          3       14       10
  STAGE II          4        8       12
  STAGE IIA         3        6        3
  STAGE IIB         1        5       11
  STAGE IIC         0        4       10
  STAGE III        14        8       15
  STAGE IIIA        0        7        6
  STAGE IIIB        7       11       13
  STAGE IIIC       17       18       14
  STAGE IV          4        8        6
[1] 14  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    27 12 14  9
  subtype2    12 33 29 18
  subtype3    19 27 30 31
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       27       12       19
  T2          12       33       27
  T3          14       29       30
  T4           9       18       31
[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       N0 N1 N2 N3
  subtype1 40 12  9 17
  subtype2 59 22 14 11
  subtype3 69 27 12 10
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       40       59       69
  N1       12       22       27
  N2        9       14       12
  N3       17       11       10
[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"
D9V7, binary
          cls
clus         0   1
  subtype1  76   5
  subtype2 101   8
  subtype3 120   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76    5
  subtype2  101    8
  subtype3  120    6
   clus
vv  subtype1 subtype2 subtype3
  0       76      101      120
  1        5        8        6
[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"
D9V8, binary
          cls
clus        0  1
  subtype1 31 13
  subtype2 44 27
  subtype3 47 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   13
  subtype2   44   27
  subtype3   47   42
     clus
vv    subtype1 subtype2 subtype3
  NO        31       44       47
  YES       13       27       42
[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"
D9V9, binary
          cls
clus         0   1
  subtype1  15  70
  subtype2  12 107
  subtype3  14 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   70
  subtype2   12  107
  subtype3   14  120
     clus
vv    subtype1 subtype2 subtype3
  NO        15       12       14
  YES       70      107      120
[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"
D9V10, continuous
D9V11, binary
          cls
clus        0  1
  subtype1 35 50
  subtype2 38 81
  subtype3 50 84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   50
  subtype2   38   81
  subtype3   50   84
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       38       50
  MALE         50       81       84
[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"
D9V12, binary
          cls
clus         0   1
  subtype1  72  13
  subtype2 105  14
  subtype3 121  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   13
  subtype2  105   14
  subtype3  121   12
     clus
vv    subtype1 subtype2 subtype3
  NO        72      105      121
  YES       13       14       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    82
  subtype2     2                         0   113
  subtype3     2                         0   130
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        2
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           82      113      130
[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"
D9V14, binary
          cls
clus         0   1
  subtype1   2  82
  subtype2   2 113
  subtype3   3 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   82
  subtype2    2  113
  subtype3    3  129
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       82      113      129
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 12 12
  subtype2  5 11
  subtype3 21 14
  subtype4 19 28
  subtype5 11 18
  subtype6  5  4
  subtype7 22 23
  subtype8 13  6
  subtype9  7  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      24       16       35       47       29        9       45       19 
subtype9 
      10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12       11       14       28       18        4       23        6 
subtype9 
       3 
$subtype1
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-3N-A9WC TCGA-D3-A2J8 TCGA-D3-A2JC 
       62.07        38.76       134.40        60.46        62.86        86.30 
TCGA-D3-A3CE TCGA-D3-A8GD TCGA-D9-A3Z1 TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A20C 
       59.70        23.61        15.02         3.91        13.15        75.55 
TCGA-EE-A29Q TCGA-EE-A2GK TCGA-EE-A2MM TCGA-ER-A199 TCGA-ER-A1A1 TCGA-FR-A8YC 
       61.12        10.62       145.45         7.82        73.05        10.06 
TCGA-FS-A1Z4 TCGA-FS-A4F8 TCGA-GN-A4U3 TCGA-W3-AA1W TCGA-WE-A8ZY TCGA-WE-AAA0 
       27.62       173.19       120.53       185.13        48.39        37.32 

$subtype2
TCGA-ER-A193 TCGA-3N-A9WD TCGA-D3-A2JG TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-DA-A1IC 
       19.04        12.99       107.61        40.01        68.68        58.85 
TCGA-EE-A29G TCGA-EE-A2GJ TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19Q TCGA-ER-A19W 
       44.28        68.65        19.86         4.54        49.71       146.63 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-WE-A8ZN 
        4.70        68.52        15.48        12.69 

$subtype3
TCGA-EE-A3JD TCGA-BF-AAP0 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JL TCGA-D3-A3CB 
       27.35        14.83        25.64       168.00       171.58       140.98 
TCGA-D3-A3CF TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F8 
       24.53        70.62        16.90        76.34       150.61         8.71 
TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F 
       72.10        14.14        18.21        20.38        26.24        79.20 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MJ 
       47.41        47.74        77.98        32.48         5.75        63.25 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A19S TCGA-FR-A3YN 
       23.51       124.31        54.51         6.28        47.18         4.50 
TCGA-FR-A7UA TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-XV-AB01 TCGA-YG-AA3O 
        5.65       130.95        35.28         6.61        28.21 

$subtype4
TCGA-D3-A2JE TCGA-EE-A180 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A51K 
        9.76        31.96         8.42        15.72        76.41        31.76 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      124.08       179.97        69.53       135.12        36.53        10.78 
TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A95W TCGA-EB-A5KH TCGA-EE-A29B TCGA-EE-A29E 
       69.21        64.83         0.76        16.41        75.22         0.26 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD 
        0.20       103.13       209.79       143.93        64.04         4.41 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL 
      111.85       135.98        16.87        10.19       173.29        32.05 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       26.20       171.78       195.98         4.47         5.29         3.06 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 
       55.59        53.29        42.48        43.23       297.01         0.20 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-Z2-AA3S 
      174.12        44.05        21.90         8.68        91.23 

$subtype5
TCGA-EE-A20H TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A3MO 
      166.75        31.89        49.35        15.75        64.83         9.34 
TCGA-D3-A3MR TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A29W 
       90.21       138.67        60.10       225.11        24.89       185.19 
TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-ER-A195 
       71.31        23.77       171.85        67.89       168.85        34.45 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A2NC TCGA-ER-A42L TCGA-FS-A1ZD TCGA-FS-A1ZM 
       11.47       150.12        22.36        74.47        32.78        78.61 
TCGA-FS-A1ZS TCGA-GF-A3OT TCGA-GN-A26A TCGA-W3-A825 TCGA-W3-A828 
      136.27         9.90         7.59         1.97       120.07 

$subtype6
TCGA-EE-A2GO TCGA-D3-A1Q5 TCGA-D3-A51J TCGA-EE-A29T TCGA-ER-A19B TCGA-ER-A19L 
       52.90       110.93       144.46       346.49        53.29        99.06 
TCGA-LH-A9QB TCGA-W3-AA1V TCGA-WE-A8ZM 
       85.05         8.09        65.42 

$subtype7
TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-WE-A8K5 TCGA-WE-AAA3 TCGA-D3-A1Q7 TCGA-D3-A1QB 
      269.03        36.95        52.73         7.40       133.25        62.60 
TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A51F TCGA-D3-A5GL TCGA-D9-A4Z6 TCGA-DA-A1I5 
       45.99        58.06        30.67        42.05        18.44       110.53 
TCGA-DA-A95Z TCGA-EB-A5UN TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A2A1 TCGA-EE-A2GE 
       12.30        52.41        76.14        12.99       115.43        12.95 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MU 
      201.60        18.35        93.63         0.76        94.19        53.26 
TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A2NG 
       45.90        10.49        39.81        59.84       120.76        28.67 
TCGA-FR-A69P TCGA-FS-A1YY TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4FD 
        4.14        49.74        43.92        36.33        66.67        80.68 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-RP-A693 TCGA-WE-A8K1 
       11.54       117.93        17.06        59.41         0.33        47.54 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA4 
       62.43         1.94        24.99 

$subtype8
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A51R TCGA-D3-A5GN TCGA-EE-A182 
       19.04        36.30        66.08        62.70        45.70         0.00 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       27.16        30.02        26.14        81.99        15.25       104.78 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FS-A1ZC TCGA-GN-A265 TCGA-GN-A4U4 
      122.73         3.35       184.60       312.07        96.92        34.49 
TCGA-GN-A4U8 
       46.92 

$subtype9
TCGA-D3-A2JP TCGA-D3-A51E TCGA-D3-A51T TCGA-DA-A95X TCGA-EE-A2MK TCGA-EE-A2MP 
       43.53       173.85        11.34        65.03        89.26       227.01 
TCGA-FS-A1Z3 TCGA-FS-A1ZW TCGA-W3-AA1R TCGA-W3-AA21 
        8.35        23.21        79.99        92.84 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    3.91     4.54     4.50     0.20     1.97     8.09     0.33     0.00 
subtype9 
    8.35 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  185.13   146.63   171.58   297.01   225.11   346.49   269.03   312.07 
subtype9 
  227.01 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  60.080   42.145   32.480   43.230   64.830   85.050   45.990   45.700 
subtype9 
  72.510 
[1] "3.9 - 185.1 (60.1)" "4.5 - 146.6 (42.1)" "4.5 - 171.6 (32.5)"
[4] "0.2 - 297.0 (43.2)" "2.0 - 225.1 (64.8)" "8.1 - 346.5 (85.0)"
[7] "0.3 - 269.0 (46.0)" "0.0 - 312.1 (45.7)" "8.3 - 227.0 (72.5)"
D10V2, survival
          sevent
clus2       0  1
  subtype1 18 17
  subtype2  5 18
  subtype3 28 23
  subtype4 23 41
  subtype5 16 21
  subtype6  9  5
  subtype7 26 35
  subtype8 16 13
  subtype9  9  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      35       23       51       64       37       14       61       29 
subtype9 
      15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      17       18       23       41       21        5       35       13 
subtype9 
       6 
$subtype1
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-3N-A9WC TCGA-D3-A2J8 TCGA-D3-A2J9 
       62.07        46.32       134.40        66.48        65.49        23.77 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A51H TCGA-D3-A8GD TCGA-D3-A8GN 
       86.76        11.87        60.23        56.35        23.61       161.00 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-EB-A44Q TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C 
      117.17        15.39        13.87         7.04        29.82       151.27 
TCGA-EE-A29Q TCGA-EE-A2GK TCGA-EE-A2MM TCGA-ER-A199 TCGA-ER-A1A1 TCGA-ER-A2NH 
       66.74        54.74       167.90         9.17       105.07        41.56 
TCGA-FR-A8YC TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-GN-A266 TCGA-GN-A4U3 
       34.82        28.08        27.72       174.84        10.13       121.91 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-Z2-AA3V 
      219.16        24.03        49.51        40.41        15.98 

$subtype2
TCGA-ER-A193 TCGA-3N-A9WD TCGA-D3-A2JG TCGA-D3-A3CC TCGA-D3-A8GB TCGA-DA-A1I1 
       31.40        12.99       113.52        86.93        30.84       222.51 
TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29V TCGA-EE-A2GJ 
       35.93        68.09        13.55        72.07        25.87       107.38 
TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND 
      134.33        77.75         6.44        50.89       148.18        23.34 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1ZB TCGA-FS-A1ZR TCGA-WE-A8ZN 
       93.01        46.98        48.85        11.41        58.98 

$subtype3
TCGA-EE-A3JD TCGA-ER-A198 TCGA-BF-AAP0 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JL 
       27.35        50.76        14.93        43.43       168.00       171.58 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A5GS TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 
      166.52        24.53        18.18       107.15       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
        3.65        22.29         9.90        76.57        36.03       176.55 
TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A5UL TCGA-EB-A6L9 
       40.60        43.36        72.10        14.14        29.29        36.46 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       33.73        26.89        91.56        64.64        56.84        18.61 
TCGA-EE-A2A6 TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MQ 
       86.14        79.66        44.88        19.76        96.23        43.23 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-ER-A19S 
       71.21       124.31        54.51        13.81        36.95        49.48 
TCGA-FR-A3YN TCGA-FR-A7UA TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-GN-A26D 
       92.98        38.27        23.93       133.55        53.16        48.00 
TCGA-GN-A4U7 TCGA-XV-AB01 TCGA-YG-AA3O 
       10.42        13.25        37.94 

$subtype4
TCGA-D3-A2JE TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A29L 
       27.65        13.87        54.02        94.98        68.15         2.60 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A51K TCGA-D3-A5GU TCGA-D3-A8GJ 
       16.57        16.67        90.90        32.94       125.19       241.38 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC 
       89.13       152.75       129.63        18.12        25.18        77.56 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A95W TCGA-EB-A5KH TCGA-EE-A17Z TCGA-EE-A185 
       65.92        10.49        37.35        20.35         8.65         4.96 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2MN 
       85.08        63.78        42.77       129.27       268.73        47.54 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JA 
      162.48        64.04        28.77       138.81       127.20        53.19 
TCGA-EE-A3JI TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 
      152.81        20.15        28.83       247.04        33.21        27.85 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.26       216.92       202.65        74.73        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A268 
       27.02        28.73        26.73        55.59       139.89        62.79 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-WE-A8ZO 
       50.10       297.90         0.20       228.16        69.07        70.52 
TCGA-WE-A8ZR TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        9.01        14.43        27.58        96.99 

$subtype5
TCGA-EE-A20H TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A3MO 
      168.26       112.04        71.80       115.53        66.48         9.34 
TCGA-D3-A3MR TCGA-D3-A8GE TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y 
      103.59        26.43       144.89        88.87       225.96        27.22 
TCGA-EE-A29A TCGA-EE-A29W TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI 
       63.35       195.02        81.21        21.67        61.51       204.66 
TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A19D TCGA-ER-A19H 
      172.18       201.80        51.35        35.44        12.59       152.35 
TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A7U9 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       43.82       149.03        18.77        53.52       101.26       148.80 
TCGA-GF-A3OT TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-W3-A825 TCGA-W3-A828 
        9.90        32.48        22.13         0.23        63.02       121.08 
TCGA-YD-A9TA 
       49.18 

$subtype6
TCGA-EE-A2GO TCGA-D3-A1Q5 TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I8 
      126.81       112.57        46.98       145.12        22.62        53.92 
TCGA-EE-A29T TCGA-ER-A19B TCGA-ER-A19L TCGA-FR-A8YE TCGA-LH-A9QB TCGA-W3-AA1V 
      369.93        98.40       131.51       104.42       368.78        42.08 
TCGA-WE-A8K6 TCGA-WE-A8ZM 
       17.95       101.33 

$subtype7
TCGA-EE-A2GD TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-AAA3 
      340.14        15.45        36.95        18.05        61.15        21.40 
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3C6 
      133.25        95.74       103.10        12.10       130.72        58.06 
TCGA-D3-A51F TCGA-D3-A5GL TCGA-D3-A8GV TCGA-D9-A4Z6 TCGA-DA-A1I5 TCGA-DA-A95Z 
       55.73       125.79       167.70        18.44       135.02        13.02 
TCGA-EB-A5UN TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
       58.92        78.97        13.97        14.47        61.28       115.96 
TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       39.29       173.79       220.24        75.48       102.12        13.91 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C 
      103.27       103.20        53.26        64.08        13.94        48.89 
TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1YX 
       13.02        61.05       162.08        48.99        15.72        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4FD 
      228.59         7.79        46.45        47.38        66.67        80.68 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-RP-A693 
       13.51       117.93        64.44        21.37        59.41         0.33 
TCGA-RP-A694 TCGA-W3-AA1O TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA4 
        0.69         4.01        49.05        63.22        12.16        24.99 
TCGA-YD-A89C 
        6.90 

$subtype8
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        31.59        42.08        66.08        45.30        63.81 
TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B 
      135.75        29.06         7.10        10.36        14.70       133.81 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       56.42        46.82        59.64        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FS-A1ZC 
      216.66       122.73        41.59        34.32       302.07       357.37 
TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 
       32.75        17.46        96.92        39.35        48.89 

$subtype9
TCGA-D3-A2JP TCGA-D3-A51E TCGA-D3-A51T TCGA-DA-A95X TCGA-EE-A2GC TCGA-EE-A2GI 
       59.57       174.84        26.89        73.94        67.43        48.72 
TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-ER-A19F TCGA-FS-A1Z3 
       47.28        16.96       180.39       248.65        26.37        20.91 
TCGA-FS-A1ZW TCGA-W3-AA1R TCGA-W3-AA21 
       49.48       111.09       105.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    7.04     6.44     3.65     0.20     0.23    17.95     0.33     7.10 
subtype9 
   16.96 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  219.16   222.51   176.55   297.90   225.96   369.93   340.14   357.37 
subtype9 
  248.65 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  49.510   50.890   43.430   53.605   66.480  102.875   55.730   46.820 
subtype9 
  59.570 
[1] "7.0 - 219.2 (49.5)"   "6.4 - 222.5 (50.9)"   "3.6 - 176.6 (43.4)"  
[4] "0.2 - 297.9 (53.6)"   "0.2 - 226.0 (66.5)"   "17.9 - 369.9 (102.9)"
[7] "0.3 - 340.1 (55.7)"   "7.1 - 357.4 (46.8)"   "17.0 - 248.7 (59.6)" 
D10V3, continuous
          vv
clus       I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1        1       1       6        4        1        1         2
  subtype2        1       0       0        1        1        2         0
  subtype3        4       2       1        3        4        3         2
  subtype4        0       2       5        2        7        6         0
  subtype5        0       2       5        0        4        3         1
  subtype6        4       0       0        1        0        2         0
  subtype7        1       0       8        3        8        1         4
  subtype8        1       0       1        1        1        4         3
  subtype9        1       0       2        1        1        2         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         2         0         3          0          3         10
  subtype2         2         1         2          4          2          3
  subtype3         2         3         8          2          4          5
  subtype4         7         3         8          2          8          7
  subtype5         1         0         7          3          3          4
  subtype6         0         1         2          0          2          0
  subtype7         2         5         3          1          4         15
  subtype8         0         1         2          1          4          3
  subtype9         1         0         2          0          1          2
          vv
clus       STAGE IV
  subtype1        0
  subtype2        3
  subtype3        2
  subtype4        1
  subtype5        1
  subtype6        1
  subtype7        6
  subtype8        3
  subtype9        1
D10V4, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  I/II NOS          1        1        4        0        0        4        1
  STAGE 0           1        0        2        2        2        0        0
  STAGE I           6        0        1        5        5        0        8
  STAGE IA          4        1        3        2        0        1        3
  STAGE IB          1        1        4        7        4        0        8
  STAGE II          1        2        3        6        3        2        1
  STAGE IIA         2        0        2        0        1        0        4
  STAGE IIB         2        2        2        7        1        0        2
  STAGE IIC         0        1        3        3        0        1        5
  STAGE III         3        2        8        8        7        2        3
  STAGE IIIA        0        4        2        2        3        0        1
  STAGE IIIB        3        2        4        8        3        2        4
  STAGE IIIC       10        3        5        7        4        0       15
  STAGE IV          0        3        2        1        1        1        6
            clus
vv           subtype8 subtype9
  I/II NOS          1        1
  STAGE 0           0        0
  STAGE I           1        2
  STAGE IA          1        1
  STAGE IB          1        1
  STAGE II          4        2
  STAGE IIA         3        0
  STAGE IIB         0        1
  STAGE IIC         1        0
  STAGE III         2        2
  STAGE IIIA        1        0
  STAGE IIIB        4        1
  STAGE IIIC        3        2
  STAGE IV          3        1
[1] 14  9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    11  5  7  6
  subtype2     3  4  8  4
  subtype3    10  9 10  9
  subtype4    11 12 15 14
  subtype5     4 14 10  2
  subtype6     4  1  2  1
  subtype7     7 19 11 14
  subtype8     6  3  7  5
  subtype9     2  5  3  3
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T0+T1       11        3       10       11        4        4        7        6
  T2           5        4        9       12       14        1       19        3
  T3           7        8       10       15       10        2       11        7
  T4           6        4        9       14        2        1       14        5
       clus
vv      subtype9
  T0+T1        2
  T2           5
  T3           3
  T4           3
[1] 4 9
[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 16  5  2  9
  subtype2 11  5  4  2
  subtype3 24  9  8  5
  subtype4 34 11  6  7
  subtype5 19 11  3  3
  subtype6  9  4  0  1
  subtype7 30 10  6  8
  subtype8 13  4  6  2
  subtype9 12  2  0  1
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       16       11       24       34       19        9       30       13
  N1        5        5        9       11       11        4       10        4
  N2        2        4        8        6        3        0        6        6
  N3        9        2        5        7        3        1        8        2
    clus
vv   subtype9
  N0       12
  N1        2
  N2        0
  N3        1
[1] 4 9
[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 34  0
  subtype2 20  3
  subtype3 44  3
  subtype4 57  1
  subtype5 35  1
  subtype6 14  1
  subtype7 55  6
  subtype8 24  3
  subtype9 14  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    0
  subtype2   20    3
  subtype3   44    3
  subtype4   57    1
  subtype5   35    1
  subtype6   14    1
  subtype7   55    6
  subtype8   24    3
  subtype9   14    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       34       20       44       57       35       14       55       24
  1        0        3        3        1        1        1        6        3
   clus
vv  subtype9
  0       14
  1        1
[1] 2 9
[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 11 12
  subtype2 12  4
  subtype3 22 10
  subtype4 26 15
  subtype5  9  7
  subtype6  3  1
  subtype7 26 20
  subtype8  8  9
  subtype9  5  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   12
  subtype2   12    4
  subtype3   22   10
  subtype4   26   15
  subtype5    9    7
  subtype6    3    1
  subtype7   26   20
  subtype8    8    9
  subtype9    5    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        11       12       22       26        9        3       26        8
  YES       12        4       10       15        7        1       20        9
     clus
vv    subtype9
  NO         5
  YES        4
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1  5 31
  subtype2  3 21
  subtype3  5 46
  subtype4  7 57
  subtype5  4 34
  subtype6  3 14
  subtype7  7 57
  subtype8  5 24
  subtype9  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   31
  subtype2    3   21
  subtype3    5   46
  subtype4    7   57
  subtype5    4   34
  subtype6    3   14
  subtype7    7   57
  subtype8    5   24
  subtype9    2   13
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         5        3        5        7        4        3        7        5
  YES       31       21       46       57       34       14       57       24
     clus
vv    subtype9
  NO         2
  YES       13
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, binary
          cls
clus        0  1
  subtype1 14 22
  subtype2  7 17
  subtype3 24 27
  subtype4 20 44
  subtype5 10 28
  subtype6  8  9
  subtype7 23 41
  subtype8 12 17
  subtype9  5 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   22
  subtype2    7   17
  subtype3   24   27
  subtype4   20   44
  subtype5   10   28
  subtype6    8    9
  subtype7   23   41
  subtype8   12   17
  subtype9    5   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       14        7       24       20       10        8       23
  MALE         22       17       27       44       28        9       41
        clus
vv       subtype8 subtype9
  FEMALE       12        5
  MALE         17       10
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus        0  1
  subtype1 28  8
  subtype2 23  1
  subtype3 44  7
  subtype4 56  7
  subtype5 37  1
  subtype6 15  2
  subtype7 59  5
  subtype8 22  7
  subtype9 14  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    8
  subtype2   23    1
  subtype3   44    7
  subtype4   56    7
  subtype5   37    1
  subtype6   15    2
  subtype7   59    5
  subtype8   22    7
  subtype9   14    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        28       23       44       56       37       15       59       22
  YES        8        1        7        7        1        2        5        7
     clus
vv    subtype9
  NO        14
  YES        1
[1] 2 9
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    34
  subtype2     0                         0    23
  subtype3     1                         1    48
  subtype4     1                         0    61
  subtype5     1                         0    36
  subtype6     0                         0    17
  subtype7     0                         0    63
  subtype8     1                         0    28
  subtype9     0                         0    15
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        1        1
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                           34       23       48       61       36
                           clus
vv                          subtype6 subtype7 subtype8 subtype9
  ASIAN                            0        0        1        0
  BLACK OR AFRICAN AMERICAN        0        0        0        0
  WHITE                           17       63       28       15
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
          cls
clus        0  1
  subtype1  0 34
  subtype2  0 24
  subtype3  1 50
  subtype4  3 60
  subtype5  1 34
  subtype6  1 16
  subtype7  1 62
  subtype8  0 29
  subtype9  0 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    0   24
  subtype3    1   50
  subtype4    3   60
  subtype5    1   34
  subtype6    1   16
  subtype7    1   62
  subtype8    0   29
  subtype9    0   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        1        3        1        1
  NOT HISPANIC OR LATINO       34       24       50       60       34       16
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       62       29       15
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
