[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/19775519/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/20140641/SKCM-TM.mergedcluster.txt"

nPatients in clinical file=368, in cluster file=368, common to both=368
[1]  10 368
[1] "CN_CNMF"
[1] 3
  1   2   3 
101 139 126 
  1   2   3 
101 139 126 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
129 144  94 
  1   2   3 
129 144  94 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
50 51 42 26 
 1  2  3  4 
50 51 42 26 
[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 
138 104 125 
  1   2   3 
138 104 125 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
108 105  96  58 
  1   2   3   4 
108 105  96  58 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
 74  94 119  21  44 
  1   2   3   4   5 
 74  94 119  21  44 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
132  93  89  38 
  1   2   3   4 
132  93  89  38 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 94 108 136 
  1   2   3 
 94 108 136 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
162  70  76  30 
  1   2   3   4 
162  70  76  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] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 368 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=189,	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=212,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=288,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=110,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 368 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=68, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 41 73 79 71 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   64    73    79    71 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 41 73 79 71 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   64    73    79    71 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
177  66  39  45 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
177  66  39  45 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
177  66  39  45 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
177  66  39  45 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=110, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 28 36
  subtype2 54 41
  subtype3 40 46
subtype1 subtype2 subtype3 
      64       95       86 
subtype1 subtype2 subtype3 
      36       41       46 
$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        76.34        53.65        45.07        64.83        58.85 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
       14.14        12.30        50.07        62.37         0.00        67.50 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GJ 
      155.90        75.22        12.99        47.74        30.02        68.65 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       71.31        81.99       143.93        23.51       122.73        64.04 
TCGA-EE-A3J7 TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A3EV TCGA-ER-A3PL 
       45.90        11.47       151.46        49.71        15.48        32.05 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZT 
       10.06       171.78       195.98         7.82        36.33        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U4 
        4.47         3.06        80.68        17.06        42.48        34.49 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA21 
       43.23        85.05         7.23        18.05        79.99        92.84 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.90        48.39        18.31        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-A95X TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       15.02        30.44        52.90        33.24        52.41        18.21 
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       115.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
      239.11        12.95       201.60        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-EE-A3JH 
      145.45        25.08        53.26       124.31         3.35        19.86 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N 
       34.45         1.58        47.31         7.82         4.54        42.48 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A3ES 
      120.76        47.18       146.63        47.97        10.95       173.29 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZS 
       74.47       174.21         5.65        49.74        27.62       136.27 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY 
       23.21        30.90       173.19        13.28        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD 
        9.90         1.91        53.29        96.92        46.92        59.41 
TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W 
        0.20       174.12       120.07        44.05         8.09       185.13 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        1.15        12.69         1.94        31.99        24.99 

$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        69.21        22.85       138.67       150.61        95.51 
TCGA-DA-A3F5 TCGA-DA-A95V TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29E 
      225.11        72.10         3.91        24.89        20.38         0.26 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB 
       63.12        27.16       346.49       185.19        77.98        26.14 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       18.35        31.00       118.32         0.76       103.13        15.25 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      209.79        89.26       227.01         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19B 
       67.89       111.85       201.80       152.81        14.56        53.29 
TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND 
       39.81       150.12        99.06        59.84        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       16.87        68.52       209.23        26.20         8.35       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZY 
       32.78        42.08        12.92        78.61       130.95         5.29 
TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 
       66.67        55.59         6.05       117.93         7.59       120.53 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      297.01         0.33         1.97        59.64        65.42        62.43 
TCGA-WE-A8ZT TCGA-Z2-AA3S 
       10.95        91.23 

subtype1 subtype2 subtype3 
    0.00     0.20     0.26 
subtype1 subtype2 subtype3 
  195.98   239.11   346.49 
subtype1 subtype2 subtype3 
   45.80    45.99    58.85 
[1] "0.0 - 196.0 (45.8)" "0.2 - 239.1 (46.0)" "0.3 - 346.5 (58.9)"
D1V2, survival
          sevent
clus2       0  1
  subtype1 38 61
  subtype2 77 59
  subtype3 55 67
subtype1 subtype2 subtype3 
      99      136      122 
subtype1 subtype2 subtype3 
      61       59       67 
$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        76.57 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A95Y 
      207.48        73.84        65.92        68.09        10.49        14.14 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 
       13.02        10.36        54.02        29.29        94.98        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       68.15         4.96       168.26        13.55        63.35        85.08 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       13.97         2.60        56.84        14.47        61.28        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MN 
       59.64        48.72       107.38        81.21        94.82        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG 
       43.23       162.48        71.21       122.73        64.04        41.59 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q 
       64.08        53.19        12.59        26.37       268.93        50.89 
TCGA-ER-A2NF TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
       16.37        46.98        33.21        92.98        15.72        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZG TCGA-FS-A1ZH 
       36.26       216.92       202.65        27.72         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD 
       47.38        23.93        53.16        26.56        27.02        80.68 
TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 
        0.20        64.44        62.79        48.00        39.35        10.42 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       22.13        50.10        21.37       368.78         7.23        18.05 
TCGA-W3-AA1O TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZO TCGA-WE-A8ZY 
        4.01       111.09       105.04        24.03        70.52        49.51 
TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YG-AA3O 
       21.40         6.90        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-D3-A8GV TCGA-D9-A148 TCGA-D9-A149 
      107.15       161.00       117.17       167.70       151.53        54.67 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 
       18.12        15.39         9.90        20.38        40.60        33.93 
TCGA-DA-A3F8 TCGA-DA-A95X TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       15.68        61.81        68.25        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29G 
       29.82        26.89       151.27        91.56        78.97        72.07 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD 
       18.61        66.74        46.82       115.96        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT 
      173.79       220.24        54.74        79.66        42.77        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU 
      204.66        96.23       216.66       167.90       134.40        53.26 
TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      124.31        36.95        34.32        27.35        51.35       134.33 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N 
       35.44        13.94        50.76         9.17        77.75        44.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH 
      162.08        49.48       148.18        79.99        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
      247.04       149.03       174.21        18.77        38.27       104.42 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW 
      228.59        28.08        48.85        74.73       148.80        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
       77.82       174.84        34.03        54.41        22.92        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         2.04        15.78       139.89        96.92 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-A828 
       10.13        48.89        59.41         0.20       228.16       121.08 
TCGA-W3-AA1Q TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y 
       69.07        42.08       219.16        49.05        58.98        12.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       40.41        24.99        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        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
      144.89       176.55        35.93       120.00        53.92       225.96 
TCGA-DA-A95V TCGA-DA-A95W TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A17Z 
       72.10        25.15        13.87        20.35        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T 
       33.73       133.81        63.78        64.64        56.42       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM 
      195.02        17.92        39.29        86.14        59.28        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF 
      102.12       126.81        13.91       129.27        28.83       268.73 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       16.96       180.39       248.65        28.77        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 
      138.81       172.18       127.20       201.80       152.81        31.40 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       98.40        48.89        13.02       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET 
       61.05         8.88        43.82        23.34        20.15        93.01 
TCGA-ER-A42K TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       12.95       220.80        27.85        48.59        20.91         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        53.52        46.45        15.45       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB 
       11.41        27.09        50.14        66.67        28.73        26.73 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-HR-A2OG 
       55.59         7.23       117.93        32.48       121.91         0.23 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-WE-A8K5 
       65.88       297.90         0.33         0.69        63.02        61.15 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YD-A9TA 
       17.95       101.33        63.22        11.80        35.80        49.18 
TCGA-YG-AA3P TCGA-Z2-AA3S 
       14.43        96.99 

subtype1 subtype2 subtype3 
    0.20     0.20     0.23 
subtype1 subtype2 subtype3 
  368.78   340.14   369.93 
subtype1 subtype2 subtype3 
  46.980   55.235   56.005 
[1] "0.2 - 368.8 (47.0)" "0.2 - 340.1 (55.2)" "0.2 - 369.9 (56.0)"
D1V3, continuous
          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           6       3      15        6       10       11         6
  subtype3           6       2       8        6        9       10         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         4         5        12          4         11         19
  subtype2        10         2        12          4          9         23
  subtype3         5         8        16          7         13         13
          vv
clus       STAGE IV
  subtype1        5
  subtype2        6
  subtype3       10
D1V4, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        1        6        6
  STAGE 0            2        3        2
  STAGE I            6       15        8
  STAGE IA           6        6        6
  STAGE IB           9       10        9
  STAGE II           4       11       10
  STAGE IIA          5        6        3
  STAGE IIB          4       10        5
  STAGE IIC          5        2        8
  STAGE III         12       12       16
  STAGE IIIA         4        4        7
  STAGE IIIB        11        9       13
  STAGE IIIC        19       23       13
  STAGE IV           5        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 22
  subtype2    19 26 33 26
  subtype3    25 25 25 22
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       20       19       25
  T2          22       26       25
  T3          20       33       25
  T4          22       26       22
[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 45 16 18 11
  subtype2 70 18 11 22
  subtype3 62 31 10 12
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       45       70       62
  N1       16       18       31
  N2       18       11       10
  N3       11       22       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  90   5
  subtype2 119   7
  subtype3 109  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90    5
  subtype2  119    7
  subtype3  109   10
   clus
vv  subtype1 subtype2 subtype3
  0       90      119      109
  1        5        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"
D1V8, binary
          cls
clus        0  1
  subtype1 40 29
  subtype2 52 31
  subtype3 42 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   29
  subtype2   52   31
  subtype3   42   30
     clus
vv    subtype1 subtype2 subtype3
  NO        40       52       42
  YES       29       31       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"
D1V9, binary
          cls
clus         0   1
  subtype1  14  87
  subtype2  17 122
  subtype3  16 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   87
  subtype2   17  122
  subtype3   16  110
     clus
vv    subtype1 subtype2 subtype3
  NO        14       17       16
  YES       87      122      110
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, binary
          cls
clus        0  1
  subtype1 40 61
  subtype2 45 94
  subtype3 52 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   61
  subtype2   45   94
  subtype3   52   74
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       45       52
  MALE         61       94       74
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus         0   1
  subtype1  94   6
  subtype2 114  24
  subtype3 109  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    6
  subtype2  114   24
  subtype3  109   17
     clus
vv    subtype1 subtype2 subtype3
  NO        94      114      109
  YES        6       24       17
[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    97
  subtype2     1                         1   136
  subtype3     3                         0   119
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           97      136      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"
D1V14, binary
          cls
clus         0   1
  subtype1   2  97
  subtype2   2 136
  subtype3   3 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   97
  subtype2    2  136
  subtype3    3  118
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       97      136      118
[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 40 48
  subtype2 59 34
  subtype3 23 42
subtype1 subtype2 subtype3 
      88       93       65 
subtype1 subtype2 subtype3 
      48       34       42 
$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        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       53.65        45.07        58.85        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B 
        3.91        13.15        62.37        67.50        75.55        75.22 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GJ 
       63.12        27.16        61.12        30.02        26.14        68.65 
TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       18.35        81.99       103.13        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
      227.01         4.41        54.51         6.28       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19G TCGA-ER-A2NE 
        3.35       152.81        14.56        47.31       151.46        16.87 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG 
       10.06       171.78        49.74       312.07        12.92         7.82 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A262 
      130.95         3.06        30.90        66.67        13.28        53.29 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A8LK TCGA-OD-A75X 
      117.93        42.48       120.53        34.49        43.23       297.01 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K5 
       18.05       174.12        44.05        79.99        92.84        59.64 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-AA3S 
       10.95        48.39        28.21        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-EB-A5SG TCGA-EB-A5UN 
       16.90        95.51        30.44       225.11        33.24        52.41 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       18.21        20.38        76.14         0.26        44.28        47.74 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      346.49       115.43        77.98       239.11        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MJ 
       10.62        32.48         5.75        23.77        94.19        63.25 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JB TCGA-EE-A3JH 
       25.08        53.26       124.31       122.73       201.80        19.86 
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        47.18       146.63        47.97 
TCGA-ER-A2NG TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1Z4 
       10.95        74.47       174.21       209.23         5.65        27.62 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       35.28        23.21       173.19        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-QB-A6FS 
        6.05        96.92         7.59        46.92        59.41         7.23 
TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN 
        0.33       120.07         8.09       185.13         1.15        12.69 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        1.94        31.99        24.99 

$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-DA-A95V TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A182 
      150.61        64.83        72.10        50.07        24.89         0.00 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29W TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      155.90        12.99       185.19        31.00       118.32         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MS 
        0.20        71.31        15.25       209.79       171.85       143.93 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       23.51        64.04        67.89        53.29        39.81        11.47 
TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       99.06        22.36         4.70       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       32.05        26.20       195.98         8.35        32.78        42.08 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD 
       36.33        78.61       136.27         4.47         5.29        80.68 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A825 
       55.59         1.91        17.06        85.05         0.20         1.97 
TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-AAA3 
       65.42        21.90        62.43         8.68        18.31 

subtype1 subtype2 subtype3 
    3.06     0.26     0.00 
subtype1 subtype2 subtype3 
  312.07   346.49   209.79 
subtype1 subtype2 subtype3 
  56.285   44.280   36.330 
[1] "3.1 - 312.1 (56.3)" "0.3 - 346.5 (44.3)" "0.0 - 209.8 (36.3)"
D2V2, survival
          sevent
clus2       0  1
  subtype1 50 74
  subtype2 87 54
  subtype3 33 60
subtype1 subtype2 subtype3 
     124      141       93 
subtype1 subtype2 subtype3 
      74       54       60 
$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-D3-A8GV TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC 
      129.63       167.70         7.10        18.12        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 
       22.95        76.57       144.89       207.48        73.84        53.92 
TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q 
       68.09        25.15        61.81        14.14        13.02        13.87 
TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       20.35        29.82        94.98        68.15         4.96       151.27 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P 
       13.55        63.35        85.08        64.64         2.60        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC 
       66.74        61.28        17.92        59.64        59.28        67.43 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML 
      107.38        75.48        94.82       129.27       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AD TCGA-EE-A3AE 
      167.90        47.54       248.65        43.23        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        41.59       138.81       127.20        64.08        34.32 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
      152.81        31.40        50.76        26.37       268.93         6.44 
TCGA-ER-A2NE TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY 
       20.15        92.98        34.82        36.26       216.92       228.59 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
       27.72       357.37        15.45         9.70       133.55        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       77.82        50.14        66.67        28.73        34.03        54.41 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
       22.92       139.89       117.93        62.79       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       10.42        50.10       297.90        18.05         0.69       228.16 
TCGA-W3-AA1O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
        4.01        69.07       111.09       105.04        24.03        61.15 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-AA3S 
       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       120.00        40.60        33.93       225.96        15.68 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 
       68.25        29.29        58.92         7.04        36.46        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       115.96        86.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      340.14       173.79       220.24        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       134.33 
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        49.48       148.18        79.99 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
       31.27        32.05       149.03       174.21       220.80        18.77 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A1ZT 
       38.27       104.42        28.08        48.85        32.75        53.16 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.48       174.84        13.51        19.30         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD 
       15.78        96.92        10.13        32.48        48.89        59.41 
TCGA-HR-A2OG TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1V 
        0.23        65.88         7.23         0.33       121.08        42.08 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
      219.16        49.05        58.98        35.80        12.16        40.41 
TCGA-WE-AAA4 TCGA-YD-A9TA TCGA-Z2-AA3V 
       24.99        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-DA-A95V 
       29.06        18.44       176.55        65.92        10.49        72.10 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20B 
       10.36        54.02        27.22         8.65        14.70       133.81 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GN 
      168.26        13.97        14.47       195.02        39.29       102.12 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF 
      126.81        13.91        42.77        81.21        28.83       268.73 
TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA 
      204.66       162.48        71.21        64.04       172.18        53.19 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19T 
       98.40        48.89        12.59        13.02       131.51         8.88 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       43.82        23.34        16.37       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 
       33.21        12.95        15.72        27.85        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.91         7.79        53.52        46.45        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
      101.26        74.73        11.41       148.80        26.56        27.09 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 
       26.73        80.68         0.20        55.59         2.04        64.44 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-RP-A690 TCGA-W3-A825 
       48.00        22.13        21.37       368.78         0.20        63.02 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZR TCGA-WE-AAA3 
       17.95       101.33        70.52        63.22         9.01        21.40 
TCGA-YD-A89C TCGA-YG-AA3P TCGA-Z2-A8RT 
        6.90        14.43        27.58 

subtype1 subtype2 subtype3 
    0.69     0.23     0.20 
subtype1 subtype2 subtype3 
  357.37   369.93   368.78 
subtype1 subtype2 subtype3 
  61.545   49.480   45.300 
[1] "0.7 - 357.4 (61.5)" "0.2 - 369.9 (49.5)" "0.2 - 368.8 (45.3)"
D2V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           7       3       9        9       11        6         6
  subtype2           5       2      14        7        9        9         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         8        13          8          9         12
  subtype2         3         1        18          5         14         27
  subtype3         7         6         9          2         10         17
          vv
clus       STAGE IV
  subtype1        8
  subtype2        9
  subtype3        4
D2V4, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        7        5        1
  STAGE 0            3        2        2
  STAGE I            9       14        6
  STAGE IA           9        7        2
  STAGE IB          11        9        8
  STAGE II           6        9       10
  STAGE IIA          6        4        4
  STAGE IIB          9        3        7
  STAGE IIC          8        1        6
  STAGE III         13       18        9
  STAGE IIIA         8        5        2
  STAGE IIIB         9       14       10
  STAGE IIIC        12       27       17
  STAGE IV           8        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 24 26 26
  subtype2    33 25 32 21
  subtype3     8 24 20 24
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       23       33        8
  T2          24       25       24
  T3          26       32       20
  T4          26       21       24
[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 70 19 15 11
  subtype2 59 29 15 24
  subtype3 48 18  9 10
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       70       59       48
  N1       19       29       18
  N2       15       15        9
  N3       11       24       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"
D2V7, binary
          cls
clus         0   1
  subtype1 114   8
  subtype2 123  10
  subtype3  82   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    8
  subtype2  123   10
  subtype3   82    4
   clus
vv  subtype1 subtype2 subtype3
  0      114      123       82
  1        8       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"
D2V8, binary
          cls
clus        0  1
  subtype1 54 35
  subtype2 56 28
  subtype3 24 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   35
  subtype2   56   28
  subtype3   24   28
     clus
vv    subtype1 subtype2 subtype3
  NO        54       56       24
  YES       35       28       28
[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  15 114
  subtype2  23 121
  subtype3   9  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15  114
  subtype2   23  121
  subtype3    9   85
     clus
vv    subtype1 subtype2 subtype3
  NO        15       23        9
  YES      114      121       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"
D2V10, continuous
D2V11, binary
          cls
clus        0  1
  subtype1 42 87
  subtype2 54 90
  subtype3 41 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   87
  subtype2   54   90
  subtype3   41   53
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42       54       41
  MALE         87       90       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"
D2V12, binary
          cls
clus         0   1
  subtype1 114  15
  subtype2 121  23
  subtype3  82  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114   15
  subtype2  121   23
  subtype3   82   10
     clus
vv    subtype1 subtype2 subtype3
  NO       114      121       82
  YES       15       23       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   125
  subtype2     1                         1   139
  subtype3     2                         0    89
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          125      139       89
[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   2 122
  subtype2   3 139
  subtype3   2  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  122
  subtype2    3  139
  subtype3    2   91
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        2
  NOT HISPANIC OR LATINO      122      139       91
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 19 15
  subtype2 15 23
  subtype3 12 19
  subtype4  4 14
subtype1 subtype2 subtype3 subtype4 
      34       38       31       18 
subtype1 subtype2 subtype3 subtype4 
      15       23       19       14 
$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        30.44       225.11        76.14         0.26        44.28 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GU 
      346.49       185.19        77.98       201.60        10.62        81.99 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MU 
       23.77       171.85       104.78       227.01        25.08        53.26 
TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG 
       19.86         4.54        11.47        59.84       146.63        10.95 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        9.90        96.92        17.06         7.59 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MO TCGA-EE-A180 
       31.89        19.04        76.41        59.70         9.34        62.37 
TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GL TCGA-EE-A2M6 TCGA-EE-A2MJ 
       75.55        27.16        30.02        32.48       103.13        63.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J3 TCGA-EE-A3J7 
       89.26       145.45       143.93        23.51        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-A1Q5 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3ML TCGA-DA-A1HV 
      110.93        86.30        64.83        43.53        13.87        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
      138.67       150.61        95.51        13.15        20.38         0.00 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GP TCGA-EE-A2GR 
       67.50        75.22        63.12        47.74         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       71.31       124.31       122.73        64.04        54.51         6.28 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19L TCGA-ER-A19N 
       14.56        34.45         1.58        47.31        99.06        42.48 
TCGA-FS-A1ZJ 
       36.33 

$subtype4
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-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q 
        5.75         4.41        39.81       150.12       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3TV 
       47.18         4.70        68.52        78.61       130.95        11.54 

subtype1 subtype2 subtype3 subtype4 
    0.26     4.47     0.00     4.41 
subtype1 subtype2 subtype3 subtype4 
  346.49   312.07   150.61   150.12 
subtype1 subtype2 subtype3 subtype4 
  61.350   46.935   54.510   48.445 
[1] "0.3 - 346.5 (61.4)" "4.5 - 312.1 (46.9)" "0.0 - 150.6 (54.5)"
[4] "4.4 - 150.1 (48.4)"
D3V2, survival
          sevent
clus2       0  1
  subtype1 22 26
  subtype2 20 31
  subtype3 15 25
  subtype4 10 16
subtype1 subtype2 subtype3 subtype4 
      48       51       40       26 
subtype1 subtype2 subtype3 subtype4 
      26       31       25       16 
$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        33.93        10.49 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
      225.96        91.56        78.97        63.78        72.07        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GH 
       61.28       369.93       195.02        46.82        86.14       220.24 
TCGA-EE-A2GK TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML 
       54.74        94.82        21.67        61.51       204.66       216.66 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A 
      248.65       134.40        53.26        27.35       134.33        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH 
       12.59        13.02        61.05       148.18        31.27        32.05 
TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       27.72         9.90        96.92        10.13        64.44        32.48 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MO 
      112.04        28.08        31.59        90.90        60.23         9.34 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 
       54.67         7.10        94.98       151.27        56.42        59.64 
TCGA-EE-A2GC TCGA-EE-A2GL TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK 
       67.43        79.66       129.27        47.28        96.23       180.39 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3J3 
      167.90        47.54       162.48        71.21        41.59       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
       64.08        53.19        51.35         9.17        98.40       268.93 
TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
        6.44        79.99        43.82        20.15        16.37       247.04 
TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
       33.21       216.92       202.65        20.91        28.08       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 TCGA-GN-A262 
       53.52         9.70        53.16        26.56         0.20       139.89 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
      117.93        62.79        48.00 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3ML TCGA-DA-A1HV 
      112.57        86.76        66.48        59.57        13.87        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X 
       36.03       144.89       176.55       120.00        40.60        29.82 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L 
       33.73        14.70        68.15        85.08        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       56.84        18.61        13.91        42.77        81.21        44.88 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A193 
      124.31       122.73        64.04        54.51        13.81        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N 
       35.44        13.94        50.76        26.37       131.51        44.05 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       32.75        47.38        23.93        74.73 

$subtype4
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A148 TCGA-D9-A1JW 
       95.74        43.43        11.87        45.30       151.53         3.65 
TCGA-D9-A3Z1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V 
       15.39        65.92        68.09        15.68         4.96        25.87 
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        49.48        23.34        93.01        92.98       101.26 
TCGA-FS-A1ZQ TCGA-FW-A3TV 
      133.55        13.51 

subtype1 subtype2 subtype3 subtype4 
    9.90     0.20     2.60     3.65 
subtype1 subtype2 subtype3 subtype4 
  369.93   357.37   176.55   162.08 
subtype1 subtype2 subtype3 subtype4 
  64.110   59.640   49.070   48.805 
[1] "9.9 - 369.9 (64.1)" "0.2 - 357.4 (59.6)" "2.6 - 176.6 (49.1)"
[4] "3.6 - 162.1 (48.8)"
D3V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       1       8        3        7        1         2
  subtype2           1       2       5        1        6        2         2
  subtype3           4       0       1        3        3        4         1
  subtype4           1       0       1        1        1        0         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         1         3          3          5          7
  subtype2         2         3         7          0          2          6
  subtype3         2         0         7          1          4          5
  subtype4         1         0         5          1          4          5
          vv
clus       STAGE IV
  subtype1        2
  subtype2        5
  subtype3        2
  subtype4        0
D3V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        1        4        1
  STAGE 0            1        2        0        0
  STAGE I            8        5        1        1
  STAGE IA           3        1        3        1
  STAGE IB           7        6        3        1
  STAGE II           1        2        4        0
  STAGE IIA          2        2        1        0
  STAGE IIB          1        2        2        1
  STAGE IIC          1        3        0        0
  STAGE III          3        7        7        5
  STAGE IIIA         3        0        1        1
  STAGE IIIB         5        2        4        4
  STAGE IIIC         7        6        5        5
  STAGE IV           2        5        2        0
[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    10 13 10  9
  subtype2     7 11  6 13
  subtype3    13  6  7  7
  subtype4     6  7  5  2
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       10        7       13        6
  T2          13       11        6        7
  T3          10        6        7        5
  T4           9       13        7        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 27  7  6  6
  subtype2 32  6  4  5
  subtype3 21  6  9  3
  subtype4  7  6  7  4
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       27       32       21        7
  N1        7        6        6        6
  N2        6        4        9        7
  N3        6        5        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"
D3V7, binary
          cls
clus        0  1
  subtype1 45  2
  subtype2 42  5
  subtype3 38  2
  subtype4 24  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    2
  subtype2   42    5
  subtype3   38    2
  subtype4   24    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       45       42       38       24
  1        2        5        2        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1 23  7
  subtype2 19 15
  subtype3 12 10
  subtype4 11  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    7
  subtype2   19   15
  subtype3   12   10
  subtype4   11    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        23       19       12       11
  YES        7       15       10        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"
D3V9, binary
          cls
clus        0  1
  subtype1  6 44
  subtype2  7 44
  subtype3  9 33
  subtype4  3 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   44
  subtype2    7   44
  subtype3    9   33
  subtype4    3   23
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        7        9        3
  YES       44       44       33       23
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, binary
          cls
clus        0  1
  subtype1 18 32
  subtype2 18 33
  subtype3 17 25
  subtype4 11 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   32
  subtype2   18   33
  subtype3   17   25
  subtype4   11   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18       18       17       11
  MALE         32       33       25       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
          cls
clus        0  1
  subtype1 44  6
  subtype2 45  5
  subtype3 38  4
  subtype4 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    6
  subtype2   45    5
  subtype3   38    4
  subtype4   23    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        44       45       38       23
  YES        6        5        4        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       WHITE
  subtype1    50
  subtype2    51
  subtype3    42
  subtype4    26
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V14, binary
          cls
clus        0
  subtype1 50
  subtype2 51
  subtype3 41
  subtype4 26
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  7 11
  subtype2 23 21
  subtype3  7 18
  subtype4 13 21
subtype1 subtype2 subtype3 subtype4 
      18       44       25       34 
subtype1 subtype2 subtype3 subtype4 
      11       21       18       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        30.44       225.11         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-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 
       53.26        19.86         4.54         9.90        96.92        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        76.34       138.67        75.22        27.16        30.02 
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        89.26 
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        64.04        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-EE-A181 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29H 
       15.02       150.61        20.38        67.50        75.55        63.12 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
       47.74       346.49         0.20         5.75        34.45         1.58 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
      150.12        99.06        59.84       146.63        10.95        68.52 
TCGA-FS-A1ZJ 
       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        95.51        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       201.60        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        47.18 
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 
  225.11   312.07   346.49   227.01 
subtype1 subtype2 subtype3 subtype4 
  27.105   50.630   62.600   60.610 
[1] "0.0 - 225.1 (27.1)" "4.5 - 312.1 (50.6)" "0.2 - 346.5 (62.6)"
[4] "4.4 - 227.0 (60.6)"
D4V2, survival
          sevent
clus2       0  1
  subtype1  8 17
  subtype2 25 32
  subtype3 12 22
  subtype4 22 27
subtype1 subtype2 subtype3 subtype4 
      25       57       34       49 
subtype1 subtype2 subtype3 subtype4 
      17       32       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        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       10.49       225.96        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       134.33        77.75         9.90        96.92 
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        76.57       144.89        53.92        85.08        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       59.64        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       180.39       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        64.04        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        48.00 

$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        40.60        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        93.01 
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       120.00        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       220.24        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        49.48 
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 
  225.96   357.37   369.93   248.65 
subtype1 subtype2 subtype3 subtype4 
  53.260   56.420   61.165   50.890 
[1] "9.9 - 226.0 (53.3)"  "6.4 - 357.4 (56.4)"  "13.9 - 369.9 (61.2)"
[4] "0.2 - 248.7 (50.9)" 
D4V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       3        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          6
  subtype2         4         4        11          0          2          7
  subtype3         0         0         4          2          3          4
  subtype4         2         0         6          1          5          6
          vv
clus       STAGE IV
  subtype1        2
  subtype2        2
  subtype3        1
  subtype4        4
D4V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        2        4        1
  STAGE 0            1        1        1        0
  STAGE I            3        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        4        0        0
  STAGE III          1       11        4        6
  STAGE IIIA         2        0        2        1
  STAGE IIIB         5        2        3        5
  STAGE IIIC         6        7        4        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
D4V5, 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 11  8  4  3
  subtype2 33  5  9  7
  subtype3 18  5  6  3
  subtype4 25  7  7  5
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       11       33       18       25
  N1        8        5        5        7
  N2        4        9        6        7
  N3        3        7        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"
D4V7, 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"
D4V8, 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"
D4V9, 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"
D4V10, continuous
D4V11, 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"
D4V12, binary
          cls
clus        0  1
  subtype1 26  1
  subtype2 47 11
  subtype3 32  3
  subtype4 45  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   47   11
  subtype3   32    3
  subtype4   45    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        26       47       32       45
  YES        1       11        3        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          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 39 56
  subtype2 47 21
  subtype3 36 47
subtype1 subtype2 subtype3 
      95       68       83 
subtype1 subtype2 subtype3 
      56       21       47 
$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-DA-A95V 
       18.44        69.21        22.85        64.83        58.85        72.10 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       14.14        12.30         3.91        50.07        52.41        13.15 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       62.37         0.00        67.50        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR 
        0.26        63.12        47.74        26.14        18.35         0.20 
TCGA-EE-A2GU TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       81.99        23.51        64.04         4.41         6.28       111.85 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A2ND 
      152.81         1.58        47.31        39.81        49.71         4.70 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW 
       16.87        10.95       173.29        15.48        26.20       171.78 
TCGA-FS-A1YY TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       49.74        42.08         7.82        36.33       130.95         4.47 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV 
        3.06        30.90        66.67        13.28        55.59        11.54 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A8LK 
      117.93        17.06        42.48       120.53        34.49        43.23 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R 
        7.23        18.05         0.20       174.12        44.05        79.99 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZR 
       92.84         1.15        59.64        12.69        21.90         8.68 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       48.39        18.31        24.99        28.21        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-EB-A5SG TCGA-EB-A6L9 
       76.34        53.65        95.51        30.44        33.24        18.21 
TCGA-EE-A181 TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GH 
       20.38        27.16       115.43        30.02        77.98       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG 
       68.65        10.62        32.48         5.75       209.79        94.19 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       63.25       104.78        25.08        53.26       124.31        54.51 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N 
       19.86        14.56         7.82         4.54       151.46        42.48 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A42L TCGA-FR-A44A 
      120.76        47.18       146.63        47.97        74.47       174.21 
TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
      209.23         5.65        27.62        35.28        23.21       173.19 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-RP-A693 
       19.30         6.05        96.92        46.92        59.41         0.33 
TCGA-W3-AA1W TCGA-WE-AAA0 
      185.13        31.99 

$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       138.67       150.61        45.07       225.11 
TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29G TCGA-EE-A29Q 
       52.90        24.89        75.55       155.90        44.28        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO 
      346.49       185.19       239.11        12.95        31.00       118.32 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI 
        0.76        71.31       103.13        15.25        23.77       171.85 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3J3 
       89.26       145.45       227.01       143.93       122.73        67.89 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D 
       45.90         3.35       201.80        34.45        53.29        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL 
      150.12        99.06        59.84        22.36        68.52        32.05 
TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       10.06       195.98         8.35       312.07        32.78        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C8 
       78.61       136.27         5.29        80.68         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A26A TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-A828 
       53.29         7.59        85.05       297.01         1.97       120.07 
TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
        8.09        65.42        62.43        10.95         1.94 

subtype1 subtype2 subtype3 
    0.00     0.33     0.76 
subtype1 subtype2 subtype3 
  174.12   209.79   346.49 
subtype1 subtype2 subtype3 
  36.530   50.615   59.700 
[1] "0.0 - 174.1 (36.5)" "0.3 - 209.8 (50.6)" "0.8 - 346.5 (59.7)"
D5V2, survival
          sevent
clus2       0  1
  subtype1 52 83
  subtype2 69 34
  subtype3 49 71
subtype1 subtype2 subtype3 
     135      103      120 
subtype1 subtype2 subtype3 
      83       34       71 
$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        77.56        22.95        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95W 
       20.38        35.93        65.92        68.09        72.10        25.15 
TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       14.14        13.02        13.87        10.36        20.35        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       29.29        58.92        29.82         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
       26.89        68.15         4.96        13.55        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V 
       13.97        63.78        64.64         2.60        56.84        25.87 
TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD 
       17.92        59.28        75.48        42.77        94.82        47.28 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       47.54        43.23        71.21        64.04        28.77        13.81 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19F 
      127.20       152.81        13.94        50.76        48.89        26.37 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       50.89         8.88        23.34        20.15        16.37        31.27 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW 
      247.04        46.98        92.98        27.85        36.26       216.92 
TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      228.59        48.85        46.45         9.70        47.38        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
      133.55        26.56        27.02        77.82        66.67        34.03 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       22.92        55.59        13.51       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-GN-A8LL 
       48.00       121.91        39.35        10.42        50.10        21.37 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O 
        7.23        18.05         0.20         0.69       228.16         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-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       70.52         9.01        49.51        21.40        24.99        37.94 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       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 
       76.57       207.48       120.00        40.60        33.93        15.68 
TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N 
       68.25         7.04        36.46        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       115.96        59.64        86.14 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       220.24        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       134.33        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        49.48 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A729 
      148.18        79.99        32.05       149.03       174.21       220.80 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW 
       18.77        38.27       104.42        28.08        53.16        49.48 
TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 
      174.84        19.30         7.23        15.78        96.92        48.89 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-W3-AA1W TCGA-WE-A8ZX TCGA-WE-AAA0 
       59.41        65.88         0.33       219.16        35.80        40.41 
TCGA-Z2-A8RT 
       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-D3-A8GV TCGA-D9-A1X3 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
      167.70        18.12       144.89       176.55        73.84        53.92 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A95X TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C 
       10.49       225.96        61.81        27.22       133.81       151.27 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
      168.26        63.35        72.07        66.74        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO 
      195.02        39.29       340.14       173.79       102.12       126.81 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        81.21        21.67       129.27        28.83        61.51 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB 
      204.66       180.39       167.90       248.65       162.48       122.73 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       41.59       138.81       172.18        64.08        34.32       201.80 
TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J 
       35.44        98.40        12.59        13.02       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
      131.51        61.05        43.82        93.01        33.21        12.95 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       15.72        34.82        48.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       27.72       357.37        53.52        15.45        32.75       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
       74.73        11.41       148.80        27.09        50.14        28.73 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A3OT TCGA-GF-A6C8 
       26.73        54.41        80.68         0.20         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB 
      139.89        10.13        32.48        22.13         0.23       368.78 
TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 
      297.90        63.02       121.08        42.08        24.03        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YD-A9TA 
      101.33        63.22        11.80        12.16         6.90        49.18 

subtype1 subtype2 subtype3 
    0.20     0.33     0.20 
subtype1 subtype2 subtype3 
  247.04   268.93   369.93 
subtype1 subtype2 subtype3 
   43.23    56.42    60.64 
[1] "0.2 - 247.0 (43.2)" "0.3 - 268.9 (56.4)" "0.2 - 369.9 (60.6)"
D5V3, continuous
          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        7         5
  subtype3           6       3      12        2       11       11         5
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9        10        13          8         13         27
  subtype2         4         2        11          1         11         17
  subtype3         6         3        16          6          9         12
          vv
clus       STAGE IV
  subtype1        7
  subtype2        4
  subtype3       10
D5V4, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        3        4        6
  STAGE 0            3        1        3
  STAGE I            6       11       12
  STAGE IA           7        9        2
  STAGE IB          10        7       11
  STAGE II           7        7       11
  STAGE IIA          4        5        5
  STAGE IIB          9        4        6
  STAGE IIC         10        2        3
  STAGE III         13       11       16
  STAGE IIIA         8        1        6
  STAGE IIIB        13       11        9
  STAGE IIIC        27       17       12
  STAGE IV           7        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 37
  subtype2    25 17 22 17
  subtype3    20 33 27 17
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       25       20
  T2          23       17       33
  T3          29       22       27
  T4          37       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 58 25 17 21
  subtype2 54 18  8 12
  subtype3 65 23 14 12
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       58       54       65
  N1       25       18       23
  N2       17        8       14
  N3       21       12       12
[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"
D5V7, binary
          cls
clus         0   1
  subtype1 121   8
  subtype2  92   4
  subtype3 106  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  121    8
  subtype2   92    4
  subtype3  106   10
   clus
vv  subtype1 subtype2 subtype3
  0      121       92      106
  1        8        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"
D5V8, binary
          cls
clus        0  1
  subtype1 56 42
  subtype2 44 22
  subtype3 34 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56   42
  subtype2   44   22
  subtype3   34   27
     clus
vv    subtype1 subtype2 subtype3
  NO        56       44       34
  YES       42       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"
D5V9, binary
          cls
clus         0   1
  subtype1  14 124
  subtype2  16  88
  subtype3  17 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  124
  subtype2   16   88
  subtype3   17  108
     clus
vv    subtype1 subtype2 subtype3
  NO        14       16       17
  YES      124       88      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"
D5V10, continuous
D5V11, binary
          cls
clus        0  1
  subtype1 46 92
  subtype2 39 65
  subtype3 52 73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   92
  subtype2   39   65
  subtype3   52   73
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       46       39       52
  MALE         92       65       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"
D5V12, binary
          cls
clus         0   1
  subtype1 120  17
  subtype2  85  19
  subtype3 112  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  120   17
  subtype2   85   19
  subtype3  112   12
     clus
vv    subtype1 subtype2 subtype3
  NO       120       85      112
  YES       17       19       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0   131
  subtype2     1                         1   101
  subtype3     1                         0   121
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          131      101      121
[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   4 131
  subtype2   1 102
  subtype3   2 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  131
  subtype2    1  102
  subtype3    2  119
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        2
  NOT HISPANIC OR LATINO      131      102      119
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 22 51
  subtype2 48 25
  subtype3 27 34
  subtype4 25 14
subtype1 subtype2 subtype3 subtype4 
      73       73       61       39 
subtype1 subtype2 subtype3 subtype4 
      51       25       34       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-DA-A95Y TCGA-DA-A95Z 
       69.21        22.85        64.83        58.85        14.14        12.30 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A29B 
       50.07        52.41        13.15        62.37         0.00        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2GM 
       76.14        12.99         0.26        44.28        61.12        18.35 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 
       31.00         0.20        23.51         4.41         6.28        45.90 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3EV 
        1.58        39.81         4.70        16.87       173.29        15.48 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       26.20        49.74         8.35        42.08         7.82        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
      130.95         4.47         5.29         3.06        30.90        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       80.68        55.59       117.93        96.92        17.06        42.48 
TCGA-GN-A4U3 TCGA-GN-A8LK TCGA-OD-A75X TCGA-RP-A690 TCGA-WE-A8ZR TCGA-WE-A8ZY 
      120.53        43.23       297.01         0.20         8.68        48.39 
TCGA-YG-AA3O 
       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-A95X TCGA-EB-A5SG 
       76.34        53.65       150.61        30.44        52.90        33.24 
TCGA-EE-A29P TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
       27.16       115.43        77.98       239.11       201.60        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 
       89.26       227.01        25.08       124.31        64.04        67.89 
TCGA-EE-A3J4 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G 
      111.85        19.86       152.81         7.82         4.54       151.46 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.48       120.76        47.18       146.63        47.97 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC 
       68.52        32.05       174.21       209.23         5.65        10.06 
TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
      171.78        27.62        78.61        35.28        23.21       173.19 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-W3-AA1Q 
       19.30         6.05        34.49        46.92        59.41        44.05 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-AA9Y TCGA-WE-AAA3 
      185.13        92.84        59.64        21.90         1.94        18.31 
TCGA-Z2-AA3S 
       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       138.67 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29T 
       45.07       225.11        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        12.95       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-ER-A42L TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       99.06        22.36        74.47       195.98       312.07        32.78 
TCGA-FS-A1ZF TCGA-FS-A1ZS TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A26A 
       12.92       136.27         9.90         1.91        53.29         7.59 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       85.05         1.97       120.07         8.09        65.42        62.43 
TCGA-WE-A8ZT 
       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-DA-A95V 
      173.85        70.62        15.02        16.90        95.51        72.10 
TCGA-EB-A44Q TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29H TCGA-EE-A29M 
        3.91        18.21        20.38        67.50        63.12        47.74 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE 
       30.02        26.14        81.99        63.25        53.26        54.51 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FS-A4F4 TCGA-FW-A3TV 
       14.56        47.31        49.71        10.95        66.67        11.54 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1R TCGA-WE-A8K1 
        7.23        18.05         0.33       174.12        79.99         1.15 
TCGA-WE-A8ZN TCGA-WE-AAA0 TCGA-WE-AAA4 
       12.69        31.99        24.99 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.76     1.91     0.33 
subtype1 subtype2 subtype3 subtype4 
  297.01   239.11   346.49   174.12 
subtype1 subtype2 subtype3 subtype4 
   36.33    59.41    62.43    47.31 
[1] "0.0 - 297.0 (36.3)" "0.8 - 239.1 (59.4)" "1.9 - 346.5 (62.4)"
[4] "0.3 - 174.1 (47.3)"
D6V2, survival
          sevent
clus2       0  1
  subtype1 30 75
  subtype2 67 37
  subtype3 40 52
  subtype4 33 24
subtype1 subtype2 subtype3 subtype4 
     105      104       92       57 
subtype1 subtype2 subtype3 subtype4 
      75       37       52       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        77.56 
TCGA-D9-A6EG TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95W TCGA-DA-A95Y 
       22.95        35.93        65.92        68.09        25.15        14.14 
TCGA-DA-A95Z TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.02        10.36        20.35        54.02        58.92        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29B TCGA-EE-A29C 
        8.65        94.98        14.70         4.96        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V 
       13.97        63.78        72.07         2.60        66.74        25.87 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AD 
       75.48       102.12        42.77        43.23        71.21        28.77 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19T 
       13.81        64.08        13.94        48.89         6.44         8.88 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 
       23.34        20.15        16.37       247.04        46.98        27.85 
TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       36.26       228.59        20.91        48.85        46.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38        23.93       133.55        11.41        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       27.02        77.82        50.14        28.73        34.03        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       80.68         0.20        22.92        55.59       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A8LK 
       64.44        62.79        48.00       121.91        10.42        50.10 
TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A690 TCGA-W3-AA1O TCGA-WE-A8ZR TCGA-WE-A8ZY 
       21.37       297.90         0.20         4.01         9.01        49.51 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
       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        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
      207.48       176.55        40.60        33.93        10.49        15.68 
TCGA-DA-A95X TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 
       61.81        68.25         7.04        56.42        61.28        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI 
      115.96        86.14        67.43       340.14       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M8 TCGA-EE-A2ME 
      107.38        54.74        79.66        13.91        19.76       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      268.73       103.20       180.39        47.54       248.65       134.40 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD 
      124.31        64.04       172.18       127.20        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G 
       51.35       134.33       152.81         9.17        77.75       268.93 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        49.48       148.18        79.99 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC 
       93.01        33.21       174.21       220.80        38.27        34.82 
TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW 
      216.92        28.08       101.26        74.73        53.16        49.48 
TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A4U4 TCGA-GN-A4U8 
      174.84        19.30         7.23        15.78        39.35        48.89 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-AA1Q TCGA-W3-AA1W TCGA-W3-AA21 
       59.41        65.88         0.69        69.07       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 
       24.03        61.15        70.52        35.80        12.16        21.40 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       27.58        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-D3-A8GV TCGA-DA-A1HY TCGA-DA-A1I7 
      178.32        26.43        29.06       167.70       144.89        73.84 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       53.92       225.96        27.22       133.81       151.27       168.26 
TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GE 
       63.35        14.47       369.93       195.02        39.29       173.79 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
      126.81        81.21        21.67       129.27        28.83        61.51 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AB 
       16.96       204.66       216.66       167.90       162.48       122.73 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B 
       41.59       138.81        34.32       201.80        35.44        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A2NH 
       12.59        13.02       152.35       131.51        43.82        32.05 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1YX 
       12.95       149.03        15.72        18.77       104.42        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      202.65         7.79        27.72       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZS TCGA-FS-A4FB TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       32.75       148.80        26.73         9.90         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A825 
       10.13        32.48        22.13         0.23       368.78        63.02 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      121.08        42.08        17.95       101.33        63.22        11.80 
TCGA-YD-A89C TCGA-YD-A9TA 
        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       120.00 
TCGA-DA-A95V TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 
       72.10        13.87        29.29        36.46        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       68.15        91.56        13.55        64.64        56.84        18.61 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2MD 
       17.92        59.64        59.28        44.88        94.82        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A198 
       96.23        53.26        54.51        36.95        31.40        50.76 
TCGA-ER-A19F TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FS-A4F4 TCGA-FW-A3TV 
       26.37        50.89        31.27        92.98        66.67        13.51 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1R TCGA-WE-A8K1 
        7.23        18.05         0.33       228.16       111.09        49.05 
TCGA-WE-A8ZN TCGA-WE-AAA0 TCGA-WE-AAA4 
       58.98        40.41        24.99 

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 
  42.770   61.215   60.870   49.050 
[1] "0.2 - 297.9 (42.8)" "0.7 - 340.1 (61.2)" "0.2 - 369.9 (60.9)"
[4] "0.3 - 228.2 (49.0)"
D6V3, continuous
          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       10        5         5
  subtype3           6       3      10        3        7       11         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        10         9          7          8         22
  subtype2         4         2        13          3         14         12
  subtype3         2         2        13          5          6         10
  subtype4         4         1         5          0          5         12
          vv
clus       STAGE IV
  subtype1        6
  subtype2        6
  subtype3        5
  subtype4        4
D6V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        2        6        3
  STAGE 0            2        0        3        2
  STAGE I            3       14       10        2
  STAGE IA           4        6        3        5
  STAGE IB           7       10        7        4
  STAGE II           5        5       11        4
  STAGE IIA          5        5        3        1
  STAGE IIB          9        4        2        4
  STAGE IIC         10        2        2        1
  STAGE III          9       13       13        5
  STAGE IIIA         7        3        5        0
  STAGE IIIB         8       14        6        5
  STAGE IIIC        22       12       10       12
  STAGE IV           6        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 36
  subtype2    25 26 21 15
  subtype3    17 23 23 10
  subtype4    11  8 12 10
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       11       25       17       11
  T2          16       26       23        8
  T3          22       21       23       12
  T4          36       15       10       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 47 18 13 15
  subtype2 50 18 15  9
  subtype3 50 21  7  9
  subtype4 30  9  4 12
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       47       50       50       30
  N1       18       18       21        9
  N2       13       15        7        4
  N3       15        9        9       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"
D6V7, binary
          cls
clus        0  1
  subtype1 92  6
  subtype2 91  6
  subtype3 84  5
  subtype4 52  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    6
  subtype2   91    6
  subtype3   84    5
  subtype4   52    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       92       91       84       52
  1        6        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"
D6V8, binary
          cls
clus        0  1
  subtype1 40 33
  subtype2 42 25
  subtype3 30 16
  subtype4 22 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   33
  subtype2   42   25
  subtype3   30   16
  subtype4   22   17
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        40       42       30       22
  YES       33       25       16       17
[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 12 96
  subtype2 18 87
  subtype3 13 83
  subtype4  4 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   96
  subtype2   18   87
  subtype3   13   83
  subtype4    4   54
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        12       18       13        4
  YES       96       87       83       54
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, binary
          cls
clus        0  1
  subtype1 37 71
  subtype2 40 65
  subtype3 39 57
  subtype4 21 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   71
  subtype2   40   65
  subtype3   39   57
  subtype4   21   37
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       37       40       39       21
  MALE         71       65       57       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"
D6V12, binary
          cls
clus        0  1
  subtype1 94 12
  subtype2 86 19
  subtype3 86 10
  subtype4 51  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94   12
  subtype2   86   19
  subtype3   86   10
  subtype4   51    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        94       86       86       51
  YES       12       19       10        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   104
  subtype2     0                         0   102
  subtype3     1                         0    93
  subtype4     2                         1    54
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        1        2
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                          104      102       93       54
[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   4 102
  subtype2   0 103
  subtype3   2  91
  subtype4   1  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  102
  subtype2    0  103
  subtype3    2   91
  subtype4    1   56
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        0        2        1
  NOT HISPANIC OR LATINO      102      103       91       56
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 28 20
  subtype2 27 34
  subtype3 36 54
  subtype4  8  4
  subtype5 17 11
subtype1 subtype2 subtype3 subtype4 subtype5 
      48       61       90       12       28 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       34       54        4       11 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2JB TCGA-D3-A2JC 
       60.46        14.83         8.42        62.60       168.00        86.30 
TCGA-D3-A2JD TCGA-D3-A3CB TCGA-D3-A8GD TCGA-DA-A1IA TCGA-DA-A95Z TCGA-EB-A44Q 
        7.27       140.98        23.61        64.83        12.30         3.91 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2A6 
       18.21        13.15        75.55         0.26       346.49        77.98 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MM 
       10.62        18.35       118.32       103.13        94.19       145.45 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-ER-A199 
       25.08       143.93        23.51        64.04        54.51         7.82 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       99.06        42.48        47.97        16.87       195.98        27.62 
TCGA-FS-A1ZE TCGA-FS-A1ZU TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A4U3 
       42.08         4.47       173.19        55.59         6.05       120.53 
TCGA-OD-A75X TCGA-RP-A690 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZR TCGA-WE-AAA0 
      297.01         0.20         8.09       185.13         8.68        31.99 

$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       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29C 
       53.65        95.51        45.07        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       115.43       239.11        12.95       201.60 
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-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET 
       11.47       150.12        59.84       146.63        22.36        68.52 
TCGA-ER-A3EV TCGA-ER-A42L TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       15.48        74.47        49.74        32.78        78.61       136.27 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A26A TCGA-LH-A9QB TCGA-W3-A825 
       80.68        11.54         9.90         7.59        85.05         1.97 
TCGA-W3-A828 TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
      120.07        12.69        62.43        48.39         1.94        18.31 
TCGA-WE-AAA4 
       24.99 

$subtype3
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL 
       15.72        76.41        25.64         9.76       107.61       171.58 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL 
       58.06        16.96        13.87       173.85        31.76        42.05 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      124.08        78.21       179.97        70.62       135.12        36.53 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV 
       10.78        15.02        16.90        18.44        69.21        76.34 
TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95Y TCGA-EB-A5SG TCGA-EB-A5SH 
      150.61        58.85        72.10        14.14        33.24        50.07 
TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29D 
       52.41        62.37        20.38        67.50        75.22        12.99 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
       63.12        47.74        68.65        32.48        31.00         0.20 
TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
      209.79        63.25        89.26       124.31         4.41         6.28 
TCGA-EE-A3J4 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
      111.85        19.86       152.81         1.58        47.31        39.81 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ES 
      120.76        49.71        47.18         4.70        10.95       173.29 
TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG 
       32.05        26.20       171.78         8.35        12.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       36.33       130.95        35.28        23.21         3.06        30.90 
TCGA-FS-A4F4 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD 
       66.67       117.93        17.06        42.48        43.23        59.41 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 
        7.23        18.05         0.33       174.12        44.05        92.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        1.15        59.64        21.90         6.61        28.21        91.23 

$subtype4
TCGA-D3-A1Q5 TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-DA-A95X TCGA-EE-A29Q 
      110.93        43.53        46.98       144.46        52.90        61.12 
TCGA-EE-A2MP TCGA-ER-A19B TCGA-FS-A1ZY TCGA-GN-A262 TCGA-WE-A8ZM TCGA-WE-A8ZT 
      227.01        53.29         5.29        53.29        65.42        10.95 

$subtype5
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       19.04        36.30        66.08        59.70        90.21        23.67 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EE-A182 
       62.70        11.34        45.70        30.44       225.11         0.00 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       27.16        30.02        26.14        81.99        15.25       104.78 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1ZC 
      122.73         3.35       151.46         5.65        10.06       312.07 
TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-W3-AA1R 
       96.92        34.49        46.92        79.99 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.76     0.20     5.29     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
  346.49   239.11   209.79   227.01   312.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  45.225   49.350   42.855   53.290   41.000 
[1] "0.2 - 346.5 (45.2)" "0.8 - 239.1 (49.4)" "0.2 - 209.8 (42.9)"
[4] "5.3 - 227.0 (53.3)" "0.0 - 312.1 (41.0)"
D7V2, survival
          sevent
clus2       0  1
  subtype1 38 33
  subtype2 41 50
  subtype3 50 68
  subtype4 11  9
  subtype5 21 22
subtype1 subtype2 subtype3 subtype4 subtype5 
      71       91      118       20       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       50       68        9       22 
$subtype1
TCGA-3N-A9WC TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J9 TCGA-D3-A2JB 
       66.48        14.93        16.57        95.74        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H TCGA-D3-A8GD 
       86.76        11.87        62.07       166.52        56.35        23.61 
TCGA-D3-A8GS TCGA-D3-A8GV TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1IA TCGA-DA-A1IB 
      117.17       167.70         9.90        25.18        65.92        40.60 
TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.02        13.87        20.35         7.04        36.46        29.82 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29X 
       26.89       151.27        63.78        18.61       369.93        17.92 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2M6 
       86.14        54.74        75.48       126.81        44.88       129.27 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      103.20       167.90        47.54       134.40       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19L 
       64.04        54.51        27.35         9.17        13.02       131.51 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-FR-A8YE TCGA-FS-A1Z0 
       44.05        79.99        20.15        16.37       104.42       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZU TCGA-FS-A4F8 
       28.08        27.72        46.45        23.93        26.56       174.84 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-OD-A75X TCGA-RP-A690 
       55.59         7.23       121.91        10.42       297.90         0.20 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZR TCGA-WE-AAA0 TCGA-Z2-AA3V 
       42.08       219.16         9.01        40.41        15.98 

$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-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3MO 
      115.53        66.48       130.72        46.32        86.93         9.34 
TCGA-D3-A51F TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN TCGA-DA-A1HY 
       55.73        30.84        26.43        89.13       161.00       144.89 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20H 
      207.48        35.93       120.00        73.84        27.22       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       63.35        78.97        72.07        61.28        25.87       195.02 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP 
      115.96        39.29       340.14       173.79       220.24        13.91 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI 
       81.21        21.67        19.76        61.51       103.27       204.66 
TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JE 
       53.26       172.18        36.95        64.08       201.80        51.35 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M 
       31.40        35.44        77.75        12.59       152.35        61.05 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
      148.18        43.82        32.05        93.01        46.98       149.03 
TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       15.72        18.77        48.59       228.59         7.79        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
       53.52       101.26       148.80        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-A8ZN 
      368.78        63.02       121.08         4.01        24.03        58.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YD-A89C 
       63.22        49.51        12.16        21.40        24.99         6.90 
TCGA-YD-A9TA 
       49.18 

$subtype3
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JK 
       16.67        90.90        43.43        27.65       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K 
      171.58        58.06        24.53        13.87       174.84        32.94 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM 
      125.79        18.18       125.19        79.59       241.38       107.15 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      152.75       129.63       151.53        54.67         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       15.39        22.29        18.44        77.56        76.57        36.03 
TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95Y TCGA-EB-A5SG 
      176.55        68.09        72.10        25.15        14.14        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       54.02        29.29        58.92         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-A3J4 
      180.39        43.23       124.31        28.77        13.81       127.20 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
       53.19       134.33       152.81        13.94        50.76        48.89 
TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
        6.44       162.08        50.89        49.48        23.34        31.27 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW 
      247.04        33.21        92.98        27.85        36.26       216.92 
TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       20.91        15.45         9.70        47.38        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.41        53.16        49.48        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD 
       28.73       117.93        64.44        62.79        50.10        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         7.23        18.05         0.33         0.69       228.16 
TCGA-W3-AA1Q TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-XV-AB01 
       69.07       105.04        49.05        61.15        70.52        13.25 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       37.94        14.43        27.58        96.99 

$subtype4
TCGA-D3-A1Q5 TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I8 
      112.57        59.57        46.98       145.12        22.62        53.92 
TCGA-DA-A3F3 TCGA-DA-A95X TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2MP TCGA-EE-A3AH 
       10.49        61.81        66.74        14.47       248.65       138.81 
TCGA-ER-A19B TCGA-ER-A42K TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-GN-A262 TCGA-WE-A8K6 
       98.40        12.95        27.09        26.73       139.89        17.95 
TCGA-WE-A8ZM TCGA-WE-A8ZT 
      101.33        11.80 

$subtype5
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR 
       28.08        31.59        42.08        66.08        60.23       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A8GQ 
       39.75        45.30        63.81        26.89       135.75        29.06 
TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
        7.10        20.38        33.93       225.96        15.68        10.36 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
       14.70       133.81        56.42        46.82        59.64        59.28 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG 
       94.82        28.83        47.28       216.66       122.73        41.59 
TCGA-EE-A3J8 TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1ZC 
       34.32        26.37       268.93        38.27        34.82       357.37 
TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U8 
       32.75         0.20        96.92        48.00        39.35        48.89 
TCGA-W3-AA1R 
      111.09 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.23     0.33    10.49     0.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
  369.93   368.78   268.73   248.65   357.37 
subtype1 subtype2 subtype3 subtype4 subtype5 
  46.450   61.050   53.175   56.745   45.300 
[1] "0.2 - 369.9 (46.5)"  "0.2 - 368.8 (61.0)"  "0.3 - 268.7 (53.2)" 
[4] "10.5 - 248.7 (56.7)" "0.2 - 357.4 (45.3)" 
D7V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           4       5       9        8        3        5         2
  subtype2           3       1       9        2       10        4         5
  subtype3           3       1       7        5       12        8         2
  subtype4           2       0       1        0        1        1         0
  subtype5           1       0       2        1        2        6         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         3         6          1          4         15
  subtype2         5         2        13          6          7         16
  subtype3        10         6        12          5         10         17
  subtype4         2         1         3          0          3          3
  subtype5         1         2         4          2          7          4
          vv
clus       STAGE IV
  subtype1        2
  subtype2        3
  subtype3        9
  subtype4        2
  subtype5        4
D7V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  I OR II NOS        4        3        3        2        1
  STAGE 0            5        1        1        0        0
  STAGE I            9        9        7        1        2
  STAGE IA           8        2        5        0        1
  STAGE IB           3       10       12        1        2
  STAGE II           5        4        8        1        6
  STAGE IIA          2        5        2        0        3
  STAGE IIB          0        5       10        2        1
  STAGE IIC          3        2        6        1        2
  STAGE III          6       13       12        3        4
  STAGE IIIA         1        6        5        0        2
  STAGE IIIB         4        7       10        3        7
  STAGE IIIC        15       16       17        3        4
  STAGE IV           2        3        9        2        4
[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    20 12  9 13
  subtype2     8 29 22 16
  subtype3    18 23 26 25
  subtype4     5  4  5  2
  subtype5     9  5 12 10
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       20        8       18        5        9
  T2          12       29       23        4        5
  T3           9       22       26        5       12
  T4          13       16       25        2       10
[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 39  8  6 12
  subtype2 43 22 10  9
  subtype3 59 17 13 16
  subtype4  9  7  1  3
  subtype5 20  8  9  3
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       39       43       59        9       20
  N1        8       22       17        7        8
  N2        6       10       13        1        9
  N3       12        9       16        3        3
[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"
D7V7, binary
          cls
clus         0   1
  subtype1  67   2
  subtype2  84   3
  subtype3 101  10
  subtype4  18   2
  subtype5  37   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    2
  subtype2   84    3
  subtype3  101   10
  subtype4   18    2
  subtype5   37    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       67       84      101       18       37
  1        2        3       10        2        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 27 16
  subtype2 39 19
  subtype3 47 32
  subtype4  2  6
  subtype5 12 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   16
  subtype2   39   19
  subtype3   47   32
  subtype4    2    6
  subtype5   12   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        27       39       47        2       12
  YES       16       19       32        6       14
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1   9  65
  subtype2   9  85
  subtype3  15 104
  subtype4   5  16
  subtype5   7  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   65
  subtype2    9   85
  subtype3   15  104
  subtype4    5   16
  subtype5    7   37
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9        9       15        5        7
  YES       65       85      104       16       37
[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, continuous
D7V11, binary
          cls
clus        0  1
  subtype1 30 44
  subtype2 30 64
  subtype3 44 75
  subtype4 11 10
  subtype5 16 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   44
  subtype2   30   64
  subtype3   44   75
  subtype4   11   10
  subtype5   16   28
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       30       44       11       16
  MALE         44       64       75       10       28
[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"
D7V12, binary
          cls
clus         0   1
  subtype1  63  10
  subtype2  85   9
  subtype3 106  13
  subtype4  20   1
  subtype5  33  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   10
  subtype2   85    9
  subtype3  106   13
  subtype4   20    1
  subtype5   33   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        63       85      106       20       33
  YES       10        9       13        1       10
[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     3                         1    70
  subtype2     1                         0    89
  subtype3     0                         0   115
  subtype4     0                         0    21
  subtype5     1                         0    43
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        1        0        0        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0        0
  WHITE                           70       89      115       21       43
[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  73
  subtype2   2  88
  subtype3   4 112
  subtype4   1  20
  subtype5   0  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   73
  subtype2    2   88
  subtype3    4  112
  subtype4    1   20
  subtype5    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        4        1        0
  NOT HISPANIC OR LATINO       73       88      112       20       44
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 47 45
  subtype2 28 32
  subtype3 27 36
  subtype4 14 10
subtype1 subtype2 subtype3 subtype4 
      92       60       63       24 
subtype1 subtype2 subtype3 subtype4 
      45       32       36       10 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JE TCGA-D3-A2JG TCGA-D3-A2JL 
       60.46        76.41        45.99         9.76       107.61       171.58 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       43.53        58.06       140.98        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        69.21        76.34 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A95V TCGA-DA-A95X TCGA-EB-A44Q TCGA-EB-A5SG 
       53.65        95.51        72.10        52.90         3.91        33.24 
TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A2GD 
       50.07        20.38        67.50        12.99        63.12       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       12.95       201.60        68.65        31.00         0.76        71.31 
TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD 
      209.79        89.26       145.45       227.01        53.26         4.41 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19M 
       54.51        67.89        19.86       152.81         1.58        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 
      120.76        49.71        47.18        68.52        15.48        26.20 
TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        5.65       171.78         8.35        12.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       130.95         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A9SD TCGA-OD-A75X 
       30.90        53.29       117.93        42.48        59.41       297.01 
TCGA-QB-AA9O TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       18.05        44.05        79.99        92.84         1.15        59.64 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.90        62.43        10.95        48.39        31.99        18.31 
TCGA-WE-AAA4 TCGA-Z2-AA3S 
       24.99        91.23 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 
       12.99        31.89       110.93        49.35        62.60        62.86 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE 
       15.75        86.30         7.27        64.83        46.98        59.70 
TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A95Z TCGA-EE-A17X TCGA-EE-A20C 
        9.34       138.67        45.07        12.30        13.15        75.55 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
      155.90        76.14        61.12       346.49       185.19       115.43 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG 
       10.62        18.35       118.32       103.13        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3JB TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 
      171.85        25.08       201.80        14.56        34.45         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19W 
        4.54        53.29        11.47       150.12        42.48       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42L TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       47.97        22.36        74.47        27.62        32.78        42.08 
TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A26A TCGA-LH-A9QB 
      136.27       173.19         9.90         6.05         7.59        85.05 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZM TCGA-WE-AA9Y 
        1.97       120.07         8.09       185.13        65.42         1.94 

$subtype3
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JB 
       14.83         8.42        15.72       133.25        25.64       168.00 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL TCGA-D3-A8GM TCGA-D3-A8GR 
       40.01        16.96        13.87        42.05        70.62        36.53 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A95Y 
       16.90        18.44       150.61        64.83        58.85        14.14 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       52.41        18.21        62.37        75.22         0.26        44.28 
TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-EE-A2MJ 
       47.74        77.98        32.48         0.20         5.75        63.25 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
      143.93        23.51       124.31        64.04         6.28       111.85 
TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE 
       45.90        47.31        39.81        99.06         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       10.95       173.29        32.05        49.74       195.98        35.28 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A267 TCGA-GN-A4U3 
       66.67        80.68        55.59        11.54        17.06       120.53 
TCGA-GN-A8LK TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-WE-A8ZN 
       43.23         7.23         0.20         0.33       174.12        12.69 
TCGA-WE-A8ZR TCGA-XV-AB01 TCGA-YG-AA3O 
        8.68         6.61        28.21 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51R TCGA-D3-A5GN 
       19.04        36.30        66.08        90.21        62.70        45.70 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A29P TCGA-EE-A2A2 
       30.44       225.11        24.89         0.00        27.16        30.02 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3J8 
       26.14        81.99        15.25       104.78       122.73         3.35 
TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 
      151.46        10.06       312.07        96.92        34.49        46.92 

subtype1 subtype2 subtype3 subtype4 
    0.76     1.94     0.20     0.00 
subtype1 subtype2 subtype3 subtype4 
  297.01   346.49   195.98   312.07 
subtype1 subtype2 subtype3 subtype4 
  53.275   48.660   39.810   41.000 
[1] "0.8 - 297.0 (53.3)" "1.9 - 346.5 (48.7)" "0.2 - 196.0 (39.8)"
[4] "0.0 - 312.1 (41.0)"
D8V2, survival
          sevent
clus2       0  1
  subtype1 59 67
  subtype2 46 45
  subtype3 37 52
  subtype4 19 18
subtype1 subtype2 subtype3 subtype4 
     126       91       89       37 
subtype1 subtype2 subtype3 subtype4 
      67       45       52       18 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JE TCGA-D3-A2JF TCGA-D3-A2JG 
       66.48        90.90       103.10        27.65        62.07       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU 
       12.10       171.58        59.57        58.06       166.52        39.75 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS 
      174.84       145.12        32.94        22.62        26.89        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP 
      125.19        79.59        23.61       241.38        89.13       152.75 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       18.12        15.39        25.18        77.56        76.57       207.48 
TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W TCGA-DA-A95X TCGA-EB-A44Q 
      120.00        10.49        72.10        25.15        61.81        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       68.25        54.02         8.65        33.73        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R 
       91.56        13.55        13.97        64.64         2.60        14.47 
TCGA-EE-A29S TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       61.28        67.43       340.14       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2ME 
      107.38       102.12        13.91        81.21        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU 
      268.73        16.96       180.39       167.90       248.65        53.26 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JH 
       28.77        54.51       138.81       172.18        53.19       134.33 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
      152.81        13.94        26.37         6.44        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       50.89        49.48        93.01        46.98        12.95        92.98 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 
       27.85        38.27        36.26       216.92        48.59        20.91 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       15.45         9.70        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        77.82        28.73 
TCGA-FS-A4FB TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U7 TCGA-GN-A8LL 
       26.73       139.89       117.93        62.79        10.42        21.37 
TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1Q TCGA-W3-AA1R 
       59.41       297.90        18.05         0.69        69.07       111.09 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      105.04        49.05        61.15        70.52        63.22        11.80 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       49.51        40.41        21.40        24.99        27.58        96.99 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 
       12.99       112.04       112.57        71.80        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3BZ 
       23.77       115.53        86.76        11.87        66.48       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H 
       46.98        46.32        60.23         9.34        55.73        56.35 
TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D3-A8GV TCGA-DA-A1HY TCGA-DA-A1I7 
       26.43       161.00       117.17       167.70       144.89        73.84 
TCGA-DA-A1I8 TCGA-DA-A95Z TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C 
       53.92        13.02        20.35         7.04        29.82       151.27 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
      168.26        63.35        78.97        66.74       369.93       195.02 
TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
      115.96        54.74        75.48       126.81        21.67       129.27 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3JB TCGA-ER-A193 
       61.51       103.20       204.66       134.40       201.80        31.40 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       35.44         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH 
      152.35        44.05       148.18        79.99        43.82        32.05 
TCGA-ER-A42L TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      149.03        15.72        18.77       104.42        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 
       27.72        48.85        53.52        46.45       148.80       174.84 
TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
       22.92         9.90         7.23        10.13        32.48        22.13 
TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.23       368.78        63.02       121.08        42.08       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-YD-A89C TCGA-YD-A9TA 
       24.03        17.95       101.33        12.16         6.90        49.18 
TCGA-Z2-AA3V 
       15.98 

$subtype3
TCGA-BF-AAP0 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JB 
       14.93        16.57        16.67       133.25        43.43       168.00 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GM 
       86.93        24.53        13.87       125.79        30.84       107.15 
TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      129.63       151.53        54.67         3.65        22.29        18.44 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.90        36.03       176.55        35.93        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A95Y TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 
       68.09        14.14        29.29        58.92        36.46        94.98 
TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N 
       26.89        85.08        63.78        72.07        56.84        18.61 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GL TCGA-EE-A2GR 
       25.87        17.92        39.29        86.14        79.66        42.77 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
       44.88        19.76        96.23        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       71.21       124.31        64.04        13.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND 
       64.08        27.35        50.76        48.89       131.51        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YY 
       20.15        16.37        31.27       247.04        33.21       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD 
      202.65        23.93        11.41        53.16        66.67        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A8LK 
       55.59        13.51        64.44        48.00       121.91        50.10 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1O 
       65.88         7.23         0.20         0.33       228.16         4.01 
TCGA-WE-A8ZN TCGA-WE-A8ZR TCGA-XV-AB01 TCGA-YG-AA3O TCGA-YG-AA3P 
       58.98         9.01        13.25        37.94        14.43 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        31.59        42.08        66.08       103.59        45.30 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 
       63.81       135.75        29.06         7.10        20.38        33.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B 
      225.96        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        59.64        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G 
      216.66       122.73        41.59        34.32        51.35       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        96.92        39.35 
TCGA-GN-A4U8 
       48.89 

subtype1 subtype2 subtype3 subtype4 
    0.69     0.23     0.20     0.20 
subtype1 subtype2 subtype3 subtype4 
  340.14   369.93   247.04   357.37 
subtype1 subtype2 subtype3 subtype4 
  58.735   56.350   44.880   45.300 
[1] "0.7 - 340.1 (58.7)" "0.2 - 369.9 (56.4)" "0.2 - 247.0 (44.9)"
[4] "0.2 - 357.4 (45.3)"
D8V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           8       0      11        9       14        6         5
  subtype2           3       3      11        4        6        7         1
  subtype3           1       4       4        2        7        7         3
  subtype4           1       0       2        1        1        4         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         8         5        11          4          9         22
  subtype2         4         3        11          4          6         16
  subtype3         5         5        13          5          7         14
  subtype4         1         1         3          1          9          3
          vv
clus       STAGE IV
  subtype1       10
  subtype2        3
  subtype3        3
  subtype4        4
D8V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        8        3        1        1
  STAGE 0            0        3        4        0
  STAGE I           11       11        4        2
  STAGE IA           9        4        2        1
  STAGE IB          14        6        7        1
  STAGE II           6        7        7        4
  STAGE IIA          5        1        3        3
  STAGE IIB          8        4        5        1
  STAGE IIC          5        3        5        1
  STAGE III         11       11       13        3
  STAGE IIIA         4        4        5        1
  STAGE IIIB         9        6        7        9
  STAGE IIIC        22       16       14        3
  STAGE IV          10        3        3        4
[1] 14  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    21 36 23 25
  subtype2    18 19 15 14
  subtype3    13 14 25 19
  subtype4     8  4 11  8
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       21       18       13        8
  T2          36       19       14        4
  T3          23       15       25       11
  T4          25       14       19        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 72 19 11 18
  subtype2 47 19  6 12
  subtype3 36 16 14 10
  subtype4 15  8  8  3
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       72       47       36       15
  N1       19       19       16        8
  N2       11        6       14        8
  N3       18       12       10        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1 115  10
  subtype2  82   3
  subtype3  78   4
  subtype4  32   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115   10
  subtype2   82    3
  subtype3   78    4
  subtype4   32    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      115       82       78       32
  1       10        3        4        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 50 33
  subtype2 29 18
  subtype3 38 23
  subtype4 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   33
  subtype2   29   18
  subtype3   38   23
  subtype4   10   13
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        50       29       38       10
  YES       33       18       23       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1  16 116
  subtype2  15  78
  subtype3   8  81
  subtype4   6  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16  116
  subtype2   15   78
  subtype3    8   81
  subtype4    6   32
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        16       15        8        6
  YES      116       78       81       32
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, binary
          cls
clus        0  1
  subtype1 57 75
  subtype2 32 61
  subtype3 30 59
  subtype4 12 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   75
  subtype2   32   61
  subtype3   30   59
  subtype4   12   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       57       32       30       12
  MALE         75       61       59       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus         0   1
  subtype1 118  14
  subtype2  81  12
  subtype3  78  10
  subtype4  30   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   14
  subtype2   81   12
  subtype3   78   10
  subtype4   30    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       118       81       78       30
  YES       14       12       10        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0   129
  subtype2     1                         0    90
  subtype3     1                         1    83
  subtype4     2                         0    36
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        2
  BLACK OR AFRICAN AMERICAN        0        0        1        0
  WHITE                          129       90       83       36
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
          cls
clus         0   1
  subtype1   3 128
  subtype2   2  87
  subtype3   2  85
  subtype4   0  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  128
  subtype2    2   87
  subtype3    2   85
  subtype4    0   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        2        0
  NOT HISPANIC OR LATINO      128       87       85       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 32 26
  subtype2 32 42
  subtype3 45 52
subtype1 subtype2 subtype3 
      58       74       97 
subtype1 subtype2 subtype3 
      26       42       52 
$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-EB-A6L9 
       16.90        76.34        53.65       150.61        58.85        18.21 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       13.15        62.37        77.98        68.65        10.62        32.48 
TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MK 
      118.32        81.99        15.25         5.75        63.25        89.26 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
       25.08        23.51       124.31        54.51         6.28       111.85 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
       19.86         1.58       151.46        99.06        49.71        47.18 
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-AA1R TCGA-W3-AA1V 
       35.28        55.59        59.41        18.05        79.99         8.09 
TCGA-W3-AA1W TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
      185.13        31.99        24.99        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       62.86        15.75       107.61        36.30        64.83        66.08 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A51R TCGA-D3-A5GN TCGA-DA-A1HY TCGA-DA-A1I5 
       58.06         9.34        62.70        45.70       138.67        95.51 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20H 
       45.07       225.11        52.41        24.89         0.00       155.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE 
       76.14        44.28       185.19       115.43       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
      201.60         0.76        71.31        23.77        94.19       171.85 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-ER-A193 
      227.01        53.26       122.73        67.89       201.80        14.56 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M 
       34.45         4.54        53.29        11.47       150.12        59.84 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FS-A1YY 
      146.63        22.36        68.52        15.48        74.47        49.74 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZS 
      312.07        32.78        42.08        12.92        78.61       136.27 
TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
      173.19        11.54         9.90       117.93        96.92         7.59 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       85.05         1.97       120.07         1.15        12.69        62.43 
TCGA-WE-AA9Y TCGA-WE-AAA3 
        1.94        18.31 

$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-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A51E 
        9.76       171.58        40.01        59.70        13.87       173.85 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GJ 
      144.46        31.76        11.34        42.05       124.08       179.97 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 
       69.53        70.62       135.12        36.53        10.78        18.44 
TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A95V TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z 
       69.21        64.83        72.10        52.90        14.14        12.30 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29B 
        3.91        50.07        20.38        67.50        75.55        75.22 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        63.12        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      346.49        30.02        26.14        18.35        31.00         0.20 
TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AC 
      103.13       209.79       104.78       145.45       143.93        64.04 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 
        4.41        45.90         3.35       152.81        47.31         7.82 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 
       39.81       120.76        16.87       173.29        32.05        26.20 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZJ TCGA-FS-A1ZU 
       10.06       171.78       195.98         8.35        36.33         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-GN-A262 
       23.21         5.29         3.06        66.67        80.68        53.29 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A8LK 
       17.06        42.48       120.53        34.49        46.92        43.23 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 
      297.01         0.20         0.33       174.12        44.05        92.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-XV-AB01 
       59.64        65.42        21.90         8.68        48.39         6.61 
TCGA-Z2-AA3S 
       91.23 

subtype1 subtype2 subtype3 
    1.58     0.00     0.20 
subtype1 subtype2 subtype3 
  185.13   312.07   346.49 
subtype1 subtype2 subtype3 
  47.080   55.675   45.900 
[1] "1.6 - 185.1 (47.1)" "0.0 - 312.1 (55.7)" "0.2 - 346.5 (45.9)"
D9V2, survival
          sevent
clus2       0  1
  subtype1 50 38
  subtype2 46 60
  subtype3 58 77
subtype1 subtype2 subtype3 
      88      106      135 
subtype1 subtype2 subtype3 
      38       60       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        76.57        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F8 
      207.48       176.55        35.93        40.60        68.09        15.68 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20F 
        7.04        36.46        29.82        94.98        26.89        91.56 
TCGA-EE-A20I TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       13.55        18.61        86.14        48.72       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       180.39        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       134.33        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 
       49.48        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-HR-A2OG TCGA-QB-AA9O TCGA-W3-AA1R TCGA-W3-AA1V TCGA-W3-AA1W 
       59.41         0.23        18.05       111.09        42.08       219.16 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3V 
       40.41        24.99        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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       65.49       115.53       113.52        42.08        12.10        66.48 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F 
       66.08       130.72        58.06         9.34        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GQ 
       56.35        63.81       135.75        26.43       161.00        29.06 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y 
      144.89       120.00        73.84       225.96        58.92        27.22 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G 
       14.70       133.81       168.26        63.35        78.97        72.07 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GD 
       61.28        25.87       195.02        46.82       115.96       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC 
      173.79       220.24        13.91        81.21        21.67        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AB 
      103.27       103.20       204.66       248.65        53.26       122.73 
TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
      172.18       201.80        51.35        31.40        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       98.40        12.59        13.02       152.35         6.44        61.05 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L TCGA-FR-A69P 
      148.18        43.82        93.01        46.98       149.03        15.72 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       18.77        48.59       228.59         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
       53.52        46.45        15.45        32.75       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 
      148.80       174.84        13.51         9.90       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 
       10.13        32.48        22.13       368.78        63.02       121.08 
TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
        4.01        24.03        49.05        17.95        58.98        63.22 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YD-A89C TCGA-YD-A9TA 
       12.16        21.40         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-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       43.43        27.65       171.58        86.93        60.23        13.87 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
      174.84       145.12        32.94        26.89       125.79        18.18 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      125.19       241.38        89.13       107.15       152.75       129.63 
TCGA-D3-A8GV TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
      167.70         7.10        18.12        18.44         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A95V TCGA-DA-A95W 
       77.56        53.92        65.92        10.49        72.10        25.15 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       61.81        14.14        13.02        13.87        10.36        20.35 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       54.02        29.29         8.65        33.73        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
      151.27        85.08        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A2 
       56.84        56.42        66.74        14.47       369.93        59.64 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       39.29        59.28        67.43        75.48       102.12        42.77 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      129.27        47.28       268.73       216.66       167.90        47.54 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J7 
      162.48        64.04        28.77        41.59       138.81        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F 
       34.32       152.81        50.76         9.17        48.89        26.37 
TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
      162.08        20.15        16.37       247.04        33.21        92.98 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       27.85        34.82        36.26       216.92       202.65        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW 
       27.72        47.38        23.93        74.73        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD 
       27.09        27.02        66.67        28.73        26.73        80.68 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 
        0.20       139.89        64.44        62.79        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X 
       39.35        10.42        48.89        50.10        21.37       297.90 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA21 
        0.20         0.33         0.69       228.16        69.07       105.04 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-XV-AB01 
       61.15       101.33        70.52         9.01        49.51        13.25 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        27.58        96.99 

subtype1 subtype2 subtype3 
    0.23     4.01     0.20 
subtype1 subtype2 subtype3 
  268.93   368.78   369.93 
subtype1 subtype2 subtype3 
  47.850   61.395   49.510 
[1] "0.2 - 268.9 (47.8)" "4.0 - 368.8 (61.4)" "0.2 - 369.9 (49.5)"
D9V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           7       2       5       11        4        6         3
  subtype2           2       2      13        2       12        7         6
  subtype3           4       3      10        3       11       11         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0        15          1          9         17
  subtype2         5         3        10          7          7         16
  subtype3        12        11        13          5         13         17
          vv
clus       STAGE IV
  subtype1        3
  subtype2        6
  subtype3        9
D9V4, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        7        2        4
  STAGE 0            2        2        3
  STAGE I            5       13       10
  STAGE IA          11        2        3
  STAGE IB           4       12       11
  STAGE II           6        7       11
  STAGE IIA          3        6        3
  STAGE IIB          0        5       12
  STAGE IIC          0        3       11
  STAGE III         15       10       13
  STAGE IIIA         1        7        5
  STAGE IIIB         9        7       13
  STAGE IIIC        17       16       17
  STAGE IV           3        6        9
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    27 13 17 13
  subtype2    14 30 25 17
  subtype3    17 29 29 31
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       27       14       17
  T2          13       30       29
  T3          17       25       29
  T4          13       17       31
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 43 13 13 16
  subtype2 56 21 11 10
  subtype3 69 27 11 12
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       56       69
  N1       13       21       27
  N2       13       11       11
  N3       16       10       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  84   4
  subtype2  94   6
  subtype3 119   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84    4
  subtype2   94    6
  subtype3  119    9
   clus
vv  subtype1 subtype2 subtype3
  0       84       94      119
  1        4        6        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1 40 14
  subtype2 39 25
  subtype3 43 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   14
  subtype2   39   25
  subtype3   43   43
     clus
vv    subtype1 subtype2 subtype3
  NO        40       39       43
  YES       14       25       43
[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  13  81
  subtype2  12  96
  subtype3  16 120
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   81
  subtype2   12   96
  subtype3   16  120
     clus
vv    subtype1 subtype2 subtype3
  NO        13       12       16
  YES       81       96      120
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, binary
          cls
clus        0  1
  subtype1 39 55
  subtype2 35 73
  subtype3 49 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   55
  subtype2   35   73
  subtype3   49   87
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39       35       49
  MALE         55       73       87
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus         0   1
  subtype1  82  12
  subtype2  96  12
  subtype3 119  15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   12
  subtype2   96   12
  subtype3  119   15
     clus
vv    subtype1 subtype2 subtype3
  NO        82       96      119
  YES       12       12       15
[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    90
  subtype2     1                         0   104
  subtype3     3                         0   131
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           90      104      131
[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  90
  subtype2   2 103
  subtype3   3 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   90
  subtype2    2  103
  subtype3    3  131
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       90      103      131
[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 57 57
  subtype2 17 29
  subtype3 22 27
  subtype4 13  7
subtype1 subtype2 subtype3 subtype4 
     114       46       49       20 
subtype1 subtype2 subtype3 subtype4 
      57       29       27        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-A2JL 
       62.60        25.64       168.00         7.27         9.76       171.58 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K 
       43.53       140.98        16.96        13.87       173.85        31.76 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL 
       11.34        42.05       124.08        23.61       179.97        69.53 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       70.62       135.12        36.53        10.78        15.02        16.90 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A95V 
       18.44        69.21        76.34       150.61        64.83        72.10 
TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN 
       52.90        14.14        12.30         3.91        50.07        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A29B 
       18.21        13.15        62.37        20.38        67.50        75.22 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GL 
       12.99         0.26        63.12        47.74        77.98        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        89.26       145.45       227.01       143.93        23.51 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3JI 
      124.31        64.04         4.41        54.51       111.85       152.81 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NG 
       47.31         7.82        39.81        47.18        16.87        10.95 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1Z0 
      173.29        32.05        26.20         5.65       171.78       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.35        42.08       130.95        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 
        5.29         3.06        66.67        55.59        53.29        17.06 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       42.48        43.23       297.01        18.05         0.20         0.33 
TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZO 
      174.12        44.05        79.99       185.13        92.84        21.90 
TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O TCGA-Z2-AA3S 
        8.68        48.39        31.99         6.61        28.21        91.23 

$subtype2
TCGA-3N-A9WD TCGA-D3-A2J7 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-DA-A1I1 
       12.99        45.99       107.61        58.06        40.01        53.65 
TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A2A1 TCGA-EE-A2GD 
       95.51        58.85        76.14        44.28       115.43       239.11 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MG 
       12.95       201.60        68.65         0.76        71.31        94.19 
TCGA-EE-A2MU TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
       53.26         6.28        45.90        19.86        14.56         1.58 
TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND 
        4.54        59.84       120.76        49.71       146.63         4.70 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YY TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A4FD 
       68.52        15.48        49.74        12.92        36.33        80.68 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A9SD TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
       11.54       117.93        59.41         1.15        59.64        12.69 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       62.43         1.94        18.31        24.99 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       31.89       110.93        49.35        62.86        15.75        86.30 
TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51J 
       64.83        46.98        59.70         9.34        90.21       144.46 
TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H 
      138.67        45.07       225.11        24.89        75.55       155.90 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2MC 
       61.12       346.49       185.19        10.62       118.32        23.77 
TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B 
      171.85        25.08        67.89       201.80        34.45        53.29 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42L 
       11.47       150.12        99.06        47.97        22.36        74.47 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT 
       27.62        32.78        78.61       136.27       173.19         9.90 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        7.59       120.53        85.05         1.97       120.07         8.09 
TCGA-WE-A8ZM 
       65.42 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A51R TCGA-D3-A5GN TCGA-EE-A182 
       19.04        36.30        66.08        62.70        45.70         0.00 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       27.16        30.02        26.14        81.99        15.25       104.78 
TCGA-EE-A3AB TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-GN-A265 
      122.73         3.35       151.46        10.06       312.07        96.92 
TCGA-GN-A4U4 TCGA-GN-A4U8 
       34.49        46.92 

subtype1 subtype2 subtype3 subtype4 
    0.20     0.76     1.97     0.00 
subtype1 subtype2 subtype3 subtype4 
  297.01   239.11   346.49   312.07 
subtype1 subtype2 subtype3 subtype4 
  43.380   49.725   64.830   41.000 
[1] "0.2 - 297.0 (43.4)" "0.8 - 239.1 (49.7)" "2.0 - 346.5 (64.8)"
[4] "0.0 - 312.1 (41.0)"
D10V2, survival
          sevent
clus2       0  1
  subtype1 79 81
  subtype2 23 44
  subtype3 36 36
  subtype4 16 14
subtype1 subtype2 subtype3 subtype4 
     160       67       72       30 
subtype1 subtype2 subtype3 subtype4 
      81       44       36       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-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
      171.58        59.57       166.52        24.53        13.87       174.84 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD 
       32.94        26.89       125.79        18.18       125.19        23.61 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GV 
      241.38        89.13       107.15       152.75       129.63       167.70 
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-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       18.44         9.90        25.18        77.56        76.57        36.03 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-DA-A95V 
      176.55        65.92        40.60        10.49        15.68        72.10 
TCGA-DA-A95W TCGA-DA-A95X TCGA-DA-A95Y TCGA-DA-A95Z TCGA-EB-A44Q TCGA-EB-A5KH 
       25.15        61.81        14.14        13.02        13.87        20.35 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        29.29        58.92        36.46        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
       94.98        33.73        26.89        68.15         4.96        91.56 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       85.08        13.97        63.78        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM 
       18.61        86.14        67.43        48.72        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD 
      102.12        42.77        44.88       129.27        19.76        47.28 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
      268.73        16.96        96.23       180.39       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65        43.23       162.48        71.21       124.31        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
       28.77        54.51       138.81       127.20        36.95        53.19 
TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F 
       27.35       152.81        50.76         9.17        48.89        26.37 
TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL 
       49.48        20.15        16.37        31.27       247.04        33.21 
TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 
       92.98        27.85        38.27        36.26       216.92       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       20.91        46.45        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        66.67        28.73 
TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       26.73        55.59       139.89        64.44        62.79        48.00 
TCGA-GN-A4U7 TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A690 TCGA-RP-A693 
       10.42        50.10       297.90        18.05         0.20         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1Q TCGA-W3-AA1R TCGA-W3-AA1W TCGA-W3-AA21 
        0.69       228.16        69.07       111.09       219.16       105.04 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-XV-AB01 TCGA-YG-AA3O 
       70.52         9.01        49.51        40.41        13.25        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-A2J7 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.99       103.10       113.52        12.10       130.72        58.06 
TCGA-D3-A3CC TCGA-D3-A51F TCGA-D3-A8GB TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       86.93        55.73        30.84       207.48        35.93       120.00 
TCGA-DA-A1IC TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S 
       68.09        13.55        78.97        72.07        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       25.87       115.96        39.29       340.14       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MU 
      107.38        13.91        81.21       103.27       103.20        53.26 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19A 
       13.81        64.08       134.33        31.40        13.94        77.75 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND 
        6.44        61.05       162.08        50.89       148.18        23.34 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       93.01        46.98        15.72        48.59       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZR TCGA-FS-A4FD TCGA-FW-A3R5 
       48.85        15.45        47.38        11.41        80.68        22.92 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-AA1O TCGA-WE-A8K1 
       13.51       117.93        21.37        59.41         4.01        49.05 
TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       61.15        58.98        63.22        12.16        21.40        24.99 
TCGA-YD-A89C 
        6.90 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
      112.04       112.57        71.80        65.49        23.77       115.53 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO 
       86.76        66.48        46.98        46.32        60.23         9.34 
TCGA-D3-A3MR TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GE TCGA-D3-A8GN 
      103.59        56.35       145.12        22.62        26.43       161.00 
TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A5VV 
      117.17       144.89        73.84        53.92       225.96         7.04 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29Q TCGA-EE-A29T 
       27.22       151.27       168.26        63.35        66.74       369.93 
TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI 
      195.02        54.74       126.81        21.67        61.51       204.66 
TCGA-EE-A2MR TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A19B 
      134.40       172.18       201.80        51.35        35.44        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2NC 
       12.59        13.02       152.35       131.51        79.99        43.82 
TCGA-ER-A2NH TCGA-ER-A42L TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       32.05       149.03        18.77       104.42        28.08        27.72 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT TCGA-GN-A266 
       53.52       101.26       148.80       174.84         9.90        10.13 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-LH-A9QB TCGA-W3-A825 
       32.48       121.91        22.13         0.23       368.78        63.02 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-YD-A9TA 
      121.08        42.08        24.03        17.95       101.33        49.18 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        31.59        42.08        66.08        45.30        63.81 
TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B 
      135.75        29.06         7.10        10.36        14.70       133.81 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       56.42        46.82        59.64        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19G TCGA-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        96.92        39.35        48.89 

subtype1 subtype2 subtype3 subtype4 
    0.20     4.01     0.23     0.20 
subtype1 subtype2 subtype3 subtype4 
  297.90   340.14   369.93   357.37 
subtype1 subtype2 subtype3 subtype4 
  49.185   55.730   65.985   46.060 
[1] "0.2 - 297.9 (49.2)" "4.0 - 340.1 (55.7)" "0.2 - 369.9 (66.0)"
[4] "0.2 - 357.4 (46.1)"
D10V3, continuous
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           6       4      10       10       14       13         5
  subtype2           1       0       7        4        7        2         3
  subtype3           5       3      10        1        5        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        10         9        19          5         12         23
  subtype2         4         3         5          4          5         15
  subtype3         2         1        12          3          8          9
  subtype4         1         1         2          1          4          3
          vv
clus       STAGE IV
  subtype1        8
  subtype2        5
  subtype3        2
  subtype4        3
D10V4, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        6        1        5        1
  STAGE 0            4        0        3        0
  STAGE I           10        7       10        1
  STAGE IA          10        4        1        1
  STAGE IB          14        7        5        1
  STAGE II          13        2        5        4
  STAGE IIA          5        3        1        3
  STAGE IIB         10        4        2        1
  STAGE IIC          9        3        1        1
  STAGE III         19        5       12        2
  STAGE IIIA         5        4        3        1
  STAGE IIIB        12        5        8        4
  STAGE IIIC        23       15        9        3
  STAGE IV           8        5        2        3
[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    28 32 33 34
  subtype2     9 20 15 14
  subtype3    15 17 15  7
  subtype4     6  3  8  6
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       28        9       15        6
  T2          32       20       17        3
  T3          33       15       15        8
  T4          34       14        7        6
[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 84 26 15 18
  subtype2 33 12  9  9
  subtype3 37 19  5  9
  subtype4 14  4  6  2
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       84       33       37       14
  N1       26       12       19        4
  N2       15        9        5        6
  N3       18        9        9        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1 142   9
  subtype2  61   5
  subtype3  69   2
  subtype4  25   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  142    9
  subtype2   61    5
  subtype3   69    2
  subtype4   25    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      142       61       69       25
  1        9        5        2        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1 63 41
  subtype2 34 17
  subtype3 17 14
  subtype4  8 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   41
  subtype2   34   17
  subtype3   17   14
  subtype4    8   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        63       34       17        8
  YES       41       17       14       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"
D10V9, binary
          cls
clus         0   1
  subtype1  18 144
  subtype2   6  64
  subtype3  12  64
  subtype4   5  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18  144
  subtype2    6   64
  subtype3   12   64
  subtype4    5   25
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        18        6       12        5
  YES      144       64       64       25
[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"
D10V10, continuous
D10V11, binary
          cls
clus         0   1
  subtype1  58 104
  subtype2  27  43
  subtype3  26  50
  subtype4  12  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58  104
  subtype2   27   43
  subtype3   26   50
  subtype4   12   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       58       27       26       12
  MALE        104       43       50       18
[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"
D10V12, binary
          cls
clus         0   1
  subtype1 143  18
  subtype2  65   5
  subtype3  67   9
  subtype4  22   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  143   18
  subtype2   65    5
  subtype3   67    9
  subtype4   22    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       143       65       67       22
  YES       18        5        9        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1   155
  subtype2     0                         0    68
  subtype3     1                         0    73
  subtype4     1                         0    29
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        1        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                          155       68       73       29
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   4 155
  subtype2   1  69
  subtype3   2  70
  subtype4   0  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  155
  subtype2    1   69
  subtype3    2   70
  subtype4    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        1        2        0
  NOT HISPANIC OR LATINO      155       69       70       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"
