[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/15087681/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/15111349/SKCM-TM.mergedcluster.txt"

nPatients in clinical file=359, in cluster file=367, common to both=359
[1]  10 359
[1] "CN_CNMF"
[1] 3
  1   2   3 
 99 135 124 
  1   2   3 
 99 135 124 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
124 143  92 
  1   2   3 
124 143  92 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
47 58 26 38 
 1  2  3  4 
47 58 26 38 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
27 58 35 49 
 1  2  3  4 
27 58 35 49 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
133 103 123 
  1   2   3 
133 103 123 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
104 104  94  57 
  1   2   3   4 
104 104  94  57 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
 46 101  77 111   8 
  1   2   3   4   5 
 46 101  77 111   8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 90 143  72  38 
  1   2   3   4 
 90 143  72  38 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 92 104 133 
  1   2   3 
 92 104 133 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
163 136  30 
  1   2   3 
163 136  30 
[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] "PRIMARY_SITE_OF_DISEASE"               
 [7] "NEOPLASM_DISEASESTAGE"                 
 [8] "PATHOLOGY_T_STAGE"                     
 [9] "PATHOLOGY_N_STAGE"                     
[10] "PATHOLOGY_M_STAGE"                     
[11] "MELANOMA_ULCERATION"                   
[12] "MELANOMA_PRIMARY_KNOWN"                
[13] "BRESLOW_THICKNESS"                     
[14] "DCC_UPLOAD_DATE"                       
[15] "GENDER"                                
[16] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[17] "RADIATION_THERAPY"                     
[18] "RADIATIONS_RADIATION_REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 359 columns.

[1] "Batch" "21"   
[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=180,	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=195,	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=282,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM_DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW_THICKNESS':	nDistinctValues=126,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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 17:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "2"     "357"  
freq.contrast "357"   "2"    
both >= 3     "FALSE" "FALSE"
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "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 359 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"          "PRIMARY_SITE_OF_DISEASE"
 [3] "NEOPLASM_DISEASESTAGE"   "PATHOLOGY_T_STAGE"      
 [5] "PATHOLOGY_N_STAGE"       "PATHOLOGY_M_STAGE"      
 [7] "MELANOMA_ULCERATION"     "MELANOMA_PRIMARY_KNOWN" 
 [9] "BRESLOW_THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM_DISEASESTAGE, 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 72 77 69 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    72    77    69 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 72 77 69 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    72    77    69 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
169  64  38  49 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
169  64  38  49 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
169  64  38  49 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
169  64  38  49 
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=126, binary=FALSE, numeric=TRUE
GENDER, 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 27 35
  subtype2 52 40
  subtype3 42 43
subtype1 subtype2 subtype3 
      62       92       85 
subtype1 subtype2 subtype3 
      35       40       43 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A3C7 TCGA-D3-A3ML 
       60.46         8.42         7.27         9.76        46.98        13.87 
TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
      173.85        62.70        45.70        69.53       135.12        36.53 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       16.90        48.66        31.96        32.42        64.83        58.85 
TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29B 
       50.07        62.37         0.00        67.50       155.90        75.22 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GS TCGA-EE-A2GU 
       12.99        47.74         7.20        68.65        71.31        81.99 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-ER-A19D 
      143.93        23.51       122.73        51.62        45.90        11.47 
TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW 
      151.46        49.71        15.48        32.05        10.06       171.78 
TCGA-FS-A1Z0 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
      195.98         7.82        36.33        35.28         4.47         3.06 
TCGA-FS-A4FD TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-LH-A9QB 
       80.68        17.06        42.48        34.49        43.23        85.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZY 
        7.23        18.05        79.99        92.84        19.00        48.39 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       16.64        28.21 

$subtype2
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.83        15.72        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH 
       76.41        62.60        45.99        62.86       168.00        36.30 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A5GL 
      171.58        66.08       140.98        16.96        90.21        42.05 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D9-A1X3 
       78.21        23.61       179.97       120.00        70.62        10.78 
TCGA-D9-A3Z1 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       15.02        25.12        14.96        33.24        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A1 
       13.15        75.55        76.14        44.28        61.12       102.38 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
      239.11         0.20       189.40        10.62        32.48         0.20 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        5.75        23.77        94.19       171.85        63.25       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3J8 TCGA-ER-A195 
      145.45        25.08        53.26       124.31         3.35        34.45 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N TCGA-ER-A19P 
        1.58        47.31         7.82         4.54        42.48       120.76 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A3ES TCGA-FR-A44A 
       34.95       146.63        47.97        10.95       173.29       174.21 
TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 
        5.65        49.74        27.62       136.27        23.21        30.90 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
      173.19        13.28        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-W3-A824 TCGA-W3-A828 
       53.29        84.72        46.92        59.41       174.12       120.07 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y 
       44.05         8.09       185.13         1.15        12.69         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 
       26.60        15.65 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JG 
       31.89       110.93        25.64        15.75        86.30       107.61 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       64.83        43.53        58.06        40.01        59.70         9.34 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU 
       23.67       144.46        31.76        11.34       177.86       124.08 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       18.44        57.90        22.85       106.85       150.61        82.85 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29H 
      214.59         3.91        24.89        20.38         0.26        63.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM 
       27.16       346.49       185.19        77.98        26.14        18.35 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF 
       31.00       118.32         0.76       103.13        15.25       209.79 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
       67.50       227.01         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
      111.85       201.80       152.81        14.56        53.29        39.81 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      150.12        99.06        59.84        22.36         4.70        16.87 
TCGA-ER-A3ET TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       55.82       209.23        26.20         8.35       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 
       35.90        12.92        78.61       130.95         5.29        66.67 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-OD-A75X 
       55.59         6.05       117.93         7.59       120.53       297.01 
TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        0.33         1.97        59.64        62.99        58.98        10.95 
TCGA-Z2-AA3S 
       91.23 

subtype1 subtype2 subtype3 
    0.00     0.20     0.26 
subtype1 subtype2 subtype3 
  195.98   239.11   346.49 
subtype1 subtype2 subtype3 
  45.800   44.165   55.820 
[1] "0.0 - 196.0 (45.8)" "0.2 - 239.1 (44.2)" "0.3 - 346.5 (55.8)"
D1V2, survival
          sevent
clus2       0  1
  subtype1 38 59
  subtype2 75 57
  subtype3 56 64
subtype1 subtype2 subtype3 
      97      132      120 
subtype1 subtype2 subtype3 
      59       57       64 
$subtype1
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A3C7 
       17.03        66.48        16.57        11.87        27.65        46.98 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GL TCGA-D3-A8GP 
       13.87       174.84        63.81       135.75        89.13       152.75 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-DA-A1HV 
       29.06       129.63         3.65         7.10        22.29        48.89 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44R 
      194.83        61.18        65.92        68.09        10.49        10.36 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       54.02        17.29        94.98        14.70        68.15         4.96 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L 
      168.26        13.55        63.35        85.08        13.97         2.60 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GI 
       56.84        14.47        61.28        25.87        36.82        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
      107.38        81.21        94.82        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA 
       71.21       122.73        51.62        41.59        64.08        53.19 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A2NF TCGA-ER-A3EV 
       12.59        26.37       268.93        50.89        16.37        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       33.21        92.98        15.72        34.82        36.26       216.92 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      202.65        27.72         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A267 
       53.16        26.56        27.02        80.68         0.20        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        39.58        39.35        10.42        22.13        50.10 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1R 
       21.37       368.78         7.23        18.05         4.01       111.09 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YD-A89C 
      105.04        24.03        67.63        49.51        19.73         6.90 
TCGA-YG-AA3O 
       37.94 

$subtype2
TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99        14.93        16.67        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 
       42.08        12.10       171.58        66.08       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A5GL 
      166.52        24.53       103.59        55.73        56.35       125.79 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        23.61        26.43       241.38       170.20 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 
      107.15       161.00       117.17       151.53        54.67        18.12 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       15.39         9.90        20.38        23.44        28.60        15.68 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 
       68.25        52.01         7.04        24.89        29.82        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q 
      151.27        91.56        78.97        72.07        18.61        66.74 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82       102.90        67.43       340.14       161.03       208.04 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 
       54.74        79.66        42.77        44.88        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.20       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3J5 
      216.66       167.90       134.40        53.26       124.31        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       34.32        27.35        51.35       109.58        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
       50.76         9.17        77.75        44.05       162.08        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A44A 
      148.18        79.99        31.27        32.05       247.04       174.21 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       18.77        38.27       104.42       228.59        28.08        48.85 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       74.73       148.80        49.48        77.82       174.84        34.03 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       54.41        22.92        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A9SD 
       15.78       139.89        84.72        10.13        48.89        59.41 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
      228.16       121.08        69.07        42.08       219.16        49.05 
TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       58.98        12.16        35.01        22.29        27.58        15.98 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC 
      112.04       112.57        31.59        43.43       115.53        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       62.07       113.52        66.48        59.57        58.06        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
       60.23         9.34        39.75        45.30       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        26.89       137.92       178.32        18.18       125.19 
TCGA-D3-A8GI TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       58.52        18.44        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
      117.21       176.55        35.93       107.34        53.92       215.44 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       13.87        20.35        27.22         8.65        33.73       133.81 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       63.78        64.64        56.42       369.93       195.02        17.92 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       39.29        86.14        59.28        75.48       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
       13.91       129.27        28.83       268.73        16.96       158.63 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      248.65        28.77        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
      127.20       201.80       152.81        31.40        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19T 
       13.02       152.35         6.44       131.51        61.05         8.88 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A729 
       43.82        23.34        20.15        80.32         6.77       220.80 
TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       27.85        48.59        20.91         7.79       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       40.27        15.45       101.26       133.55        11.41        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A4EO 
       50.14        66.67        28.73        26.73        55.59         7.23 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
      117.93        32.48       121.91         0.23        65.88       297.90 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.33         0.69        63.02        61.15        15.98        98.89 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YD-A9TA TCGA-YG-AA3P TCGA-Z2-AA3S 
       59.77        11.80        32.58        49.18        14.43        96.99 

subtype1 subtype2 subtype3 
    0.20     2.04     0.23 
subtype1 subtype2 subtype3 
  368.78   340.14   369.93 
subtype1 subtype2 subtype3 
  46.980   54.540   56.005 
[1] "0.2 - 368.8 (47.0)" "2.0 - 340.1 (54.5)" "0.2 - 369.9 (56.0)"
D1V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 26             1
  subtype2                 15             1
  subtype3                 24             3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        13                  59
  subtype2                                        29                  89
  subtype3                                        30                  67
D1V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              26       15       24
  PRIMARY TUMOR                                    1        1        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       13       29       30
  REGIONAL LYMPH NODE                             59       89       67
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       2       6        6        9        4         5
  subtype2           5       3      15        6        9       10         6
  subtype3           6       2       7        6        9       10         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         4         4        11          4         11         20
  subtype2        10         2        12          4          9         23
  subtype3         5         6        14          7         12         17
          vv
clus       STAGE IV
  subtype1        4
  subtype2        6
  subtype3       10
D1V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        1        5        6
  STAGE 0            2        3        2
  STAGE I            6       15        7
  STAGE IA           6        6        6
  STAGE IB           9        9        9
  STAGE II           4       10       10
  STAGE IIA          5        6        3
  STAGE IIB          4       10        5
  STAGE IIC          4        2        6
  STAGE III         11       12       14
  STAGE IIIA         4        4        7
  STAGE IIIB        11        9       12
  STAGE IIIC        20       23       17
  STAGE IV           4        6       10
[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    20 22 20 21
  subtype2    19 25 32 26
  subtype3    25 25 25 21
D1V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       20       19       25
  T2          22       25       25
  T3          20       32       25
  T4          21       26       21
[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 16 17 12
  subtype2 67 18 11 22
  subtype3 59 29 10 15
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       67       59
  N1       16       18       29
  N2       17       11       10
  N3       12       22       15
[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"
D1V8, binary
          cls
clus         0   1
  subtype1  89   4
  subtype2 116   7
  subtype3 108  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89    4
  subtype2  116    7
  subtype3  108   10
   clus
vv  subtype1 subtype2 subtype3
  0       89      116      108
  1        4        7       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"
D1V9, binary
          cls
clus        0  1
  subtype1 40 28
  subtype2 50 31
  subtype3 42 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   28
  subtype2   50   31
  subtype3   42   29
     clus
vv    subtype1 subtype2 subtype3
  NO        40       50       42
  YES       28       31       29
[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, binary
          cls
clus         0   1
  subtype1  13  86
  subtype2  16 119
  subtype3  15 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   86
  subtype2   16  119
  subtype3   15  108
     clus
vv    subtype1 subtype2 subtype3
  NO        13       16       15
  YES       86      119      108
[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"
D1V11, continuous
D1V12, binary
          cls
clus        0  1
  subtype1 40 59
  subtype2 44 91
  subtype3 51 73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   59
  subtype2   44   91
  subtype3   51   73
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       44       51
  MALE         59       91       73
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    95
  subtype2     1                         1   132
  subtype3     3                         0   117
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           95      132      117
[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   2  95
  subtype2   2 132
  subtype3   3 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   95
  subtype2    2  132
  subtype3    3  117
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       95      132      117
[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 38 47
  subtype2 60 32
  subtype3 23 40
subtype1 subtype2 subtype3 
      85       92       63 
subtype1 subtype2 subtype3 
      47       32       40 
$subtype1
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML 
       15.72        76.41       107.61       171.58        58.06        13.87 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       23.67       173.85       144.46        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       45.70       124.08        78.21        69.53        70.62       135.12 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       36.53        10.78        57.90        22.85        48.66       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A180 
       31.96        32.42        58.85         3.91        13.15        62.37 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       67.50        75.55        75.22        63.12        27.16        61.12 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 
        7.20        26.14        68.65        18.35        81.99       103.13 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE 
       67.50       104.78       145.45       227.01         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 
        6.28       111.85        45.90         3.35       152.81        14.56 
TCGA-ER-A198 TCGA-ER-A19G TCGA-ER-A2NE TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       47.31       151.46        16.87        10.06       171.78        49.74 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 
      312.07        12.92         7.82       130.95         3.06        30.90 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U3 
       66.67        13.28        53.29       117.93        42.48       120.53 
TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1Q 
       34.49        43.23       297.01        18.05       174.12        44.05 
TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O 
       79.99        92.84        59.64        10.95        48.39        28.21 
TCGA-Z2-AA3S 
       91.23 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       60.46        12.99        14.83        49.35       133.25        19.04 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
        7.27        36.30        64.83        66.08        43.53       140.98 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D9-A3Z1 
       16.96        90.21       177.86        23.61       179.97        15.02 
TCGA-D9-A3Z3 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       16.90        82.85        25.12       214.59        14.96        33.24 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       45.50         6.64        20.38        76.14         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
       47.74       346.49       102.38        77.98       239.11         0.20 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
      189.40        10.62        32.48         5.75        23.77        94.19 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JB 
       63.25        25.08        53.26       124.31       122.73       201.80 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19H TCGA-ER-A19M 
       34.45         1.58         7.82         4.54       150.12        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.48       120.76        49.71        34.95       146.63        47.97 
TCGA-ER-A2NG TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZT 
       10.95       174.21       209.23         5.65        27.62        35.28 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       23.21       173.19        11.54        19.30         9.90         6.05 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A693 
       84.72         7.59        46.92        59.41         7.23         0.33 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y 
      120.07         8.09       185.13         1.15        12.69         1.94 
TCGA-WE-AAA0 TCGA-WE-AAA4 
       26.60        15.65 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JE TCGA-D3-A3C7 
        8.42        31.89       110.93        25.64         9.76        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51K TCGA-D3-A8GK TCGA-D9-A4Z6 
       40.01        59.70         9.34        31.76       120.00        18.44 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20H 
      150.61        64.83        50.07        24.89         0.00       155.90 
TCGA-EE-A29D TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       12.99       185.19        31.00       118.32         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT 
       71.31        15.25       209.79       171.85       143.93        23.51 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       51.62        67.89        53.29        39.81        11.47        99.06 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       22.36         4.70       173.29        55.82        15.48        32.05 
TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ 
       26.20       195.98         8.35        32.78        35.90        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TU 
       78.61       136.27         4.47         5.29        80.68        55.59 
TCGA-GF-A6C8 TCGA-GN-A267 TCGA-LH-A9QB TCGA-W3-A825 TCGA-WE-A8ZM TCGA-WE-A8ZO 
        1.91        17.06        85.05         1.97        62.99        19.00 
TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-AAA3 
       58.98         8.68        16.64 

subtype1 subtype2 subtype3 
    3.06     0.20     0.00 
subtype1 subtype2 subtype3 
  312.07   346.49   209.79 
subtype1 subtype2 subtype3 
  57.900   43.005   35.900 
[1] "3.1 - 312.1 (57.9)" "0.2 - 346.5 (43.0)" "0.0 - 209.8 (35.9)"
D2V2, survival
          sevent
clus2       0  1
  subtype1 47 72
  subtype2 87 53
  subtype3 35 56
subtype1 subtype2 subtype3 
     119      140       91 
subtype1 subtype2 subtype3 
      72       53       56 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG 
       17.03        16.67        31.59        90.90        62.07       113.52 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
      171.58        58.06        13.87        39.75       174.84       145.12 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
      125.19        79.59        58.52        89.13       107.15       152.75 
TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
      129.63         7.10        18.12        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC 
       48.89       117.21       194.83        61.18        53.92        68.09 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 
       13.87        20.35        29.82        94.98        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L 
      151.27        13.55        63.35        85.08        64.64         2.60 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB 
       56.42        66.74        61.28        17.92        36.82        59.28 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK 
       67.43       107.38        75.48        94.82       129.27       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AD 
      216.66       167.90        47.54       248.65        43.23        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
       54.51        13.81        41.59       138.81       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19G 
       34.32       152.81        31.40        50.76        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A2NE TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
        6.44        20.15        92.98        34.82        36.26       216.92 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZQ 
      228.59        27.72       357.37        15.45         9.70       133.55 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67        28.73        34.03 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U3 
       54.41        22.92       139.89       117.93        62.79       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 
       39.35        10.42        50.10       297.90        18.05         0.69 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ 
      228.16         4.01        69.07       111.09       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-AA3S 
       61.15        11.80        49.51        37.94        96.99 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       66.48        12.99        14.93        71.80       133.25        28.08 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       86.76        11.87        42.08        12.10        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       59.57       130.72        46.32       166.52        24.53       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD 
       55.73        56.35        22.62       178.32        30.84        23.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
       26.43       241.38       161.00       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 
        3.65        15.39        22.29         9.90        36.03        20.38 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       35.93       107.34        23.44        28.60       215.44        15.68 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 
       68.25        17.29        52.01         7.04        24.89        33.73 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       26.89        91.56        78.97        63.78        72.07        56.84 
TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       18.61       369.93        25.87        46.82       102.90        86.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       161.03       208.04        48.72        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
      103.20        16.96        96.23       134.40        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      122.73        36.95       201.80        27.35        51.35       109.58 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19H TCGA-ER-A19M 
       35.44        13.94         9.17        77.75       152.35        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       31.27        32.05       174.21       220.80        18.77        38.27 
TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A1ZT TCGA-FS-A1ZW 
      104.42        28.08        48.85        32.75        53.16        49.48 
TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
      174.84        13.51        19.30         9.90         7.23        15.78 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OG 
       84.72        10.13        32.48        48.89        59.41         0.23 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
       65.88         7.23         0.33       121.08        42.08       219.16 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       49.05        58.98        32.58        12.16        35.01        22.29 
TCGA-YD-A9TA TCGA-Z2-AA3V 
       49.18        15.98 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JE TCGA-D3-A3C7 
       16.57       112.04       112.57        43.43        27.65        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A8GK 
       86.93        60.23         9.34        45.30        32.94       170.20 
TCGA-D3-A8GQ TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44R 
       29.06        18.44       176.55        65.92        10.49        10.36 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H 
       54.02        27.22         8.65        14.70       133.81       168.26 
TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO 
       13.97        14.47       195.02        39.29       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MI 
       13.91        42.77        81.21        28.83       268.73       204.66 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19B 
      162.48        71.21        51.62       172.18        53.19        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2NC 
       48.89        12.59        13.02       131.51         8.88        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        16.37       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.77        15.72        27.85        48.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
        7.79        53.52        40.27        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB 
       74.73        11.41       148.80        26.56        27.09        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D 
       80.68         0.20        55.59         2.04        64.44        39.58 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-W3-A825 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       22.13        21.37       368.78        63.02        15.98        98.89 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YG-AA3P 
       67.63        59.77         9.01        19.73         6.90        14.43 
TCGA-Z2-A8RT 
       27.58 

subtype1 subtype2 subtype3 
    0.69     0.23     0.20 
subtype1 subtype2 subtype3 
  357.37   369.93   368.78 
subtype1 subtype2 subtype3 
   61.18    49.33    43.43 
[1] "0.7 - 357.4 (61.2)" "0.2 - 369.9 (49.3)" "0.2 - 368.8 (43.4)"
D2V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 28             2
  subtype2                 15             1
  subtype3                 22             2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        25                  69
  subtype2                                        25                 101
  subtype3                                        22                  46
D2V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              28       15       22
  PRIMARY TUMOR                                    2        1        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       25       25       22
  REGIONAL LYMPH NODE                             69      101       46
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           6       3       9        9       10        6         6
  subtype2           5       2      13        7        9        8         4
  subtype3           1       2       6        2        8       10         4
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         6        11          8          8         15
  subtype2         3         1        18          5         14         28
  subtype3         7         5         8          2         10         18
          vv
clus       STAGE IV
  subtype1        7
  subtype2        9
  subtype3        4
D2V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        6        5        1
  STAGE 0            3        2        2
  STAGE I            9       13        6
  STAGE IA           9        7        2
  STAGE IB          10        9        8
  STAGE II           6        8       10
  STAGE IIA          6        4        4
  STAGE IIB          9        3        7
  STAGE IIC          6        1        5
  STAGE III         11       18        8
  STAGE IIIA         8        5        2
  STAGE IIIB         8       14       10
  STAGE IIIC        15       28       18
  STAGE IV           7        9        4
[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    23 23 26 25
  subtype2    33 25 31 21
  subtype3     8 24 20 23
D2V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       23       33        8
  T2          23       25       24
  T3          26       31       20
  T4          25       21       23
[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 65 17 14 14
  subtype2 57 29 15 25
  subtype3 47 18  9 10
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       65       57       47
  N1       17       29       18
  N2       14       15        9
  N3       14       25       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"
D2V8, binary
          cls
clus         0   1
  subtype1 110   7
  subtype2 122  10
  subtype3  82   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110    7
  subtype2  122   10
  subtype3   82    4
   clus
vv  subtype1 subtype2 subtype3
  0      110      122       82
  1        7       10        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1 53 34
  subtype2 55 28
  subtype3 24 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   34
  subtype2   55   28
  subtype3   24   27
     clus
vv    subtype1 subtype2 subtype3
  NO        53       55       24
  YES       34       28       27
[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"
D2V10, binary
          cls
clus         0   1
  subtype1  13 111
  subtype2  23 120
  subtype3   8  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  111
  subtype2   23  120
  subtype3    8   83
     clus
vv    subtype1 subtype2 subtype3
  NO        13       23        8
  YES      111      120       83
[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"
D2V11, continuous
D2V12, binary
          cls
clus        0  1
  subtype1 42 82
  subtype2 54 89
  subtype3 39 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   82
  subtype2   54   89
  subtype3   39   53
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42       54       39
  MALE         82       89       53
[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   120
  subtype2     1                         1   138
  subtype3     2                         0    87
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          120      138       87
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
          cls
clus         0   1
  subtype1   2 118
  subtype2   3 138
  subtype3   2  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  118
  subtype2    3  138
  subtype3    2   89
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        2
  NOT HISPANIC OR LATINO      118      138       89
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 17 13
  subtype2 18 26
  subtype3  7 13
  subtype4 11 16
subtype1 subtype2 subtype3 subtype4 
      30       44       20       27 
subtype1 subtype2 subtype3 subtype4 
      13       26       13       16 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
        8.42        49.35       133.25        62.86        66.08       140.98 
TCGA-D3-A3MR TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       90.21        25.12       214.59        76.14         0.26        44.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MI 
      346.49       185.19       189.40        81.99        23.77       171.85 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19M 
      104.78       227.01        53.26         4.54        11.47        59.84 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
      146.63        10.95         9.90        84.72        17.06         7.59 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3ML 
       31.89       110.93        19.04        76.41        59.70        13.87 
TCGA-D3-A3MO TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GK 
        9.34        62.37        75.55        27.16         7.20        10.62 
TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       32.48        71.31       103.13        63.25        67.50       145.45 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3J7 
       25.08       143.93        23.51        51.62        67.89        45.90 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        7.82        53.29       151.46        47.97        22.36        16.87 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      173.29        32.05       171.78       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A262 
      312.07        32.78         7.82        35.28         4.47        53.29 
TCGA-GN-A264 TCGA-GN-A268 
      117.93        42.48 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D9-A3Z1 TCGA-DA-A1IA TCGA-DA-A1IC 
       62.60        25.64         7.27        15.02        64.83        58.85 
TCGA-DA-A3F8 TCGA-EE-A2A6 TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H 
       14.96        77.98         5.75         4.41        39.81       150.12 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FS-A1ZM 
      120.76        49.71        34.95         4.70        55.82        78.61 
TCGA-FS-A1ZQ TCGA-FW-A3TV 
      130.95        11.54 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
       86.30        64.83        43.53        48.66       106.85       150.61 
TCGA-DA-A1I5 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29B 
       82.85        13.15        20.38         0.00        67.50        75.22 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A3AA TCGA-EE-A3AB 
       63.12        47.74         0.76         0.20       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       54.51         6.28        14.56        34.45         1.58        47.31 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZJ 
       99.06        42.48        36.33 

subtype1 subtype2 subtype3 subtype4 
    0.26     4.47     4.41     0.00 
subtype1 subtype2 subtype3 subtype4 
  346.49   312.07   150.12   150.61 
subtype1 subtype2 subtype3 subtype4 
  64.470   46.935   44.760   47.740 
[1] "0.3 - 346.5 (64.5)" "4.5 - 312.1 (46.9)" "4.4 - 150.1 (44.8)"
[4] "0.0 - 150.6 (47.7)"
D3V2, survival
          sevent
clus2       0  1
  subtype1 21 24
  subtype2 25 33
  subtype3 11 15
  subtype4 13 23
subtype1 subtype2 subtype3 subtype4 
      45       58       26       36 
subtype1 subtype2 subtype3 subtype4 
      24       33       15       23 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       16.57        71.80       133.25        65.49        66.08       166.52 
TCGA-D3-A3MR TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 
      103.59        20.38        35.93        53.92        28.60        10.49 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
      215.44        91.56        78.97        63.78        72.07        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH TCGA-EE-A2GU 
       61.28       369.93       195.02        46.82       208.04        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       21.67        61.51       204.66       216.66       248.65        53.26 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M 
       27.35       109.58        77.75        12.59        13.02        61.05 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 
      148.18        31.27        32.05        27.72         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        64.44        32.48 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE 
      112.04       112.57        28.08        31.59        90.90        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-EE-A180 
       13.87         9.34       151.53        54.67         7.10        94.98 
TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
      151.27        56.42        36.82        67.43        54.74        79.66 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       81.21       129.27        47.28        96.23       158.63       167.90 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG 
       47.54       134.40       162.48        71.21        51.62        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B 
      172.18        64.08        53.19        51.35         9.17        98.40 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
      268.93         6.44        79.99        43.82        20.15        16.37 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      247.04        33.21       216.92       202.65        20.91        28.08 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 
      357.37        53.52         9.70        53.16        26.56         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
      139.89       117.93        62.79        39.58 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A1JW TCGA-D9-A3Z1 
       95.74        43.43        11.87        45.30         3.65        15.39 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A6 
       65.92        68.09        15.68         4.96        25.87        86.14 
TCGA-EE-A2GI TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P 
       48.72        19.76        28.77        48.89       152.35       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZM 
       50.89        37.25        23.34        80.32        92.98       101.26 
TCGA-FS-A1ZQ TCGA-FW-A3TV 
      133.55        13.51 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       86.76        66.48        59.57        48.89        36.03       117.21 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
      176.55       107.34        23.44        29.82        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       68.15        85.08        64.64         2.60        56.84        18.61 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
       13.91        42.77        44.88       124.31       122.73        54.51 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F 
       13.81        31.40        35.44        13.94        50.76        26.37 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      131.51        44.05        32.75        47.38        23.93        74.73 

subtype1 subtype2 subtype3 subtype4 
    9.90     0.20     3.65     2.60 
subtype1 subtype2 subtype3 subtype4 
  369.93   357.37   162.08   176.55 
subtype1 subtype2 subtype3 subtype4 
  63.780   58.325   47.010   46.130 
[1] "9.9 - 369.9 (63.8)" "0.2 - 357.4 (58.3)" "3.6 - 162.1 (47.0)"
[4] "2.6 - 176.6 (46.1)"
D3V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2             0
  subtype2                 11             1
  subtype3                  4             0
  subtype4                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        14                  31
  subtype2                                        10                  36
  subtype3                                         5                  17
  subtype4                                         3                  29
D3V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               2       11        4        5
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       14       10        5        3
  REGIONAL LYMPH NODE                             31       36       17       29
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       1       5        2        7        1         2
  subtype2           2       2       7        1        7        2         2
  subtype3           1       0       1        2        1        0         0
  subtype4           3       0       1        3        2        4         1
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         0         3          3          5          9
  subtype2         2         3         8          1          2          6
  subtype3         1         0         5          1          4          5
  subtype4         2         0         4          0          4          7
          vv
clus       STAGE IV
  subtype1        2
  subtype2        5
  subtype3        0
  subtype4        2
D3V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        2        1        3
  STAGE 0            1        2        0        0
  STAGE I            5        7        1        1
  STAGE IA           2        1        2        3
  STAGE IB           7        7        1        2
  STAGE II           1        2        0        4
  STAGE IIA          2        2        0        1
  STAGE IIB          1        2        1        2
  STAGE IIC          0        3        0        0
  STAGE III          3        8        5        4
  STAGE IIIA         3        1        1        0
  STAGE IIIB         5        2        4        4
  STAGE IIIC         9        6        5        7
  STAGE IV           2        5        0        2
[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     8 12 10  9
  subtype2     9 13  7 13
  subtype3     7  7  5  2
  subtype4    12  5  6  7
D3V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        8        9        7       12
  T2          12       13        7        5
  T3          10        7        5        6
  T4           9       13        2        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 22  7  6  8
  subtype2 36  6  6  6
  subtype3  8  6  7  3
  subtype4 19  5  7  4
D3V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       22       36        8       19
  N1        7        6        6        5
  N2        6        6        7        7
  N3        8        6        3        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1 42  2
  subtype2 48  6
  subtype3 25  0
  subtype4 34  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    2
  subtype2   48    6
  subtype3   25    0
  subtype4   34    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       42       48       25       34
  1        2        6        0        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1 21  7
  subtype2 23 15
  subtype3 11  5
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    7
  subtype2   23   15
  subtype3   11    5
  subtype4   10   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       23       11       10
  YES        7       15        5       10
[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"
D3V10, binary
          cls
clus        0  1
  subtype1  6 41
  subtype2  8 50
  subtype3  3 23
  subtype4  8 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   41
  subtype2    8   50
  subtype3    3   23
  subtype4    8   30
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        8        3        8
  YES       41       50       23       30
[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"
D3V11, continuous
D3V12, binary
          cls
clus        0  1
  subtype1 17 30
  subtype2 20 38
  subtype3 11 15
  subtype4 16 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   30
  subtype2   20   38
  subtype3   11   15
  subtype4   16   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       20       11       16
  MALE         30       38       15       22
[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       WHITE
  subtype1    47
  subtype2    58
  subtype3    26
  subtype4    38
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V14, binary
          cls
clus        0
  subtype1 47
  subtype2 58
  subtype3 26
  subtype4 37
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  8  9
  subtype2 23 21
  subtype3  9 17
  subtype4 13 21
subtype1 subtype2 subtype3 subtype4 
      17       44       26       34 
subtype1 subtype2 subtype3 subtype4 
       9       21       17       21 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EE-A182 
        8.42        49.35        62.86        25.12       214.59         0.00 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2GP TCGA-EE-A2MC 
       76.14         0.26        44.28       185.19         0.76        23.77 
TCGA-EE-A2MU TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 
       53.26         4.54         9.90        84.72        17.06 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
       31.89       133.25        19.04        86.30        66.08        59.70 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2A2 
        9.34        48.66       106.85        75.22        27.16         7.20 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MK 
       10.62        32.48        81.99       103.13       171.85        67.50 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      145.45        25.08       124.31       122.73        51.62        54.51 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
        6.28        45.90        14.56         7.82        53.29        11.47 
TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ES 
      151.46        42.48        47.97        22.36        16.87       173.29 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU 
      195.98        27.62       312.07        32.78        35.28         4.47 
TCGA-GN-A264 TCGA-GN-A268 
      117.93        42.48 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
      110.93        62.60        64.83        43.53       140.98        13.87 
TCGA-D9-A3Z1 TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20C 
       15.02       150.61        14.96        20.38        67.50        75.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 
       63.12        47.74       346.49         0.20         5.75        34.45 
TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG 
        1.58       150.12        99.06        59.84       146.63        10.95 
TCGA-ER-A3ET TCGA-FS-A1ZJ 
       55.82        36.33 

$subtype4
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-DA-A1I5 TCGA-DA-A1IA 
       76.41        25.64         7.27        90.21        82.85        64.83 
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GS 
       58.85        13.15        62.37        77.98       189.40        71.31 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD 
       63.25       104.78       227.01       143.93        23.51         4.41 
TCGA-EE-A3J3 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       67.89        47.31        39.81       120.76        49.71        34.95 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZM 
        4.70        32.05       171.78         8.35         7.82        78.61 
TCGA-FS-A1ZQ TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26A 
      130.95        11.54        53.29         7.59 

subtype1 subtype2 subtype3 subtype4 
    0.00     4.47     0.20     4.41 
subtype1 subtype2 subtype3 subtype4 
  214.59   312.07   346.49   227.01 
subtype1 subtype2 subtype3 subtype4 
  25.120   48.315   57.830   60.610 
[1] "0.0 - 214.6 (25.1)" "4.5 - 312.1 (48.3)" "0.2 - 346.5 (57.8)"
[4] "4.4 - 227.0 (60.6)"
D4V2, survival
          sevent
clus2       0  1
  subtype1 10 15
  subtype2 26 31
  subtype3 12 22
  subtype4 22 27
subtype1 subtype2 subtype3 subtype4 
      25       57       34       49 
subtype1 subtype2 subtype3 subtype4 
      15       31       22       27 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F2 
       16.57        71.80        65.49        20.38        35.93        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       10.49       215.44        14.70        78.97        63.78        72.07 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 
       14.47        25.87       195.02        46.82        13.91        21.67 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 
       61.51        53.26       109.58        77.75         9.90        84.72 
TCGA-GN-A267 
       64.44 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
      112.04       133.25        28.08        86.76        66.08        60.23 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29B TCGA-EE-A29P 
        9.34        48.89       117.21        53.92        85.08        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       36.82        54.74        79.66        44.88        94.82       129.27 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
      204.66       158.63       167.90        47.54       134.40       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J7 
      122.73        51.62        54.51        13.81        41.59        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       53.19        27.35        31.40         9.17        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       13.02        26.37       268.93         6.44        44.05        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       43.82        20.15        16.37       247.04       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A264 
       27.72       357.37        53.52        53.16        26.56       117.93 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        62.79        39.58 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
      112.57        95.74        66.48        59.57       166.52        13.87 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 
       15.39        36.03       176.55        23.44        15.68        33.73 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       68.15       151.27        91.56        64.64        56.84        18.61 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
       61.28       369.93        42.77        19.76        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
      152.35       131.51        61.05       148.18        31.27        80.32 
TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       92.98        32.75        47.38        74.73 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A3MV 
       31.59        90.90        43.43        11.87       103.59        45.30 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1I5 TCGA-DA-A1IA 
      151.53        54.67         3.65         7.10       107.34        65.92 
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A2A6 
       68.09        29.82        94.98         4.96         2.60        86.14 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MJ 
       67.43       208.04        48.72        81.21        47.28        96.23 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3J3 
      216.66       248.65       162.48        71.21        28.77       172.18 
TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       51.35        50.76        48.89       162.08        50.89        37.25 
TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZG 
       23.34        32.05        33.21       216.92        20.91         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GN-A262 
       23.93       101.26       133.55         0.20        13.51       139.89 
TCGA-GN-A26A 
       32.48 

subtype1 subtype2 subtype3 subtype4 
    9.90     6.44    13.87     0.20 
subtype1 subtype2 subtype3 subtype4 
  215.44   357.37   369.93   248.65 
subtype1 subtype2 subtype3 subtype4 
  53.260   53.920   61.165   50.890 
[1] "9.9 - 215.4 (53.3)"  "6.4 - 357.4 (53.9)"  "13.9 - 369.9 (61.2)"
[4] "0.2 - 248.7 (50.9)" 
D4V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  3             0
  subtype2                  9             1
  subtype3                  2             0
  subtype4                  8             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         8                  16
  subtype2                                         8                  40
  subtype3                                         4                  28
  subtype4                                        12                  29
D4V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               3        9        2        8
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        8        8        4       12
  REGIONAL LYMPH NODE                             16       40       28       29
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       2        1        3        0         1
  subtype2           2       1       7        3        5        0         3
  subtype3           4       1       2        1        4        3         1
  subtype4           1       0       3        3        5        4         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0         1          2          5          7
  subtype2         4         3        10          0          2          9
  subtype3         0         0         3          2          3          5
  subtype4         2         0         6          1          5          6
          vv
clus       STAGE IV
  subtype1        2
  subtype2        2
  subtype3        1
  subtype4        4
D4V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        2        4        1
  STAGE 0            1        1        1        0
  STAGE I            2        7        2        3
  STAGE IA           1        3        1        3
  STAGE IB           3        5        4        5
  STAGE II           0        0        3        4
  STAGE IIA          1        3        1        0
  STAGE IIB          0        4        0        2
  STAGE IIC          0        3        0        0
  STAGE III          1       10        3        6
  STAGE IIIA         2        0        2        1
  STAGE IIIB         5        2        3        5
  STAGE IIIC         7        9        5        6
  STAGE IV           2        2        1        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     4  6  7  7
  subtype2    16 12  4 11
  subtype3     6  9  8  3
  subtype4    10 10  9 10
D4V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        4       16        6       10
  T2           6       12        9       10
  T3           7        4        8        9
  T4           7       11        3       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 10  8  4  4
  subtype2 32  4  9  9
  subtype3 18  5  6  3
  subtype4 25  7  7  5
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       10       32       18       25
  N1        8        4        5        7
  N2        4        9        6        7
  N3        4        9        3        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"
D4V8, binary
          cls
clus        0  1
  subtype1 24  2
  subtype2 51  2
  subtype3 32  1
  subtype4 42  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    2
  subtype2   51    2
  subtype3   32    1
  subtype4   42    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       24       51       32       42
  1        2        2        1        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"
D4V9, binary
          cls
clus        0  1
  subtype1 11  6
  subtype2 19 14
  subtype3 12  5
  subtype4 23 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    6
  subtype2   19   14
  subtype3   12    5
  subtype4   23   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11       19       12       23
  YES        6       14        5       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"
D4V10, binary
          cls
clus        0  1
  subtype1  3 24
  subtype2 14 44
  subtype3  3 32
  subtype4  5 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   24
  subtype2   14   44
  subtype3    3   32
  subtype4    5   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3       14        3        5
  YES       24       44       32       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"
D4V11, continuous
D4V12, binary
          cls
clus        0  1
  subtype1  6 21
  subtype2 25 33
  subtype3 15 20
  subtype4 18 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   21
  subtype2   25   33
  subtype3   15   20
  subtype4   18   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       25       15       18
  MALE         21       33       20       31
[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       WHITE
  subtype1    27
  subtype2    58
  subtype3    35
  subtype4    49
[1] "NOT AVAILABLE: table dimension [4x1]"
D4V14, binary
          cls
clus        0
  subtype1 27
  subtype2 58
  subtype3 35
  subtype4 48
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 37 54
  subtype2 47 20
  subtype3 37 45
subtype1 subtype2 subtype3 
      91       67       82 
subtype1 subtype2 subtype3 
      54       20       45 
$subtype1
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A3CC 
       76.41        62.60        25.64         7.27       107.61        40.01 
TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A8GC 
       13.87        23.67       173.85        31.76        42.05        78.21 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      120.00        69.53        70.62        36.53        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44Q 
       18.44        57.90        22.85        64.83        58.85         3.91 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
       50.07        45.50        13.15        62.37         0.00        67.50 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99         0.26        63.12        47.74 
TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MT TCGA-EE-A3AC 
       26.14        18.35         0.20        81.99        23.51        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
        4.41         6.28       111.85       152.81         1.58        47.31 
TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       39.81        49.71         4.70        16.87        10.95       173.29 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZE TCGA-FS-A1ZG 
       15.48        26.20       171.78        49.74        35.90         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33       130.95         4.47         3.06        30.90        66.67 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       13.28        55.59        11.54       117.93        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 
      120.53        34.49        43.23         7.23        18.05       174.12 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       44.05        79.99        92.84         1.15        59.64        12.69 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       19.00         8.68        48.39        16.64        15.65        28.21 
TCGA-Z2-AA3S 
       91.23 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 
       60.46        12.99        14.83        15.72       133.25        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CB 
       62.86       168.00        36.30       171.58        66.08       140.98 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A8GD TCGA-D3-A8GJ 
       16.96        90.21       144.46        11.34        23.61       179.97 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG 
       48.66        31.96        82.85        25.12        14.96        33.24 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.64        20.38        27.16       102.38         7.20        77.98 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MF 
      189.40        68.65        10.62        32.48         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       94.19        63.25       104.78        25.08        53.26       124.31 
TCGA-EE-A3AE TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N 
       54.51        14.56         7.82         4.54       151.46        42.48 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FR-A729 
      120.76        34.95       146.63        47.97       174.21       209.23 
TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY 
        5.65        27.62        35.28        23.21       173.19        19.30 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1W 
        6.05        84.72        46.92        59.41         0.33       185.13 
TCGA-WE-AAA0 
       26.60 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
        8.42        31.89       110.93        49.35        19.04        15.75 
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       86.30         9.76        64.83        43.53        58.06        46.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       59.70         9.34        62.70        45.70       177.86       124.08 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
      135.12        10.78       106.85       150.61        32.42       214.59 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29T 
       24.89        75.55       155.90        44.28        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      185.19       239.11         0.20        31.00       118.32         0.76 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK 
       71.31       103.13        15.25        23.77       171.85        67.50 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 
      145.45       227.01       143.93       122.73        67.89        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H 
        3.35       201.80        34.45        53.29        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A8YC 
       99.06        59.84        22.36        55.82        32.05        10.06 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM 
      195.98         8.35       312.07        32.78        12.92        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
      136.27         5.29        80.68         9.90         1.91        53.29 
TCGA-GN-A26A TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        7.59        85.05       297.01         1.97       120.07         8.09 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       62.99        58.98        10.95         1.94 

subtype1 subtype2 subtype3 
    0.00     0.33     0.20 
subtype1 subtype2 subtype3 
  174.12   209.79   346.49 
subtype1 subtype2 subtype3 
   36.53    46.92    58.52 
[1] "0.0 - 174.1 (36.5)" "0.3 - 209.8 (46.9)" "0.2 - 346.5 (58.5)"
D5V2, survival
          sevent
clus2       0  1
  subtype1 49 81
  subtype2 69 33
  subtype3 51 67
subtype1 subtype2 subtype3 
     130      102      118 
subtype1 subtype2 subtype3 
      81       33       67 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD 
       17.03        31.59        90.90        95.74        43.43        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E 
      113.52        12.10        86.93        13.87        39.75       174.84 
TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL 
       32.94       125.79        79.59        58.52       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      107.15       129.63       151.53         3.65        15.39        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       18.44         9.90        25.18        66.25        22.95        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A44R 
       20.38        35.93        65.92        68.09        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
       20.35        54.02        17.29        52.01        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20I 
       94.98        14.70        26.89        68.15         4.96        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       85.08        78.97        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR 
       56.84        25.87        17.92        59.28        75.48        42.77 
TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC 
       94.82        47.28        47.54        43.23        71.21        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
       28.77        13.81       127.20       152.81        13.94        50.76 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
       48.89        26.37        50.89         8.88        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 
       16.37        31.27       247.04        46.98        92.98        27.85 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       36.26       216.92       228.59        48.85        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       47.38        23.93       133.55        26.56        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 
       66.67        34.03        22.92        55.59        13.51       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        39.58       121.91        39.35        10.42 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       50.10        21.37         7.23        18.05         0.69       228.16 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01        69.07       111.09       105.04        49.05        61.15 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 
       58.98        67.63         9.01        49.51        19.73        22.29 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       37.94        14.43        96.99        15.98 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 
       66.48        12.99        14.93        16.67       133.25       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       65.49        23.77       168.00        62.07        42.08       171.58 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       66.08       130.72        46.32       166.52        24.53       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB 
       55.73        56.35       145.12        26.89       137.92        30.84 
TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
       23.61       241.38       161.00       117.17        54.67         7.10 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       48.89       194.83       107.34        23.44        28.60        15.68 
TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N 
       68.25         7.04        24.89        33.73        91.56        18.61 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       56.42        61.28        46.82       102.90        36.82        86.14 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       208.04        48.72       107.38        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       44.88        19.76       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       96.23       216.66       134.40        53.26       124.31        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       36.95        53.19        27.35        51.35       109.58        31.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        9.17        77.75       268.93        44.05       162.08        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
      148.18        79.99        32.05       174.21       220.80        18.77 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
       38.27       104.42        28.08        53.16        49.48       174.84 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD 
       19.30         7.23        15.78        84.72        48.89        59.41 
TCGA-HR-A2OH TCGA-RP-A693 TCGA-W3-AA1W TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-Z2-A8RT 
       65.88         0.33       219.16        32.58        35.01        27.58 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       16.57       112.04       112.57        71.80        28.08       115.53 
TCGA-D3-A2JC TCGA-D3-A2JE TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       86.76        27.65        66.48        59.57        58.06        46.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       60.23         9.34        45.30        22.62        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GE TCGA-D3-A8GP TCGA-D3-A8GQ 
      178.32        18.18       125.19        26.43       152.75        29.06 
TCGA-D9-A1X3 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 
       18.12       117.21       176.55        61.18        53.92        10.49 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
      215.44        27.22       133.81       151.27       168.26        63.35 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 
       72.07        66.74        14.47       369.93       195.02        39.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
      340.14       161.03       102.12       126.81        13.91        81.21 
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       158.63 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH 
      167.90       248.65       162.48       122.73        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B 
      172.18        64.08        34.32       201.80        35.44        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        13.02       152.35         6.44       131.51        61.05 
TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A8YC 
       43.82        80.32        33.21         6.77        15.72        34.82 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        20.91         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       53.52        15.45        32.75       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC 
      148.80        27.09        50.14        28.73        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       80.68         0.20         9.90         2.04       139.89        10.13 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 
       32.48        22.13         0.23       368.78       297.90        63.02 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      121.08        42.08        24.03        15.98        98.89        59.77 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YD-A9TA 
       11.80        12.16         6.90        49.18 

subtype1 subtype2 subtype3 
    0.69     0.33     0.20 
subtype1 subtype2 subtype3 
  247.04   268.93   369.93 
subtype1 subtype2 subtype3 
  43.000   55.235   59.670 
[1] "0.7 - 247.0 (43.0)" "0.3 - 268.9 (55.2)" "0.2 - 369.9 (59.7)"
D5V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 32             5
  subtype2                 11             0
  subtype3                 22             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        19                  76
  subtype2                                        14                  78
  subtype3                                        39                  62
D5V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              32       11       22
  PRIMARY TUMOR                                    5        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       19       14       39
  REGIONAL LYMPH NODE                             76       78       62
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           3       3       6        7       10        7         4
  subtype2           4       1      11        9        7        6         5
  subtype3           5       3      11        2       10       11         5
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         8        13          8         12         27
  subtype2         4         2        10          1         11         18
  subtype3         6         2        14          6          9         16
          vv
clus       STAGE IV
  subtype1        6
  subtype2        4
  subtype3       10
D5V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        3        4        5
  STAGE 0            3        1        3
  STAGE I            6       11       11
  STAGE IA           7        9        2
  STAGE IB          10        7       10
  STAGE II           7        6       11
  STAGE IIA          4        5        5
  STAGE IIB          9        4        6
  STAGE IIC          8        2        2
  STAGE III         13       10       14
  STAGE IIIA         8        1        6
  STAGE IIIB        12       11        9
  STAGE IIIC        27       18       16
  STAGE IV           6        4       10
[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    19 23 29 35
  subtype2    25 17 21 17
  subtype3    20 32 27 17
D5V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       25       20
  T2          23       17       32
  T3          29       21       27
  T4          35       17       17
[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 55 24 17 21
  subtype2 53 18  7 13
  subtype3 61 22 14 15
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       55       53       61
  N1       24       18       22
  N2       17        7       14
  N3       21       13       15
[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"
D5V8, binary
          cls
clus         0   1
  subtype1 119   7
  subtype2  91   4
  subtype3 104  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119    7
  subtype2   91    4
  subtype3  104   10
   clus
vv  subtype1 subtype2 subtype3
  0      119       91      104
  1        7        4       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"
D5V9, binary
          cls
clus        0  1
  subtype1 56 40
  subtype2 43 22
  subtype3 33 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56   40
  subtype2   43   22
  subtype3   33   27
     clus
vv    subtype1 subtype2 subtype3
  NO        56       43       33
  YES       40       22       27
[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"
D5V10, binary
          cls
clus         0   1
  subtype1  11 122
  subtype2  16  87
  subtype3  17 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  122
  subtype2   16   87
  subtype3   17  105
     clus
vv    subtype1 subtype2 subtype3
  NO        11       16       17
  YES      122       87      105
[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"
D5V11, continuous
D5V12, binary
          cls
clus        0  1
  subtype1 44 89
  subtype2 39 64
  subtype3 52 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   89
  subtype2   39   64
  subtype3   52   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       39       52
  MALE         89       64       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0   126
  subtype2     1                         1   100
  subtype3     1                         0   119
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          126      100      119
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   4 127
  subtype2   1 101
  subtype3   2 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  127
  subtype2    1  101
  subtype3    2  117
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        2
  NOT HISPANIC OR LATINO      127      101      117
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 21 49
  subtype2 49 23
  subtype3 27 33
  subtype4 24 14
subtype1 subtype2 subtype3 subtype4 
      70       72       60       38 
subtype1 subtype2 subtype3 subtype4 
      49       23       33       14 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JE TCGA-D3-A2JG 
        8.42        76.41        25.64        45.99         9.76       107.61 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GC 
       40.01        13.87        31.76        42.05       124.08        78.21 
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-EB-A5SH TCGA-EB-A5UN 
       57.90        22.85        64.83        58.85        50.07        45.50 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       13.15        62.37         0.00        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
        0.26        44.28        61.12        18.35        31.00         0.20 
TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C 
       23.51         4.41         6.28        45.90         1.58        39.81 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YY 
        4.70        16.87       173.29        15.48        26.20        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZU 
        8.35        35.90         7.82        36.33       130.95         4.47 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        5.29         3.06        30.90        13.28        80.68        55.59 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A8LK 
      117.93        84.72        17.06        42.48       120.53        43.23 
TCGA-OD-A75X TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-YG-AA3O 
      297.01         8.68        48.39        28.21 

$subtype2
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2JC TCGA-D3-A2JH 
       60.46        14.83        15.72       133.25        86.30        36.30 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A8GD TCGA-D3-A8GJ 
      140.98        90.21        23.67        11.34        23.61       179.97 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG 
       48.66        31.96       150.61        25.12        14.96        33.24 
TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
       27.16       102.38        77.98       239.11       189.40        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG 
       10.62        32.48         0.76         5.75       209.79        94.19 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 
       67.50       227.01        25.08       124.31        51.62        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19M 
      111.85       152.81         7.82         4.54       151.46        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A3ET 
       42.48       120.76        34.95       146.63        47.97        55.82 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       32.05       174.21       209.23         5.65        10.06       171.78 
TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY 
       27.62        78.61        35.28        23.21       173.19        19.30 
TCGA-GF-A4EO TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-W3-AA1Q TCGA-W3-AA1W 
        6.05        34.49        46.92        59.41        44.05       185.13 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-Z2-AA3S 
       92.84        59.64        19.00         1.94        16.64        91.23 

$subtype3
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 
       12.99        31.89       110.93        49.35        19.04        62.86 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       15.75        64.83        43.53        58.06        46.98        59.70 
TCGA-D3-A3MO TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-DA-A1HY 
        9.34       144.46        62.70        45.70       177.86       106.85 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29T 
       32.42       214.59        24.89        75.55       155.90       346.49 
TCGA-EE-A29W TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
      185.19         0.20       118.32        71.31       103.13        15.25 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AB 
       23.77       171.85       104.78       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       201.80        34.45        53.29        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A2NC TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       99.06        22.36       195.98       312.07        32.78        12.92 
TCGA-FS-A1ZS TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A26A TCGA-LH-A9QB 
      136.27         9.90         1.91        53.29         7.59        85.05 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        1.97       120.07         8.09        62.99        58.98        10.95 

$subtype4
TCGA-D3-A1QB TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CF 
       62.60       168.00         7.27       171.58        66.08        16.96 
TCGA-D3-A51E TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I5 TCGA-EB-A44Q 
      173.85        70.62        15.02        16.90        82.85         3.91 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A2 
        6.64        20.38        67.50        63.12        47.74         7.20 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE TCGA-ER-A193 
       26.14        81.99        63.25        53.26        54.51        14.56 
TCGA-ER-A198 TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FS-A4F4 TCGA-FW-A3TV TCGA-QB-A6FS 
       47.31        49.71        10.95        66.67        11.54         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZN 
       18.05         0.33       174.12        79.99         1.15        12.69 
TCGA-WE-AAA0 TCGA-WE-AAA4 
       26.60        15.65 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.76     0.20     0.33 
subtype1 subtype2 subtype3 subtype4 
  297.01   239.11   346.49   174.12 
subtype1 subtype2 subtype3 subtype4 
  36.430   50.140   59.340   36.955 
[1] "0.0 - 297.0 (36.4)" "0.8 - 239.1 (50.1)" "0.2 - 346.5 (59.3)"
[4] "0.3 - 174.1 (37.0)"
D6V2, survival
          sevent
clus2       0  1
  subtype1 29 72
  subtype2 67 36
  subtype3 41 49
  subtype4 32 24
subtype1 subtype2 subtype3 subtype4 
     101      103       90       56 
subtype1 subtype2 subtype3 subtype4 
      72       36       49       24 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JE 
       17.03        16.57        90.90        43.43       103.10        27.65 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A51K TCGA-D3-A5GL 
      113.52        12.10        86.93        13.87        32.94       125.79 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL 
      137.92       125.19        79.59        58.52       170.20        89.13 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
      152.75       129.63        18.12        18.44        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44R TCGA-EB-A5KH 
       22.95        35.93        65.92        68.09        10.36        20.35 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       54.02        52.01        29.82         8.65        94.98        14.70 
TCGA-EE-A185 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        4.96        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
        2.60        66.74        25.87        75.48       102.12        42.77 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A197 
       43.23        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        16.37 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z3 
      247.04        46.98        27.85        36.26       228.59        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       48.85        40.27         9.70        47.38        23.93       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       11.41        26.56        27.09        27.02        77.82        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        34.03        54.41        80.68         0.20        22.92 
TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       55.59       117.93        84.72        64.44        62.79        39.58 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-W3-AA1O 
      121.91        10.42        50.10        21.37       297.90         4.01 
TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
        9.01        49.51        37.94        14.43        15.98 

$subtype2
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JC 
       66.48        14.93        16.67       133.25        23.77        86.76 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU 
       62.07        42.08        46.32       166.52       103.59        39.75 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GD TCGA-D3-A8GJ 
       55.73        56.35        26.89        18.18        23.61       241.38 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A1JX TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW 
      161.00       117.17         7.10         9.90        48.89        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
      194.83       176.55        23.44        28.60        10.49        15.68 
TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 
       68.25         7.04        56.42        61.28        46.82       102.90 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        67.43       340.14       208.04        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF 
       54.74        79.66        13.91        19.76       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AA 
      103.20       158.63        47.54       248.65       134.40       124.31 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       51.62       172.18       127.20        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19M 
      109.58       152.81         9.17        77.75       268.93        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A3ET 
       44.05       162.08        37.25       148.18        79.99        80.32 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       33.21       174.21       220.80        38.27        34.82       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
       28.08       101.26        74.73        53.16        49.48       174.84 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD 
       19.30         7.23        15.78        39.35        48.89        59.41 
TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       65.88         0.69        69.07       219.16       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-Z2-A8RT 
       61.15        67.63        32.58        12.16        19.73        27.58 
TCGA-Z2-AA3S 
       96.99 

$subtype3
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 
       12.99       112.04       112.57        71.80        28.08        65.49 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
      115.53        66.48        59.57        58.06        46.98        60.23 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
        9.34        45.30       145.12        22.62        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 
      178.32        26.43        29.06       117.21        61.18        53.92 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
      215.44        27.22       133.81       151.27       168.26        63.35 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GO 
       14.47       369.93       195.02        39.29       161.03       126.81 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MH 
       81.21        21.67       129.27        28.83        61.51        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG 
      204.66       216.66       167.90       162.48       122.73        41.59 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D 
      138.81        34.32       201.80        35.44        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A2NH TCGA-ER-A42K 
       13.02       152.35       131.51        43.82        32.05         6.77 
TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 
       15.72        18.77       104.42        48.59       202.65         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZS 
       27.72       357.37        53.52        15.45        32.75       148.80 
TCGA-FS-A4FB TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A 
       26.73         9.90         2.04       139.89        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-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-YD-A89C TCGA-YD-A9TA 
       15.98        98.89        59.77        11.80         6.90        49.18 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO 
       31.59        95.74       168.00        11.87       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A8GB TCGA-D3-A8GM TCGA-D9-A148 
      130.72        24.53       174.84        30.84       107.15       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I0 TCGA-DA-A1I5 
       54.67         3.65        15.39        22.29        20.38       107.34 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       13.87        17.29        24.89        33.73        26.89        68.15 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29X 
       91.56        13.55        64.64        56.84        18.61        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MJ 
       36.82        59.28        44.88        94.82        47.28        96.23 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F 
       53.26        54.51        36.95        31.40        50.76        26.37 
TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FS-A4F4 TCGA-FW-A3TV TCGA-QB-A6FS 
       50.89        31.27        92.98        66.67        13.51         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1R TCGA-WE-A8K1 TCGA-WE-A8ZN 
       18.05         0.33       228.16       111.09        49.05        58.98 
TCGA-WE-AAA0 TCGA-WE-AAA4 
       35.01        22.29 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.69     0.23     0.33 
subtype1 subtype2 subtype3 subtype4 
  297.90   340.14   369.93   228.16 
subtype1 subtype2 subtype3 subtype4 
   42.77    59.41    59.67    46.08 
[1] "0.2 - 297.9 (42.8)" "0.7 - 340.1 (59.4)" "0.2 - 369.9 (59.7)"
[4] "0.3 - 228.2 (46.1)"
D6V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 35             4
  subtype2                 12             1
  subtype3                 15             0
  subtype4                  3             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        18                  46
  subtype2                                        17                  74
  subtype3                                        25                  54
  subtype4                                        12                  42
D6V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              35       12       15        3
  PRIMARY TUMOR                                    4        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       18       17       25       12
  REGIONAL LYMPH NODE                             46       74       54       42
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       2       3        4        7        5         5
  subtype2           2       0      14        6        9        5         5
  subtype3           5       3       9        3        7       10         3
  subtype4           3       2       2        5        4        4         1
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         9         9          7          7         22
  subtype2         4         2        11          3         14         14
  subtype3         2         1        12          5          6         13
  subtype4         4         0         5          0          5         12
          vv
clus       STAGE IV
  subtype1        5
  subtype2        6
  subtype3        5
  subtype4        4
D6V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        2        5        3
  STAGE 0            2        0        3        2
  STAGE I            3       14        9        2
  STAGE IA           4        6        3        5
  STAGE IB           7        9        7        4
  STAGE II           5        5       10        4
  STAGE IIA          5        5        3        1
  STAGE IIB          9        4        2        4
  STAGE IIC          9        2        1        0
  STAGE III          9       11       12        5
  STAGE IIIA         7        3        5        0
  STAGE IIIB         7       14        6        5
  STAGE IIIC        22       14       13       12
  STAGE IV           5        6        5        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    11 16 22 35
  subtype2    25 25 21 15
  subtype3    17 23 22 10
  subtype4    11  8 12  9
D6V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       11       25       17       11
  T2          16       25       23        8
  T3          22       21       22       12
  T4          35       15       10        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 45 17 13 15
  subtype2 49 18 14 10
  subtype3 46 20  7 12
  subtype4 29  9  4 12
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       45       49       46       29
  N1       17       18       20        9
  N2       13       14        7        4
  N3       15       10       12       12
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 90  5
  subtype2 90  6
  subtype3 82  5
  subtype4 52  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90    5
  subtype2   90    6
  subtype3   82    5
  subtype4   52    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       90       90       82       52
  1        5        6        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"
D6V9, binary
          cls
clus        0  1
  subtype1 40 32
  subtype2 41 25
  subtype3 29 16
  subtype4 22 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   32
  subtype2   41   25
  subtype3   29   16
  subtype4   22   16
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        40       41       29       22
  YES       32       25       16       16
[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"
D6V10, binary
          cls
clus        0  1
  subtype1  9 95
  subtype2 18 86
  subtype3 13 80
  subtype4  4 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   95
  subtype2   18   86
  subtype3   13   80
  subtype4    4   53
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         9       18       13        4
  YES       95       86       80       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"
D6V11, continuous
D6V12, binary
          cls
clus        0  1
  subtype1 36 68
  subtype2 40 64
  subtype3 39 55
  subtype4 20 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   68
  subtype2   40   64
  subtype3   39   55
  subtype4   20   37
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       36       40       39       20
  MALE         68       64       55       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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   100
  subtype2     0                         0   101
  subtype3     1                         0    91
  subtype4     2                         1    53
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        1        2
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                          100      101       91       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"
D6V14, binary
          cls
clus         0   1
  subtype1   4  99
  subtype2   0 102
  subtype3   2  89
  subtype4   1  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   99
  subtype2    0  102
  subtype3    2   89
  subtype4    1   55
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        0        2        1
  NOT HISPANIC OR LATINO       99      102       89       55
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 22  9
  subtype2 29 34
  subtype3 29 23
  subtype4 30 52
  subtype5  4  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      31       63       52       82        4 
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       34       23       52        0 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR 
       60.46        19.04        36.30        66.08        59.70        90.21 
TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-DA-A3F2 TCGA-DA-A3F5 
       23.67        62.70        11.34        45.70        25.12       214.59 
TCGA-DA-A3F8 TCGA-EE-A182 TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU 
       14.96         0.00        27.16         7.20        26.14        81.99 
TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G 
       15.25       104.78       227.01       122.73         3.35       151.46 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 
        5.65        10.06       312.07        84.72        34.49        46.92 
TCGA-W3-AA1R 
       79.99 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99        31.89        49.35       133.25        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A8GL TCGA-DA-A1HY 
       15.75        64.83        40.01         9.34        69.53       106.85 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29C 
       31.96        82.85        32.42        24.89       155.90        76.14 
TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       44.28       185.19       102.38       239.11         0.20       189.40 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MU 
        0.76        71.31         5.75        23.77       171.85        53.26 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       67.89        45.90       201.80        14.56        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC 
       53.29        11.47       150.12        59.84       146.63        22.36 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM 
       10.95        55.82        15.48        49.74        32.78        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A26A 
      136.27        35.28        80.68        11.54         9.90         7.59 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       85.05         1.97       120.07        12.69        58.98        48.39 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
        1.94        16.64        15.65 

$subtype3
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JB 
       14.83         8.42       110.93        62.60        25.64       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A3CB TCGA-D3-A8GD TCGA-D9-A6EC TCGA-DA-A1IA 
       86.30         7.27       140.98        23.61        57.90        64.83 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29E 
        3.91        33.24         6.64        13.15        75.55         0.26 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO 
       61.12       346.49        77.98        10.62        18.35       118.32 
TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      103.13        94.19       145.45        25.08       143.93        23.51 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-ER-A199 TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
       51.62        54.51         7.82        99.06        42.48        47.97 
TCGA-ER-A2NE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       16.87       195.98        27.62        35.90       130.95         4.47 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A4U3 TCGA-OD-A75X 
      173.19        55.59         6.05        53.29       120.53       297.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZR TCGA-WE-AAA0 
        8.09       185.13         8.68        26.60 

$subtype4
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 
       15.72        76.41         9.76       107.61       171.58        58.06 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU 
       16.96        13.87       173.85        31.76        42.05       124.08 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
       78.21       179.97        70.62       135.12        36.53        10.78 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1IC 
       15.02        16.90        18.44        48.66       150.61        58.85 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B 
       50.07        45.50        62.37        20.38        67.50        75.22 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN 
       12.99        63.12        47.74        68.65        32.48        31.00 
TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A3AA TCGA-EE-A3AD 
        0.20       209.79        63.25        67.50       124.31         4.41 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
        6.28       111.85       152.81         1.58        47.31        39.81 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3PL 
      120.76        49.71        34.95         4.70       173.29        32.05 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       26.20       171.78         8.35        12.92         7.82        36.33 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-GN-A264 
       23.21         5.29         3.06        30.90        66.67       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O 
       17.06        42.48        43.23        59.41         7.23        18.05 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        0.33       174.12        44.05        92.84         1.15        59.64 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-YG-AA3O TCGA-Z2-AA3S 
       19.00        10.95        28.21        91.23 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-WE-A8ZM 
       43.53        46.98       144.46        62.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.00     0.20     0.26     0.20    43.53 
subtype1 subtype2 subtype3 subtype4 subtype5 
  312.07   239.11   346.49   209.79   144.46 
subtype1 subtype2 subtype3 subtype4 subtype5 
  45.700   45.990   52.455   42.855   54.985 
[1] "0.0 - 312.1 (45.7)"  "0.2 - 239.1 (46.0)"  "0.3 - 346.5 (52.5)" 
[4] "0.2 - 209.8 (42.9)"  "43.5 - 144.5 (55.0)"
D7V2, survival
          sevent
clus2       0  1
  subtype1 26 19
  subtype2 46 52
  subtype3 39 35
  subtype4 42 68
  subtype5  6  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      45       98       74      110        7 
subtype1 subtype2 subtype3 subtype4 subtype5 
      19       52       35       68        1 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE 
       66.48        28.08        31.59        42.08        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-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       29.06         7.10        20.38        28.60       215.44        15.68 
TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 
       10.36        14.70       133.81        56.42        46.82        36.82 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP 
       59.28        94.82        28.83        47.28       216.66       248.65 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A7UA 
      122.73        41.59        34.32        26.37       268.93        38.27 
TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D 
       34.82       357.37        32.75         0.20        84.72        39.58 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-W3-AA1R 
       39.35        48.89       111.09 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99       112.04        71.80       133.25       103.10        65.49 
TCGA-D3-A2JA TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC 
      115.53        12.10        66.48       130.72        46.32        86.93 
TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN 
        9.34        55.73        30.84        26.43        89.13       161.00 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
      117.21       194.83        35.93       107.34        61.18        27.22 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S 
      168.26        63.35        78.97        72.07        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE 
       25.87       195.02       102.90        39.29       340.14       161.03 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
      208.04        13.91        81.21        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
      103.27       204.66        53.26       172.18        36.95        64.08 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
      201.80        51.35       109.58        31.40        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W 
       98.40        12.59       152.35         6.44        61.05       148.18 
TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P 
       43.82        31.27        32.05        80.32        46.98        15.72 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       18.77        48.59       228.59         7.79        48.85        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
      101.26       148.80        53.16        80.68        22.92        13.51 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OG 
        9.90        10.13        32.48        22.13        21.37         0.23 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 
      368.78        63.02       121.08         4.01        24.03        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       58.98        59.77        49.51        12.16        19.73        22.29 
TCGA-YD-A89C TCGA-YD-A9TA 
        6.90        49.18 

$subtype3
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 
       14.93        16.57       112.57        95.74        43.43        23.77 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H 
      168.00        86.76        11.87        62.07       166.52        56.35 
TCGA-D3-A8GD TCGA-D3-A8GS TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1IA 
       23.61       117.17         9.90        25.18        66.25        65.92 
TCGA-DA-A1IB TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 
       23.44        13.87        20.35        68.25         7.04        24.89 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q 
       29.82        26.89       151.27        63.78        18.61        66.74 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO 
      369.93        17.92        86.14        54.74        75.48       126.81 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR 
       44.88       129.27       103.20       167.90        47.54       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JD TCGA-ER-A199 
      162.48        71.21        51.62        54.51        27.35         9.17 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       13.02       131.51        44.05        79.99        20.15        16.37 
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        40.27        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         7.23       139.89 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-OD-A75X TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZR 
      121.91        10.42       297.90        42.08       219.16         9.01 
TCGA-WE-AAA0 TCGA-Z2-AA3V 
       35.01        15.98 

$subtype4
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 
       16.67        90.90        27.65       113.52       171.58        58.06 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GS 
       24.53        13.87       174.84        32.94       125.79        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      125.19        79.59       241.38       107.15       152.75       129.63 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65        18.12        15.39        22.29 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F3 
       18.44        48.89        36.03       176.55        68.09        10.49 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       54.02        17.29        52.01         8.65        94.98        33.73 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
       68.15         4.96        91.56        13.55        85.08        13.97 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
       64.64         2.60        56.84        67.43        48.72       107.38 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ 
       79.66       102.12        42.77       268.73        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      158.63        43.23       124.31        28.77        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
      127.20        53.19       152.81        13.94        50.76        48.89 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3PL 
      162.08        50.89        37.25        23.34       247.04        33.21 
TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF 
       92.98        27.85        36.26       216.92        20.91        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZY 
        9.70        47.38        74.73        11.41        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A264 
       27.02        77.82        66.67        28.73        26.73       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS 
       64.44        62.79        50.10        59.41        65.88         7.23 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 
       18.05         0.33         0.69       228.16        69.07       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-YG-AA3O TCGA-YG-AA3P 
       49.05        61.15        67.63        11.80        37.94        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       27.58        96.99 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I8 TCGA-ER-A42K 
       59.57        46.98       145.12        22.62        53.92         6.77 
TCGA-WE-A8ZM 
       98.89 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.23     7.04     0.33     6.77 
subtype1 subtype2 subtype3 subtype4 subtype5 
  357.37   368.78   369.93   268.73   145.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
  42.080   54.625   53.065   50.825   53.920 
[1] "0.2 - 357.4 (42.1)" "0.2 - 368.8 (54.6)" "7.0 - 369.9 (53.1)"
[4] "0.3 - 268.7 (50.8)" "6.8 - 145.1 (53.9)"
D7V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  5             0
  subtype2                 18             0
  subtype3                 16             4
  subtype4                 22             0
  subtype5                  0             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         9                  32
  subtype2                                        35                  48
  subtype3                                         5                  52
  subtype4                                        17                  71
  subtype5                                         3                   5
D7V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               5       18       16       22
  PRIMARY TUMOR                                    0        0        4        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        9       35        5       17
  REGIONAL LYMPH NODE                             32       48       52       71
                                           clus
vv                                          subtype5
  DISTANT METASTASIS                               0
  PRIMARY TUMOR                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        3
  REGIONAL LYMPH NODE                              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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       0       2        1        2        6         4
  subtype2           3       1       9        2       11        3         5
  subtype3           5       5       9        8        3        5         1
  subtype4           2       1       7        5       11        8         2
  subtype5           1       0       0        0        0        0         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         2         4          2          7          5
  subtype2         5         2        12          6          8         21
  subtype3         2         3         6          2          4         15
  subtype4        10         4        11          4         10         16
  subtype5         0         0         2          0          1          3
          vv
clus       STAGE IV
  subtype1        4
  subtype2        4
  subtype3        1
  subtype4        9
  subtype5        1
D7V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  I OR II NOS        1        3        5        2        1
  STAGE 0            0        1        5        1        0
  STAGE I            2        9        9        7        0
  STAGE IA           1        2        8        5        0
  STAGE IB           2       11        3       11        0
  STAGE II           6        3        5        8        0
  STAGE IIA          4        5        1        2        0
  STAGE IIB          1        5        2       10        0
  STAGE IIC          2        2        3        4        0
  STAGE III          4       12        6       11        2
  STAGE IIIA         2        6        2        4        0
  STAGE IIIB         7        8        4       10        1
  STAGE IIIC         5       21       15       16        3
  STAGE IV           4        4        1        9        1
[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     9  7 12 10
  subtype2     8 31 23 17
  subtype3    20 11 12 13
  subtype4    19 22 25 22
  subtype5     4  1  0  2
D7V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        9        8       20       19        4
  T2           7       31       11       22        1
  T3          12       23       12       25        0
  T4          10       17       13       22        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20  8  9  4
  subtype2 44 24 10 13
  subtype3 41  9  6 12
  subtype4 56 16 13 14
  subtype5  1  3  0  4
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       20       44       41       56        1
  N1        8       24        9       16        3
  N2        9       10        6       13        0
  N3        4       13       12       14        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"
D7V8, binary
          cls
clus        0  1
  subtype1 39  4
  subtype2 90  4
  subtype3 70  1
  subtype4 95 10
  subtype5  7  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    4
  subtype2   90    4
  subtype3   70    1
  subtype4   95   10
  subtype5    7    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       39       90       70       95        7
  1        4        4        1       10        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 12 15
  subtype2 38 22
  subtype3 29 17
  subtype4 46 29
  subtype5  0  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   15
  subtype2   38   22
  subtype3   29   17
  subtype4   46   29
  subtype5    0    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        12       38       29       46        0
  YES       15       22       17       29        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"
D7V10, binary
          cls
clus        0  1
  subtype1  7 39
  subtype2 10 91
  subtype3  7 70
  subtype4 14 97
  subtype5  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   39
  subtype2   10   91
  subtype3    7   70
  subtype4   14   97
  subtype5    4    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7       10        7       14        4
  YES       39       91       70       97        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"
D7V11, continuous
D7V12, binary
          cls
clus        0  1
  subtype1 17 29
  subtype2 32 69
  subtype3 32 45
  subtype4 42 69
  subtype5  5  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   29
  subtype2   32   69
  subtype3   32   45
  subtype4   42   69
  subtype5    5    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17       32       32       42        5
  MALE         29       69       45       69        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 BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    45
  subtype2     1                         0    96
  subtype3     3                         1    73
  subtype4     0                         0   107
  subtype5     0                         0     8
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        3        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                           45       96       73      107        8
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
          cls
clus         0   1
  subtype1   0  46
  subtype2   2  95
  subtype3   0  76
  subtype4   4 105
  subtype5   1   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   46
  subtype2    2   95
  subtype3    0   76
  subtype4    4  105
  subtype5    1    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        0        4        1
  NOT HISPANIC OR LATINO       46       95       76      105        7
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 25 38
  subtype2 49 47
  subtype3 23 25
  subtype4 17  8
subtype1 subtype2 subtype3 subtype4 
      63       96       48       25 
subtype1 subtype2 subtype3 subtype4 
      38       47       25        8 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 
       60.46        14.83         8.42        15.72       133.25        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL 
       45.99       168.00        40.01        16.96        13.87        42.05 
TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA 
       70.62        36.53        16.90        18.44       150.61        64.83 
TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A29B TCGA-EE-A29E 
       58.85        45.50         6.64        62.37        75.22         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GL 
       44.28        63.12        47.74        77.98       239.11        32.48 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MS 
        0.20        71.31         5.75        63.25       145.45       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
       23.51       124.31        51.62         6.28       111.85        45.90 
TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       47.31        39.81        99.06         4.70        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD 
      173.29        32.05       195.98        35.28        66.67        80.68 
TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-QB-A6FS TCGA-RP-A693 
       55.59        17.06       120.53        43.23         7.23         0.33 
TCGA-W3-A824 TCGA-WE-A8ZR TCGA-YG-AA3O 
      174.12         8.68        28.21 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JP 
       12.99        76.41         9.76       107.61       171.58        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       58.06       140.98         9.34        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ 
       31.76        11.34       124.08        78.21        23.61       179.97 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV 
       69.53       135.12        10.78        15.02        57.90        48.66 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       31.96        82.85        32.42         3.91        33.24        50.07 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A2A1 
       20.38        67.50       155.90        76.14        12.99       102.38 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MF 
        0.20       189.40        68.65        31.00         0.76       209.79 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       67.50       227.01        53.26         4.41        54.51        67.89 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19P 
      152.81        14.56         1.58         4.54        59.84       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 
       49.71        34.95       146.63        55.82        15.48        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG 
        5.65       171.78        49.74         8.35        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       36.33        78.61       130.95         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
        3.06        30.90        11.54        53.29       117.93        42.48 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 
       59.41       297.01        18.05        44.05        79.99        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        1.15        59.64        12.69        19.00        58.98        10.95 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S 
       48.39         1.94        26.60        16.64        15.65        91.23 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA 
       31.89       110.93        49.35        62.60        62.86        15.75 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-DA-A1HY 
       86.30         7.27        64.83        46.98        59.70       106.85 
TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GK 
       13.15        75.55        61.12       346.49       185.19        10.62 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
       18.35       118.32       103.13        23.77        94.19       171.85 
TCGA-EE-A2MR TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       25.08       201.80        34.45         7.82        53.29        11.47 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-FS-A1Z4 TCGA-FS-A1ZD 
      150.12        42.48        47.97        22.36        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A26A 
       35.90       136.27       173.19         9.90         6.05         7.59 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM 
       85.05         1.97       120.07         8.09       185.13        62.99 

$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 
       25.12       214.59        14.96        24.89         0.00        27.16 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AB 
        7.20        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       151.46        10.06       312.07        84.72        34.49 
TCGA-GN-A4U8 
       46.92 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.20     1.97     0.00 
subtype1 subtype2 subtype3 subtype4 
  239.11   297.01   346.49   312.07 
subtype1 subtype2 subtype3 subtype4 
   45.50    46.22    51.32    36.30 
[1] "0.2 - 239.1 (45.5)" "0.2 - 297.0 (46.2)" "2.0 - 346.5 (51.3)"
[4] "0.0 - 312.1 (36.3)"
D8V2, survival
          sevent
clus2       0  1
  subtype1 37 53
  subtype2 66 71
  subtype3 35 35
  subtype4 21 16
subtype1 subtype2 subtype3 subtype4 
      90      137       70       37 
subtype1 subtype2 subtype3 subtype4 
      53       71       35       16 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 
       66.48        14.93        16.57        16.67       133.25        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      103.10       168.00        62.07        86.93        24.53        13.87 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A148 
      125.79        18.18        30.84       107.15       129.63       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW 
       54.67         3.65        22.29        18.44         9.90        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EB-A5UL 
      176.55        35.93        65.92        23.44        68.09        17.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E 
       52.01        24.89        94.98        26.89        85.08        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X 
       72.07        64.64        56.84        18.61        25.87        17.92 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS 
       39.29        86.14       340.14        79.66        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       44.88        19.76        96.23       167.90        47.54        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
      162.48        71.21       124.31        51.62        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L 
       36.95        64.08        27.35        50.76        48.89       131.51 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL 
       23.34        20.15        16.37        31.27       247.04        33.21 
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-GN-A267 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-HR-A2OH 
       55.59        64.44        39.58       121.91        50.10        65.88 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-WE-A8ZR TCGA-YG-AA3O TCGA-YG-AA3P 
        7.23         0.33       228.16         9.01        37.94        14.43 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       12.99        90.90        27.65       113.52        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3MO 
       59.57       130.72        58.06        46.32       166.52         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       39.75       174.84        55.73       145.12        32.94        22.62 
TCGA-D3-A51T TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL 
       26.89       125.19        79.59        23.61       241.38        89.13 
TCGA-D3-A8GP TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
      152.75        18.12        15.39        25.18        66.25        48.89 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SG 
      194.83       107.34        61.18        10.49        13.87        68.25 
TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
       54.02         8.65        33.73        68.15         4.96        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
      168.26        13.55        78.97        13.97         2.60        14.47 
TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       61.28       102.90        67.43       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
      107.38       102.12        13.91        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE 
       16.96       158.63       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-A193 
      138.81       172.18        53.19       109.58       152.81        31.40 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
       13.94        77.75        26.37         6.44        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       50.89        37.25       148.18        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
       92.98        15.72        27.85        38.27        36.26       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZF 
       48.59       228.59        20.91         7.79        48.85        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU 
        9.70        47.38       101.26        74.73       133.55        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB 
       49.48        27.09        27.02        77.82        28.73        26.73 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U7 
       22.92        13.51       139.89       117.93        62.79        10.42 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1O 
       21.37        59.41       297.90        18.05         0.69         4.01 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       69.07       111.09       105.04        49.05        61.15        58.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       67.63        59.77        11.80        49.51        12.16        35.01 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.73        22.29         6.90        27.58        96.99 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      112.04       112.57        71.80        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE 
      115.53        86.76        11.87        66.48        46.98        60.23 
TCGA-D3-A51H TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I8 
       56.35        26.43       161.00       117.17       117.21        53.92 
TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29Q 
       20.35         7.04        29.82       151.27        63.35        66.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 
      369.93       195.02        54.74        75.48       126.81        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3JB 
      129.27        61.51       103.20       204.66       134.40       201.80 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
       35.44         9.17        98.40        12.59        13.02       152.35 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A7U9 TCGA-FR-A8YE 
       44.05        79.99        43.82        32.05        18.77       104.42 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 
       28.08        27.72        53.52        40.27       148.80       174.84 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG 
        9.90         7.23        10.13        32.48        22.13         0.23 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
      368.78        63.02       121.08        42.08       219.16        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-YD-A9TA TCGA-Z2-AA3V 
       15.98        98.89        49.18        15.98 

$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        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B 
      215.44        15.68        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        36.82        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       268.93 
TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U4 
       34.82       357.37        32.75         0.20        84.72        39.35 
TCGA-GN-A4U8 
       48.89 

subtype1 subtype2 subtype3 subtype4 
    0.33     0.69     0.23     0.20 
subtype1 subtype2 subtype3 subtype4 
  340.14   297.90   369.93   357.37 
subtype1 subtype2 subtype3 subtype4 
   50.43    50.89    60.87    42.08 
[1] "0.3 - 340.1 (50.4)" "0.7 - 297.9 (50.9)" "0.2 - 369.9 (60.9)"
[4] "0.2 - 357.4 (42.1)"
D8V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 19             2
  subtype2                 23             2
  subtype3                 14             0
  subtype4                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        16                  53
  subtype2                                        27                  90
  subtype3                                        15                  43
  subtype4                                        11                  22
D8V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              19       23       14        5
  PRIMARY TUMOR                                    2        2        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       16       27       15       11
  REGIONAL LYMPH NODE                             53       90       43       22
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       4       5        4        8        6         3
  subtype2           8       0      11        8       14        7         5
  subtype3           2       3      10        3        4        5         1
  subtype4           1       0       1        1        1        4         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         5         4        10          5          7         16
  subtype2        10         4        14          5          9         27
  subtype3         2         2         8          3          5         13
  subtype4         1         1         3          1          9          4
          vv
clus       STAGE IV
  subtype1        4
  subtype2       10
  subtype3        1
  subtype4        4
D8V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        8        2        1
  STAGE 0            4        0        3        0
  STAGE I            5       11       10        1
  STAGE IA           4        8        3        1
  STAGE IB           8       14        4        1
  STAGE II           6        7        5        4
  STAGE IIA          3        5        1        3
  STAGE IIB          5       10        2        1
  STAGE IIC          4        4        2        1
  STAGE III         10       14        8        3
  STAGE IIIA         5        5        3        1
  STAGE IIIB         7        9        5        9
  STAGE IIIC        16       27       13        4
  STAGE IV           4       10        1        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    15 17 24 18
  subtype2    21 37 25 27
  subtype3    16 14 12 11
  subtype4     8  4 11  8
D8V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       15       21       16        8
  T2          17       37       14        4
  T3          24       25       12       11
  T4          18       27       11        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 39 18 12 10
  subtype2 73 19 15 22
  subtype3 36 15  3 11
  subtype4 14  8  8  4
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       39       73       36       14
  N1       18       19       15        8
  N2       12       15        3        8
  N3       10       22       11        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus         0   1
  subtype1  79   5
  subtype2 125  10
  subtype3  65   1
  subtype4  32   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79    5
  subtype2  125   10
  subtype3   65    1
  subtype4   32    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       79      125       65       32
  1        5       10        1        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"
D8V9, binary
          cls
clus        0  1
  subtype1 40 25
  subtype2 56 31
  subtype3 19 16
  subtype4 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   25
  subtype2   56   31
  subtype3   19   16
  subtype4   10   13
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        40       56       19       10
  YES       25       31       16       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"
D8V10, binary
          cls
clus         0   1
  subtype1   6  84
  subtype2  19 123
  subtype3  11  61
  subtype4   6  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   84
  subtype2   19  123
  subtype3   11   61
  subtype4    6   32
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       19       11        6
  YES       84      123       61       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"
D8V11, continuous
D8V12, binary
          cls
clus        0  1
  subtype1 30 60
  subtype2 58 85
  subtype3 28 44
  subtype4 12 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   60
  subtype2   58   85
  subtype3   28   44
  subtype4   12   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30       58       28       12
  MALE         60       85       44       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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    85
  subtype2     1                         0   139
  subtype3     1                         0    69
  subtype4     2                         0    36
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        2
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                           85      139       69       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   2  86
  subtype2   4 139
  subtype3   1  67
  subtype4   0  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   86
  subtype2    4  139
  subtype3    1   67
  subtype4    0   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        1        0
  NOT HISPANIC OR LATINO       86      139       67       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 33 24
  subtype2 32 38
  subtype3 41 54
subtype1 subtype2 subtype3 
      57       70       95 
subtype1 subtype2 subtype3 
      24       38       54 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JP 
       60.46        14.83       168.00        86.30         7.27        43.53 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A8GD TCGA-D9-A3Z1 
       46.98       140.98        16.96        90.21        23.61        15.02 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F8 
       16.90        48.66        31.96       150.61        58.85        14.96 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK 
        6.64        13.15        62.37        77.98        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MJ 
       32.48       118.32        81.99        15.25         5.75        63.25 
TCGA-EE-A2MK TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
       67.50        25.08        23.51       124.31        54.51         6.28 
TCGA-EE-A3J4 TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
      111.85         1.58       151.46        99.06        49.71        34.95 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZQ 
       47.97         4.70        10.95         5.65        27.62       130.95 
TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1W TCGA-WE-A8K1 
       35.28        55.59        59.41        18.05       185.13         1.15 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       26.60        15.65        28.21 

$subtype2
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-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 
       62.86        15.75        36.30        64.83        66.08        58.06 
TCGA-D3-A3MO TCGA-D3-A51R TCGA-D3-A5GN TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.34        62.70        45.70       106.85        82.85        32.42 
TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29C 
      214.59        45.50        24.89         0.00       155.90        76.14 
TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       44.28       185.19       102.38       239.11         0.20       189.40 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MU 
        0.76        71.31        23.77        94.19       171.85        53.26 
TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
      122.73        67.89       201.80        14.56        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC 
       53.29        11.47       150.12        59.84       146.63        22.36 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       55.82        15.48        49.74       312.07        32.78        35.90 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT 
       12.92        78.61       136.27       173.19        11.54         9.90 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 
      117.93        84.72         7.59        85.05         1.97       120.07 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
       12.69        58.98         1.94        16.64 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
        8.42        15.72       110.93        76.41        62.60        25.64 
TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
        9.76       107.61       171.58        40.01        59.70        13.87 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU 
      173.85       144.46        31.76        11.34        42.05       124.08 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 
      179.97        69.53        70.62       135.12        36.53        10.78 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EE-A181 
       18.44        57.90        64.83         3.91        50.07        20.38 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       67.50        75.55        75.22        12.99         0.26        63.12 
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         7.20        26.14 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2ML 
       18.35        31.00         0.20       103.13       209.79       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J7 
      145.45       227.01       143.93        51.62         4.41        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19P 
        3.35       152.81        47.31         7.82        39.81       120.76 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1YW 
       16.87       173.29        32.05        26.20        10.06       171.78 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZJ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      195.98         8.35        36.33         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
        3.06        66.67        80.68        53.29        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A693 
      120.53        34.49        46.92        43.23       297.01         0.33 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 
      174.12        44.05        79.99         8.09        92.84        59.64 
TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-Z2-AA3S 
       62.99        19.00         8.68        48.39        91.23 

subtype1 subtype2 subtype3 
    1.15     0.00     0.20 
subtype1 subtype2 subtype3 
  185.13   312.07   346.49 
subtype1 subtype2 subtype3 
  35.280   53.275   47.310 
[1] "1.1 - 185.1 (35.3)" "0.0 - 312.1 (53.3)" "0.2 - 346.5 (47.3)"
D9V2, survival
          sevent
clus2       0  1
  subtype1 48 38
  subtype2 47 55
  subtype3 55 77
subtype1 subtype2 subtype3 
      86      102      132 
subtype1 subtype2 subtype3 
      38       55       77 
$subtype1
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-A2JF TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       62.07        59.57        46.98        46.32       166.52        24.53 
TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GS TCGA-D9-A148 
      103.59        22.62        30.84        23.61       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       54.67         3.65        15.39        22.29        48.89        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F8 
      194.83       176.55        35.93        23.44        68.09        15.68 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20F 
        7.04        24.89        29.82        94.98        26.89        91.56 
TCGA-EE-A20I TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK 
       13.55        18.61        25.87        86.14       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       79.66       126.81        44.88        94.82        28.83        19.76 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       16.96        96.23       158.63        43.23       134.40        71.21 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      124.31        54.51        13.81       127.20        36.95        53.19 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19Q 
       27.35       109.58        13.94       268.93       131.51        50.89 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A7UA 
       37.25        79.99        23.34        31.27        32.05        38.27 
TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FW-A3R5 TCGA-FW-A3TU 
      104.42        28.08       133.55        53.16        22.92        55.59 
TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.41        18.05       219.16        49.05        35.01        22.29 
TCGA-YG-AA3O TCGA-Z2-AA3V 
       37.94        15.98 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       12.99       112.04        71.80       133.25        28.08       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       65.49       115.53        42.08        12.10        66.48        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
      130.72        58.06         9.34        45.30        55.73        56.35 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-DA-A1HY 
       63.81       135.75        26.43       161.00        29.06       117.21 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 
      107.34        61.18       215.44        52.01        27.22        14.70 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29S 
      133.81       168.26        63.35        78.97        72.07        61.28 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82       102.90       340.14       161.03       208.04 
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-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       31.40        35.44        77.75        98.40        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET 
      152.35         6.44        61.05       148.18        43.82        80.32 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       46.98        15.72        18.77        48.59       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.85       357.37        53.52        40.27        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT 
      101.26        11.41       148.80       174.84        13.51         9.90 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG 
      117.93        84.72        10.13        32.48        22.13         0.23 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 
      368.78        63.02       121.08         4.01        24.03        15.98 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA 
       58.98        59.77        12.16        19.73         6.90        49.18 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.57        16.67       112.57        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CE 
       43.43        27.65       113.52       171.58        86.93        60.23 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL 
       13.87       174.84       145.12        32.94        26.89       125.79 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       18.18       125.19       241.38        89.13       107.15       152.75 
TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
      129.63         7.10        18.12        18.44         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       66.25        53.92        65.92        10.49        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 
       20.35        54.02        17.29         8.65        33.73        68.15 
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-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
        2.60        56.84        56.42        66.74        14.47       369.93 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM 
       36.82        39.29        59.28        67.43        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2ML 
      102.12        42.77       129.27        47.28       268.73       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD 
      167.90        47.54       248.65       162.48        51.62        28.77 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 
       41.59       138.81        64.08        34.32       152.81        50.76 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A2NF 
        9.17        48.89        26.37       162.08        20.15        16.37 
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-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      216.92       202.65        20.91        27.72        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       74.73        26.56        49.48        27.09        27.02        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A267 
       28.73        26.73        80.68         0.20       139.89        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        39.58       121.91        39.35        10.42        48.89 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       50.10        21.37       297.90         0.33         0.69       228.16 
TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM 
       69.07       111.09        42.08       105.04        61.15        98.89 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       67.63         9.01        49.51        14.43        27.58        96.99 

subtype1 subtype2 subtype3 
    3.65     0.23     0.20 
subtype1 subtype2 subtype3 
  268.93   368.78   369.93 
subtype1 subtype2 subtype3 
  46.650   60.410   49.805 
[1] "3.6 - 268.9 (46.6)" "0.2 - 368.8 (60.4)" "0.2 - 369.9 (49.8)"
D9V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 11             0
  subtype2                 21             0
  subtype3                 28             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        12                  68
  subtype2                                        31                  52
  subtype3                                        23                  78
D9V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              11       21       28
  PRIMARY TUMOR                                    0        0        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       12       31       23
  REGIONAL LYMPH NODE                             68       52       78
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           7       2       5       10        4        4         3
  subtype2           2       2      11        2       12        6         6
  subtype3           3       3      11        4       10       12         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0        13          1          9         21
  subtype2         5         3         9          6          7         16
  subtype3        12         8        13          6         12         18
          vv
clus       STAGE IV
  subtype1        3
  subtype2        6
  subtype3        8
D9V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        7        2        3
  STAGE 0            2        2        3
  STAGE I            5       11       11
  STAGE IA          10        2        4
  STAGE IB           4       12       10
  STAGE II           4        6       12
  STAGE IIA          3        6        3
  STAGE IIB          0        5       12
  STAGE IIC          0        3        8
  STAGE III         13        9       13
  STAGE IIIA         1        6        6
  STAGE IIIB         9        7       12
  STAGE IIIC        21       16       18
  STAGE IV           3        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    26 13 17 13
  subtype2    14 29 21 17
  subtype3    18 29 31 29
D9V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       26       14       18
  T2          13       29       29
  T3          17       21       31
  T4          13       17       29
[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 14 12 18
  subtype2 53 18 11 11
  subtype3 67 27 11 13
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       40       53       67
  N1       14       18       27
  N2       12       11       11
  N3       18       11       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"
D9V8, binary
          cls
clus         0   1
  subtype1  83   4
  subtype2  89   6
  subtype3 119   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   83    4
  subtype2   89    6
  subtype3  119    8
   clus
vv  subtype1 subtype2 subtype3
  0       83       89      119
  1        4        6        8
[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 38 16
  subtype2 37 23
  subtype3 45 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   16
  subtype2   37   23
  subtype3   45   41
     clus
vv    subtype1 subtype2 subtype3
  NO        38       37       45
  YES       16       23       41
[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, binary
          cls
clus         0   1
  subtype1  13  79
  subtype2  12  92
  subtype3  13 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   79
  subtype2   12   92
  subtype3   13  120
     clus
vv    subtype1 subtype2 subtype3
  NO        13       12       13
  YES       79       92      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"
D9V11, continuous
D9V12, binary
          cls
clus        0  1
  subtype1 38 54
  subtype2 34 70
  subtype3 48 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   54
  subtype2   34   70
  subtype3   48   85
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       34       48
  MALE         54       70       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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    89
  subtype2     1                         0    99
  subtype3     3                         0   128
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           89       99      128
[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  89
  subtype2   2  98
  subtype3   3 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   89
  subtype2    2   98
  subtype3    3  129
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       89       98      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 55 60
  subtype2 38 49
  subtype3 13  7
subtype1 subtype2 subtype3 
     115       87       20 
subtype1 subtype2 subtype3 
      60       49        7 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       60.46        14.83         8.42        15.72       133.25        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JG 
       62.60        25.64       168.00         7.27         9.76       107.61 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
      171.58        43.53       140.98        16.96        13.87       173.85 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ 
       31.76        11.34        42.05       124.08        23.61       179.97 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 
       69.53        70.62       135.12        36.53        10.78        15.02 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 
       16.90        18.44        57.90        48.66        31.96       150.61 
TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       64.83        14.96         3.91        50.07        45.50         6.64 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29D 
       13.15        62.37        20.38        67.50        75.22        12.99 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GL 
        0.26        63.12        47.74        77.98        68.65        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF 
       18.35        31.00         0.20       103.13         5.75       209.79 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        67.50       145.45       227.01       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31        51.62         4.41        54.51         6.28       111.85 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S 
      152.81         1.58        47.31         7.82        39.81        34.95 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7UA 
       16.87        10.95       173.29        32.05        26.20         5.65 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      171.78       195.98         8.35        35.90        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       35.28         4.47        23.21         5.29         3.06        66.67 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-OD-A75X 
       55.59        53.29        17.06        42.48        43.23       297.01 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
       18.05         0.33       174.12        44.05        79.99       185.13 
TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O 
       92.84        19.00         8.68        48.39        26.60        28.21 
TCGA-Z2-AA3S 
       91.23 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99        31.89       110.93        49.35        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       15.75        86.30        64.83        58.06        46.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51J TCGA-DA-A1HY TCGA-DA-A1I5 
       59.70         9.34        90.21       144.46       106.85        82.85 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H 
       32.42        58.85       214.59        24.89        75.55       155.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       76.14        44.28        61.12       346.49       185.19       102.38 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GP 
      239.11         0.20       189.40        10.62       118.32         0.76 
TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MU 
       71.31        23.77        94.19       171.85        25.08        53.26 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       67.89        45.90       201.80        14.56        34.45         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       53.29        11.47       150.12        99.06        59.84       120.76 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ET 
       49.71       146.63        47.97        22.36         4.70        55.82 
TCGA-ER-A3EV TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM 
       15.48        49.74        27.62        32.78        12.92        78.61 
TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 
      136.27       173.19        80.68        11.54         9.90       117.93 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 
        7.59       120.53        59.41        85.05         1.97       120.07 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ 
        8.09         1.15        59.64        62.99        12.69        58.98 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
        1.94        16.64        15.65 

$subtype3
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         7.20        26.14        81.99        15.25       104.78 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-GN-A265 
      122.73         3.35       151.46        10.06       312.07        84.72 
TCGA-GN-A4U4 TCGA-GN-A4U8 
       34.49        46.92 

subtype1 subtype2 subtype3 
     0.2      0.2      0.0 
subtype1 subtype2 subtype3 
  297.01   346.49   312.07 
subtype1 subtype2 subtype3 
   42.48    58.06    41.00 
[1] "0.2 - 297.0 (42.5)" "0.2 - 346.5 (58.1)" "0.0 - 312.1 (41.0)"
D10V2, survival
          sevent
clus2       0  1
  subtype1 75 85
  subtype2 59 71
  subtype3 16 14
subtype1 subtype2 subtype3 
     160      130       30 
subtype1 subtype2 subtype3 
      85       71       14 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       66.48        14.93        16.57        16.67       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JE TCGA-D3-A2JF 
       95.74        43.43       168.00        11.87        27.65        62.07 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF 
      113.52        12.10       171.58        59.57       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       13.87       174.84        32.94        26.89       125.79        18.18 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
      125.19        23.61       241.38        89.13       107.15       152.75 
TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       151.53        54.67         3.65        18.12        15.39 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       22.29        18.44         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F3 
       36.03       194.83       176.55        65.92        23.44        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        13.87        20.35        54.02        17.29        52.01 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       24.89        29.82         8.65        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       68.15         4.96        91.56        85.08        13.97        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GC 
       64.64         2.60        56.84        18.61        86.14        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       48.72       107.38        79.66        75.48       102.12        42.77 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH 
       44.88       129.27        19.76        47.28       268.73        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21       124.31        51.62        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       13.81       138.81       127.20        36.95        53.19        27.35 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F 
      152.81        13.94        50.76         9.17        48.89        26.37 
TCGA-ER-A19J TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
        6.44        37.25        20.15        16.37        31.27       247.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
       33.21        92.98        27.85        38.27        36.26       216.92 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      202.65        20.91        40.27        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 
       66.67        28.73        26.73        55.59       139.89        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O 
       62.79        39.58        10.42        50.10       297.90        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W 
        0.33         0.69       228.16        69.07       111.09       219.16 
TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O 
      105.04        67.63         9.01        49.51        35.01        37.94 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        27.58        96.99        15.98 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99       112.04       112.57        71.80       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       23.77       115.53        86.76        66.48       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        86.93        60.23         9.34       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GE 
       55.73        56.35       145.12        22.62        30.84        26.43 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      161.00       117.17       117.21        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5VV TCGA-EE-A17Y TCGA-EE-A20C 
       53.92        68.09       215.44         7.04        27.22       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29Q 
      168.26        13.55        63.35        78.97        72.07        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 
       14.47        61.28       369.93        25.87       195.02       102.90 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GO 
       39.29       340.14       161.03       208.04        54.74       126.81 
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-A2MR TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      204.66       134.40        53.26       172.18        64.08       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       109.58        31.40        35.44        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       12.59        13.02       152.35       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH 
       50.89       148.18        79.99        43.82        23.34        32.05 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1YX 
       80.32        46.98        15.72        18.77       104.42        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
      228.59        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FS-A4FD 
       15.45       101.26        11.41       148.80       174.84        80.68 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
       22.92        13.51         9.90       117.93        10.13        32.48 
TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG TCGA-LH-A9QB 
      121.91        22.13        21.37        59.41         0.23       368.78 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 
       63.02       121.08         4.01        42.08        24.03        49.05 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y 
       61.15        15.98        98.89        58.98        59.77        12.16 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C TCGA-YD-A9TA 
       19.73        22.29         6.90        49.18 

$subtype3
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        36.82        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC 
      216.66       122.73        41.59        34.32       268.93        34.82 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 
      357.37        32.75         0.20        84.72        39.35        48.89 

subtype1 subtype2 subtype3 
    0.33     0.23     0.20 
subtype1 subtype2 subtype3 
  297.90   369.93   357.37 
subtype1 subtype2 subtype3 
  48.805   60.640   43.690 
[1] "0.3 - 297.9 (48.8)" "0.2 - 369.9 (60.6)" "0.2 - 357.4 (43.7)"
D10V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 32             4
  subtype2                 23             0
  subtype3                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        17                 109
  subtype2                                        43                  70
  subtype3                                         6                  19
D10V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              32       23        5
  PRIMARY TUMOR                                    4        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       17       43        6
  REGIONAL LYMPH NODE                            109       70       19
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           5       4      11       11       13       12         5
  subtype2           6       3      15        4       12        6         4
  subtype3           1       0       1        1        1        4         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        10         7        18          6         13         27
  subtype2         6         3        15          6         11         25
  subtype3         1         1         2          1          4          3
          vv
clus       STAGE IV
  subtype1        8
  subtype2        6
  subtype3        3
D10V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        5        6        1
  STAGE 0            4        3        0
  STAGE I           11       15        1
  STAGE IA          11        4        1
  STAGE IB          13       12        1
  STAGE II          12        6        4
  STAGE IIA          5        4        3
  STAGE IIB         10        6        1
  STAGE IIC          7        3        1
  STAGE III         18       15        2
  STAGE IIIA         6        6        1
  STAGE IIIB        13       11        4
  STAGE IIIC        27       25        3
  STAGE IV           8        6        3
[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    31 32 34 34
  subtype2    21 36 27 19
  subtype3     6  3  8  6
D10V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       31       21        6
  T2          32       36        3
  T3          34       27        8
  T4          34       19        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 81 28 16 21
  subtype2 65 27 12 19
  subtype3 14  4  6  2
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       81       65       14
  N1       28       27        4
  N2       16       12        6
  N3       21       19        2
[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"
D10V8, binary
          cls
clus         0   1
  subtype1 145   9
  subtype2 121   6
  subtype3  25   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  145    9
  subtype2  121    6
  subtype3   25    3
   clus
vv  subtype1 subtype2 subtype3
  0      145      121       25
  1        9        6        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1 65 41
  subtype2 47 29
  subtype3  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65   41
  subtype2   47   29
  subtype3    8   10
     clus
vv    subtype1 subtype2 subtype3
  NO        65       47        8
  YES       41       29       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"
D10V10, binary
          cls
clus         0   1
  subtype1  18 145
  subtype2  15 121
  subtype3   5  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18  145
  subtype2   15  121
  subtype3    5   25
     clus
vv    subtype1 subtype2 subtype3
  NO        18       15        5
  YES      145      121       25
[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"
D10V11, continuous
D10V12, binary
          cls
clus         0   1
  subtype1  59 104
  subtype2  49  87
  subtype3  12  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59  104
  subtype2   49   87
  subtype3   12   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       59       49       12
  MALE        104       87       18
[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     3                         1   156
  subtype2     1                         0   131
  subtype3     1                         0    29
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        1        1
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                          156      131       29
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   4 157
  subtype2   3 129
  subtype3   0  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  157
  subtype2    3  129
  subtype3    0   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        0
  NOT HISPANIC OR LATINO      157      129       30
[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"
