[1] "ofn"         "-oTKIPAN-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/15165233/KIPAN-TP.mergedcluster.txt"

nPatients in clinical file=914, in cluster file=893, common to both=869
[1]  10 869
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
34 24 13 17 
 1  2  3  4 
34 24 13 17 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
21 24 18 13 12 
 1  2  3  4  5 
21 24 18 13 12 
[1] "CN_CNMF"
[1] 3
  1   2   3 
267 304 288 
  1   2   3 
267 304 288 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
125 301 210 
  1   2   3 
125 301 210 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
118 196 298 253 
  1   2   3   4 
118 196 298 253 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 88 138 208 159 111 161 
  1   2   3   4   5   6 
 88 138 208 159 111 161 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
316 188 345 
  1   2   3 
316 188 345 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 77 574 198 
  1   2   3 
 77 574 198 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
145  68  59 126 
  1   2   3   4 
145  68  59 126 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 51  82  88 131  46 
  1   2   3   4   5 
 51  82  88 131  46 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 869 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=200,	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=595,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "868"  
freq.contrast "868"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=44,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 869 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
470 123 253  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
470 123 253  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
470 123 253  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
470 123 253  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
323  43   6 
[1] "table(vv)"
vv
 N0  N1  N2 
323  43   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
323  43   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
323  43   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=42, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=39, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 30  4
  subtype2 16  8
  subtype3 12  1
  subtype4 14  3
subtype1 subtype2 subtype3 subtype4 
      34       24       13       17 
subtype1 subtype2 subtype3 subtype4 
       4        8        1        3 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       36.82        47.21        49.58        48.59        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       37.38        23.21        48.82        31.07        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 
       18.44        82.32        51.25        28.70        24.16        18.64 
TCGA-A3-3383 TCGA-AK-3444 TCGA-AK-3455 TCGA-AS-3778 TCGA-B2-3924 TCGA-B2-4099 
       28.31        48.36        22.45         1.41        35.90        12.30 
TCGA-B2-4102 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 
       31.30        27.55        24.66        17.19       101.06        32.61 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       59.84        75.88        58.95        11.05 

$subtype2
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 
        0.53        39.16        49.08        49.02        37.15        36.36 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 
       21.86         4.50        52.93        43.20        20.71        18.87 
TCGA-AK-3426 TCGA-B8-4143 TCGA-B8-4620 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 
       29.10        23.31        25.55        90.28        93.34        89.36 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-AL-3473 
       63.25        73.22        14.17        65.69        54.61        25.08 

$subtype3
TCGA-A3-3313 TCGA-A3-3328 TCGA-A3-3336 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 
       24.16        45.53        34.29        84.36        57.37        46.78 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 
       40.01        45.93        12.13        40.70        32.61        27.16 
TCGA-B3-4104 
       34.49 

$subtype4
TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       10.49        37.58         1.68         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 
       13.55        30.35        33.83        10.09        30.58        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       28.18        26.40        20.61         0.46         1.15 

subtype1 subtype2 subtype3 subtype4 
    1.41     0.53    12.13     0.46 
subtype1 subtype2 subtype3 subtype4 
  101.06    93.34    84.36    76.64 
subtype1 subtype2 subtype3 subtype4 
  31.955   38.155   40.010   26.400 
[1] "1.4 - 101.1 (32.0)" "0.5 - 93.3 (38.2)"  "12.1 - 84.4 (40.0)"
[4] "0.5 - 76.6 (26.4)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      23        4         6        1
  subtype2       8        4         8        4
  subtype3       8        5         0        0
  subtype4       6        3         1        1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         23        8        8        6
  STAGE II         4        4        5        3
  STAGE III        6        8        0        1
  STAGE IV         1        4        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 23  4  7
  subtype2  9  5 10
  subtype3  8  5  0
  subtype4  8  7  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       23        9        8        8
  T2        4        5        5        7
  T3        7       10        0        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1
  subtype1 18  0
  subtype2 11  3
  subtype3  5  0
  subtype4  3  1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       18       11        5        3
  N1        0        3        0        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"
D1V6, binary
          cls
clus        0  1
  subtype1 33  1
  subtype2 20  4
  subtype3 13  0
  subtype4 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    1
  subtype2   20    4
  subtype3   13    0
  subtype4   11    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       33       20       13       11
  1        1        4        0        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 15 19
  subtype2  9 15
  subtype3  4  9
  subtype4  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   19
  subtype2    9   15
  subtype3    4    9
  subtype4    5   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       15        9        4        5
  MALE         19       15        9       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"
D1V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype2 subtype4 
       1        1 
character(0)
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                34
  subtype2                                23
  subtype3                                12
  subtype4                                 3
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     0
  subtype2                                     1
  subtype3                                     1
  subtype4                                    14
D1V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CLEAR CELL RENAL CARCINOMA           34       23       12        3
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        0        1        1       14
[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"
D1V10, continuous
D1V11, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype4 
       2 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    32
  subtype2     0                         1    21
  subtype3     0                         2    11
  subtype4     1                         9     7
D1V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        1        2        9
  WHITE                           32       21       11        7
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
          cls
clus        0  1
  subtype1  5 19
  subtype2  2 11
  subtype3  0 12
  subtype4  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   19
  subtype2    2   11
  subtype3    0   12
  subtype4    0   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        0        0
  NOT HISPANIC OR LATINO       19       11       12       16
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 20  1
  subtype2 16  8
  subtype3 14  4
  subtype4 10  3
  subtype5 12  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      21       24       18       13       12 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        8        4        3        0 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       36.82        47.21        48.59        38.99        24.69        37.38 
TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 
       23.21        31.07        45.53        29.92        18.44        51.25 
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3383 TCGA-AS-3778 TCGA-B2-3924 
       28.70        24.16        18.64        28.31         1.41        35.90 
TCGA-B2-4099 TCGA-B2-4102 TCGA-CJ-4634 
       12.30        31.30        59.84 

$subtype2
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 
        0.53        39.16        49.08        49.02        37.15        36.36 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 
       21.86         4.50        52.93        43.20        20.71        18.87 
TCGA-AK-3426 TCGA-B8-4143 TCGA-B8-4620 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 
       29.10        23.31        25.55        90.28        93.34        89.36 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-AL-3473 
       63.25        73.22        14.17        65.69        54.61        25.08 

$subtype3
TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 TCGA-AL-3466 TCGA-AL-3467 
       24.16        10.49        37.58         1.68         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       76.64        13.55        30.35        33.83        10.09        30.58 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 

$subtype4
TCGA-A3-3320 TCGA-A3-3331 TCGA-A3-3359 TCGA-AK-3444 TCGA-AK-3455 TCGA-B8-4151 
       49.58        48.82        82.32        48.36        22.45        27.55 
TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 TCGA-CJ-4639 TCGA-CJ-4643 
       24.66        17.19       101.06        32.61        75.88        58.95 
TCGA-CJ-4644 
       11.05 

$subtype5
TCGA-A3-3328 TCGA-A3-3336 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       45.53        34.29        84.36        57.37        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 TCGA-B3-4104 
       45.93        12.13        40.70        32.61        27.16        34.49 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.41     0.53     0.46    11.05    12.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   59.84    93.34    76.64   101.06    84.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  31.070   38.155   25.280   48.360   40.355 
[1] "1.4 - 59.8 (31.1)"   "0.5 - 93.3 (38.2)"   "0.5 - 76.6 (25.3)"  
[4] "11.1 - 101.1 (48.4)" "12.1 - 84.4 (40.4)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      16        2         3        0
  subtype2       8        4         8        4
  subtype3       7        3         1        1
  subtype4       7        2         3        1
  subtype5       7        5         0        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         16        8        7        7        7
  STAGE II         2        4        3        2        5
  STAGE III        3        8        1        3        0
  STAGE IV         0        4        1        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 16  2  3
  subtype2  9  5 10
  subtype3  9  7  2
  subtype4  7  2  4
  subtype5  7  5  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       16        9        9        7        7
  T2        2        5        7        2        5
  T3        3       10        2        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1
  subtype1  9  0
  subtype2 11  3
  subtype3  4  1
  subtype4  9  0
  subtype5  4  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        9       11        4        9        4
  N1        0        3        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 21  0
  subtype2 20  4
  subtype3 12  1
  subtype4 12  1
  subtype5 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    0
  subtype2   20    4
  subtype3   12    1
  subtype4   12    1
  subtype5   12    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       21       20       12       12       12
  1        0        4        1        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  3 18
  subtype2  9 15
  subtype3  5 13
  subtype4 12  1
  subtype5  4  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   18
  subtype2    9   15
  subtype3    5   13
  subtype4   12    1
  subtype5    4    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        3        9        5       12        4
  MALE         18       15       13        1        8
[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"
D2V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       1        1 
character(0)
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                21
  subtype2                                23
  subtype3                                 4
  subtype4                                13
  subtype5                                11
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     0
  subtype2                                     1
  subtype3                                    14
  subtype4                                     0
  subtype5                                     1
D2V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CLEAR CELL RENAL CARCINOMA           21       23        4       13
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        0        1       14        0
                                       clus
vv                                      subtype5
  KIDNEY CLEAR CELL RENAL CARCINOMA           11
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype3 
       2 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    19
  subtype2     0                         1    21
  subtype3     1                        10     7
  subtype4     0                         0    13
  subtype5     0                         1    11
D2V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        1       10        0        1
  WHITE                           19       21        7       13       11
[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"
D2V13, binary
          cls
clus        0  1
  subtype1  2 12
  subtype2  2 11
  subtype3  0 16
  subtype4  3  7
  subtype5  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   12
  subtype2    2   11
  subtype3    0   16
  subtype4    3    7
  subtype5    0   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        2        0        3        0
  NOT HISPANIC OR LATINO       12       11       16        7       12
[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(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 215  40
  subtype2 223  78
  subtype3 194  93
subtype1 subtype2 subtype3 
     255      301      287 
subtype1 subtype2 subtype3 
      40       78       93 
$subtype1
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        84.89        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.56        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 
       28.80        54.74        62.37       151.96        44.91        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8424 
       49.97       123.12       129.37        23.47        25.48        65.19 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       76.90        74.93        79.04        92.71        16.67       103.27 
TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 
       86.10        61.58        63.95        10.49        43.20        65.52 
TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 
       84.36        57.37        40.01        45.93        12.13        40.70 
TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-4839 
        3.32        28.47         1.38         3.62        68.71        53.88 
TCGA-B0-5106 TCGA-B0-5117 TCGA-B2-3923 TCGA-B8-4619 TCGA-B8-4621 TCGA-BP-4177 
       52.54        17.59        32.61        17.19        25.91        54.90 
TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 TCGA-BP-4967 TCGA-BP-4994 
       21.21        12.30        10.82        37.25         6.74        43.00 
TCGA-CJ-4875 TCGA-CW-6087 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       77.36         1.35         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JE 
      100.27        56.91         4.57        67.30        34.85        56.81 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       35.67        26.43        30.71        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       16.18        22.49         0.13        12.82        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
       61.05         0.10        35.18        19.13         0.89        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       30.48        29.46        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ 
       15.75        12.46        76.64        13.55        30.35        49.25 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20         7.33        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 
        0.46         6.58        33.83        10.09        30.58        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5879 TCGA-BQ-5880 
        0.16        17.49        86.76        19.27        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
       47.80        26.04        25.35         0.95         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       48.26        96.92        50.40         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       61.02        34.19        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 
        1.18         0.43        51.78        11.05        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 
       25.84         6.38        17.98        80.65       194.79        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
        1.05        12.43        17.95         0.89        11.21        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        20.25        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        6.61        52.27        16.01        50.60        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        27.06        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 
       30.67        25.68        27.39        12.99        15.91        18.64 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.62        25.28         6.02 

$subtype2
TCGA-KL-8326 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8437 
      109.22        23.28        28.80        51.06        31.33       100.87 
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3326 
       12.16        47.21         0.53        39.16        36.36        37.38 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 
       31.07        45.53        29.92        82.32        51.25        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
       74.63        74.76        53.29        55.76        20.71        28.31 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 
       15.39        22.65         0.10        11.18        10.62        73.08 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3455 
       60.92        46.78        48.36        58.49        48.69        22.45 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 
       37.58        31.27         1.41         2.53        19.00        65.10 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4816 
        7.82         2.14         3.25        20.25         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4841 
       33.50        16.77         6.02        14.93        29.10         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       56.68        11.64        39.45        26.07        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 
       20.94        11.24        11.90        25.32        18.51         2.24 
TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5115 
       21.86        62.89        90.48        30.48        35.90        26.20 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       48.89       101.13        46.68        84.92        90.12        52.77 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
      120.59        79.36       102.48        96.36        61.32        97.41 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-A4SR 
        1.68        12.30        21.30        31.30        10.36        16.67 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        5.75         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5164 
       27.55        25.05        24.66        23.01         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       24.23        17.16        16.60        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       29.88        17.06         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 
       14.17        85.51        90.28        93.34        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       77.03        62.24        53.42        27.78        62.07        37.25 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4354 
       15.16        18.48        52.24        54.77        12.23        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 
       31.33        72.59        77.98        77.62        44.15        71.80 
TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
       61.68         5.33        61.97        13.51        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
       48.95        36.53        20.38        36.95        47.97         6.94 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 
       63.62        61.22        61.51        14.24        49.38         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4988 
       47.11        53.65        14.93        36.07        33.34        27.22 
TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
       46.45        30.64        41.62        38.70        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 
       35.21        36.23        28.87        48.10        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       52.27        38.30        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4637 
       23.47        13.41        24.62        44.55         0.95        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4869 TCGA-CJ-4870 
       14.17        75.88        54.61        53.52        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 
       47.18        75.06        61.91        57.83        64.18        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       63.98        68.55        26.93        49.97        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5678 
       38.56        45.14         3.06         4.57        18.81        18.87 
TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6031 TCGA-CW-5581 
       18.15        73.35        67.00        53.26        62.66        92.02 
TCGA-CW-5583 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4861 
       81.83        78.18       105.93       103.43         0.59        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       60.59        63.39         5.46        63.42         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5986 TCGA-CZ-5988 
       18.44        55.33        21.76         2.40        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 
       62.63        45.96        65.88        11.67        66.28        23.90 
TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-MM-A84U TCGA-2Z-A9J9 
       18.12         6.77         7.96        10.29        15.25        75.42 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7915 TCGA-A4-8312 
       38.99        24.33        31.20        11.57         0.23        23.28 
TCGA-A4-A5Y0 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47O 
        8.28        58.45        25.08        44.61        19.56        16.87 
TCGA-B3-4104 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
       34.49        14.86        12.30        63.72        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       30.28        10.88         7.92        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7839 TCGA-DZ-6135 
       49.84        26.27        11.28         7.63        13.78        54.90 
TCGA-G7-6792 TCGA-G7-6796 TCGA-GL-7773 TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A561 
       48.62        34.82        12.92         4.60        19.99        27.65 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5ED TCGA-P4-AAVO 
        0.36        12.13        25.97        21.44        92.58        78.90 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 
       11.93        38.63        26.01        29.00        18.64        18.05 
TCGA-Y8-A8S1 
       13.28 

$subtype3
TCGA-KL-8324 TCGA-KL-8333 TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      141.73        98.33        87.91        25.91       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8409 TCGA-KO-8410 
        0.99         2.50        42.35        10.68        80.38        87.78 
TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 
       77.85        57.17        12.66        36.82        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       49.02        37.15        49.58        48.59        38.99        24.69 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       48.82        21.86        34.29         4.50        52.93        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 
       88.37        42.97        24.16        18.64        18.87        20.28 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 
        0.10       109.91        29.10        66.31        15.78        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 
       68.61        67.20        42.08        28.73        38.40        28.04 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 
        1.41         4.57         3.48         5.98        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 
       43.96         6.64        15.72        46.59         0.59        52.21 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       40.44        36.53        54.48        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-4849 
       45.30        27.42        10.29        65.29        29.03         2.27 
TCGA-B0-5077 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5098 
       43.30         7.30        15.09        10.95         8.05        52.08 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 
       15.95        90.87        29.95        19.30        11.80        21.60 
TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 
        1.94        14.76        15.78        56.78        60.33        56.94 
TCGA-B0-5703 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5639 
       39.55        47.97        89.49        35.90        11.77        32.98 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
       21.57         9.57         0.23         0.53         5.46        23.31 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5549 
       27.16        25.55        20.91        23.74        27.02         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 
       14.27         0.53         1.74         4.93       111.02        94.72 
TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4176 
      101.06        32.61         0.43        89.36        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 
       97.45         3.58        80.68         0.07        93.99        74.17 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       62.86        49.08        44.94        31.89        11.31        12.33 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4777 
        5.98        41.75        48.07        13.15        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4959 
       68.38        15.78        36.39        10.98         6.71        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 
       71.41        58.68        60.30        57.40        58.98        48.89 
TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
       45.50        46.45        31.30        25.81        36.95         3.88 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 
       16.47         5.82        45.07        18.51        37.02         6.35 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
        1.78        30.64         9.63        62.86        74.40        49.15 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
       42.44        37.22        27.02        31.79        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 
       34.95        31.27        59.84        46.55        63.25        65.69 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 
       58.95        11.05        21.24        79.66        74.27        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4892 TCGA-CJ-4893 
       71.87        66.21        69.86        30.64        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5672 
       51.29        58.92        49.28        54.48        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
       79.89        84.66        25.71        22.32        25.25        61.91 
TCGA-CJ-5683 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 
       62.10        60.99        53.42        75.58        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 
       64.57         5.39        85.78        73.18        66.31        74.66 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
       83.90        18.77        25.45        46.16        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 
       58.75         6.77        93.04        61.41        58.82        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5464 
       55.33        56.94        47.01        10.85        10.22        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 
       67.96        65.65        14.63        43.69        12.16        37.15 
TCGA-DV-5575 TCGA-DV-A4W0 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-G6-A8L8 
       56.84        66.02         3.91         4.18        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI 
        2.01        19.43        19.96        10.85        54.64        51.52 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B9-A44B TCGA-BQ-5877 TCGA-BQ-5882 
        8.48        12.99         9.63         2.10         8.88        21.63 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-EV-5902 
       13.25         7.66        11.97        20.12        79.86        19.00 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
        4.01        13.68        17.33        16.90         3.68         2.04 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-Y8-A8RZ 
        0.13        84.95        14.07        86.27         6.74 

subtype1 subtype2 subtype3 
    0.10     0.10     0.07 
subtype1 subtype2 subtype3 
  194.79   120.59   141.73 
subtype1 subtype2 subtype3 
   26.40    31.20    36.53 
[1] "0.1 - 194.8 (26.4)" "0.1 - 120.6 (31.2)" "0.1 - 141.7 (36.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     156       38        43       15
  subtype2     176       32        60       33
  subtype3     116       33        87       52
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        156      176      116
  STAGE II        38       32       33
  STAGE III       43       60       87
  STAGE IV        15       33       52
[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        T1  T2  T3  T4
  subtype1 162  45  48   6
  subtype2 180  39  80   3
  subtype3 120  39 123   6
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      162      180      120
  T2       45       39       39
  T3       48       80      123
  T4        6        3        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  76  12   3
  subtype2 116   9   2
  subtype3 125  22   1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       76      116      125
  N1       12        9       22
  N2        3        2        1
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 114   8
  subtype2 221  32
  subtype3 207  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    8
  subtype2  221   32
  subtype3  207   49
   clus
vv  subtype1 subtype2 subtype3
  0      114      221      207
  1        8       32       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  67 200
  subtype2 131 173
  subtype3  89 199
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67  200
  subtype2  131  173
  subtype3   89  199
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       67      131       89
  MALE        200      173      199
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 46                                29
  subtype2                  6                               247
  subtype3                 14                               248
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   192
  subtype2                                    51
  subtype3                                    26
D3V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          46        6       14
  KIDNEY CLEAR CELL RENAL CARCINOMA           29      247      248
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      192       51       26
[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"
D3V10, continuous
D3V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                        44
  subtype2                                0     2                        52
  subtype3                                0     5                        20
          vv
clus       WHITE
  subtype1   199
  subtype2   247
  subtype3   256
D3V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   8        2        5
  BLACK OR AFRICAN AMERICAN              44       52       20
  WHITE                                 199      247      256
[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"
D3V13, binary
          cls
clus         0   1
  subtype1  10 201
  subtype2  16 208
  subtype3  16 188
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  201
  subtype2   16  208
  subtype3   16  188
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10       16       16
  NOT HISPANIC OR LATINO      201      208      188
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  92  29
  subtype2 207  93
  subtype3 180  19
subtype1 subtype2 subtype3 
     121      300      199 
subtype1 subtype2 subtype3 
      29       93       19 
$subtype1
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E 
       86.10        77.85        57.17        61.58        63.95        12.16 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 
       72.07        57.37        45.93         3.32        28.47         3.62 
TCGA-B0-5083 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5702 
       34.36        52.08        62.89        19.30        17.59        52.77 
TCGA-B2-5636 TCGA-B4-5378 TCGA-B8-A54E TCGA-B8-A54K TCGA-BP-4177 TCGA-BP-4760 
       30.21         5.75        29.88        15.42        54.90        77.62 
TCGA-BP-4770 TCGA-BP-4795 TCGA-CJ-5681 TCGA-DV-5567 TCGA-DV-5576 TCGA-2K-A9WE 
       10.82        20.38        18.15        65.88        23.90         7.04 
TCGA-2Z-A9J9 TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7915 
       75.42        24.33        31.20        11.57        19.63         0.23 
TCGA-A4-8312 TCGA-AL-A5DJ TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 
       23.28        49.25        22.92        40.83        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-DZ-6131 
       10.88         7.92         2.76        44.84        26.27        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM 
       10.68        13.08         1.18        11.05         3.68         1.05 
TCGA-J7-8537 TCGA-MH-A857 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 
        0.13        21.44        42.94         6.61        92.58        12.85 
TCGA-Y8-A8S1 
       13.28 

$subtype2
TCGA-3Z-A93Z TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       12.66        88.37        42.97        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       55.76        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 
        0.10        11.18        10.62       109.91        73.08        60.92 
TCGA-AK-3434 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
       68.61        42.08        58.49        28.73        38.40        31.27 
TCGA-AK-3461 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       28.04         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       29.10        10.09         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       70.52        11.24        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       21.86        15.95        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       29.95        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 TCGA-B0-5703 
       60.33        84.92        90.12        35.57        56.94        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       61.32        97.41        35.90        21.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.53         4.64         5.46         0.36         0.23        16.80 
TCGA-B8-4153 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.05        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
        0.85        24.23        17.16         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4782 TCGA-BP-4801 
        4.93        17.36        16.27        14.17        11.64        36.95 
TCGA-BP-4993 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
        5.82        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4869 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 
        0.95        83.97        61.91        59.44        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       66.31        78.18        35.34        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
       83.90       103.43        18.77        25.45         0.59        58.75 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       43.69        45.96        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-7585 
       19.96        15.25        10.85        51.52        38.99        35.18 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5882 
       19.56         0.46        14.86         8.88        43.20        21.63 
TCGA-BQ-5884 TCGA-BQ-5892 TCGA-F9-A97G TCGA-HE-A5NK TCGA-WN-A9G9 TCGA-WN-AB4C 
       26.04        11.97         0.43        73.25        26.01        29.00 

$subtype3
TCGA-B0-5707 TCGA-B8-4621 TCGA-B8-5546 TCGA-CZ-5469 TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       92.98        25.91        16.60        31.10        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JD 
       58.22       100.27        56.91         4.57        67.30        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP 
       56.81        54.64        35.67        26.43        30.71        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
       18.21        61.05         0.10        19.13         0.89        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       30.48        29.46        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-7173 
       16.31        15.75         8.28        12.99        12.46        44.61 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-5156 
       16.77         6.58        12.46        10.16        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5885 
       12.30        86.76        19.27        63.72        47.80        30.28 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       26.04         7.66         0.95       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-6789 
       54.90        34.19        19.00        24.89         2.40         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79        12.92        27.65        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25         0.36        12.13        25.97        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       87.22        84.95        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       17.75        12.49        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       28.80        26.89        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       52.11        30.67        25.68        27.39        12.99        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 
        6.02 

subtype1 subtype2 subtype3 
    0.13     0.10     0.10 
subtype1 subtype2 subtype3 
  151.96   120.59   194.79 
subtype1 subtype2 subtype3 
  42.350   28.935   21.340 
[1] "0.1 - 152.0 (42.4)" "0.1 - 120.6 (28.9)" "0.1 - 194.8 (21.3)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      52       30        27       15
  subtype2     139       28        80       53
  subtype3     147       16        30        7
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         52      139      147
  STAGE II        30       28       16
  STAGE III       27       80       30
  STAGE IV        15       53        7
[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        T1  T2  T3  T4
  subtype1  53  30  35   6
  subtype2 143  38 115   5
  subtype3 152  20  30   1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       53      143      152
  T2       30       38       20
  T3       35      115       30
  T4        6        5        1
[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
  subtype1  54  13   3
  subtype2 124  10   0
  subtype3  36  10   3
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       54      124       36
  N1       13       10       10
  N2        3        0        3
[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"
D4V6, binary
          cls
clus         0   1
  subtype1  66   9
  subtype2 221  51
  subtype3  62   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    9
  subtype2  221   51
  subtype3   62    3
   clus
vv  subtype1 subtype2 subtype3
  0       66      221       62
  1        9       51        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1  58  67
  subtype2 102 199
  subtype3  49 161
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   67
  subtype2  102  199
  subtype3   49  161
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       58      102       49
  MALE         67      199      161
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 66                                25
  subtype2                  0                               286
  subtype3                  0                                 4
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    34
  subtype2                                    15
  subtype3                                   206
D4V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          66        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           25      286        4
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       34       15      206
[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"
D4V10, continuous
D4V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                        23
  subtype2                                0     2                        36
  subtype3                                2     1                        43
          vv
clus       WHITE
  subtype1    93
  subtype2   258
  subtype3   153
D4V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        2
  ASIAN                                   5        2        1
  BLACK OR AFRICAN AMERICAN              23       36       43
  WHITE                                  93      258      153
[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"
D4V13, binary
          cls
clus         0   1
  subtype1   7  77
  subtype2   9 239
  subtype3  10 177
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   77
  subtype2    9  239
  subtype3   10  177
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        9       10
  NOT HISPANIC OR LATINO       77      239      177
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  97  18
  subtype2  99  96
  subtype3 228  69
  subtype4 214  28
subtype1 subtype2 subtype3 subtype4 
     115      195      297      242 
subtype1 subtype2 subtype3 subtype4 
      18       96       69       28 
$subtype1
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3328 TCGA-A3-3374 
       57.17        61.58        63.95        24.16        45.53        43.20 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 
       84.36        72.07        57.37        46.78        40.01        45.93 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-5083 TCGA-B0-5117 
       12.13        40.70         3.62        68.71        34.36        17.59 
TCGA-B0-5691 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B8-4619 
      112.80        52.77        32.61        30.21         5.75        17.19 
TCGA-B8-5546 TCGA-B8-A54K TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4760 TCGA-BP-4769 
       16.60        15.42        54.90        21.21        77.62        61.68 
TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4994 TCGA-BP-4995 TCGA-CJ-4642 TCGA-CJ-5681 
       60.95        20.38        43.00        45.07        53.52        18.15 
TCGA-CW-5591 TCGA-DV-5567 TCGA-DV-5573 TCGA-DV-5576 TCGA-2Z-A9J9 TCGA-2Z-A9JN 
       74.66        65.88        37.15        23.90        75.42        24.33 
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8312 TCGA-B3-4104 TCGA-B9-A69E TCGA-BQ-5883 
       19.63         0.23        23.28        34.49        14.86        40.83 
TCGA-BQ-5889 TCGA-BQ-7055 TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-6793 TCGA-GL-7966 
       10.88        26.27        79.86         1.18        11.05         3.68 
TCGA-MH-A857 
       21.44 

$subtype2
TCGA-KN-8427 TCGA-KO-8404 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.99        10.68         0.53        49.08        49.02        37.15 
TCGA-A3-3323 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 
       36.36         4.50        52.93        20.71        18.87        20.28 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4688 
      109.91        29.10        60.92        67.20        42.08         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 
       65.10         5.98        19.73        43.96         6.64        15.72 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        0.59        52.21        33.50         6.02        40.44        36.53 
TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       29.10        40.70        45.30        56.68        11.64        10.29 
TCGA-B0-4848 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 
       29.03        11.24        11.90         7.30        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5108 
        8.05         2.24        21.86        62.89        52.54        29.95 
TCGA-B0-5109 TCGA-B0-5400 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5709 TCGA-B2-5633 
       19.30        37.22        56.94        79.36       102.48        11.77 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5158 
       21.57         0.23         5.46        23.31        25.55        20.91 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54F 
        1.18        27.02        17.16        14.27         0.53        17.06 
TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        4.93        14.17        93.34        89.36        23.05        62.24 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 
       64.27        53.42         0.07        93.99        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 
       49.84        11.31        12.33        33.99         5.98        41.75 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 
       10.82         5.33        68.38        15.78        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 
       10.98        37.25         6.71        47.97        71.41        58.68 
TCGA-BP-4967 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
        6.74        14.24        48.89        46.45        31.30        25.81 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5009 TCGA-BP-5010 
       27.22         3.88        16.47        30.64        36.23        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 
        6.35        79.30        30.64        62.86        74.40        38.30 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       13.35        27.02        31.79        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4641 TCGA-CJ-4868 
       44.55        46.55        63.25        73.22        54.61        21.24 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 
       83.97        79.66        47.18        74.27        66.21        61.91 
TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 
       51.52        68.55        26.93        39.45        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       49.97        54.48         3.06         4.57        18.81        63.88 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       84.66        25.71        22.32        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       62.66         7.36        66.31         1.35        83.90        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4865 
       46.16        47.08        69.21         6.77        14.66         5.46 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       56.28        10.85        57.21        22.52         1.94        31.10 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5568 TCGA-DV-5574 
       67.96        65.65        14.63        22.78        12.16        66.28 
TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A564 TCGA-MM-A84U TCGA-2Z-A9JK TCGA-4A-A93Y 
        3.91        70.13        19.96        15.25        38.99        11.57 
TCGA-BQ-5879 TCGA-BQ-5887 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-F9-A4JJ 
       22.92        25.35         7.92         2.76        44.84        10.68 
TCGA-G7-6789 TCGA-P4-A5E8 TCGA-P4-A5EA 
        4.01        42.94         6.61 

$subtype3
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 
       12.66        36.82        47.21        39.16        49.58        48.59 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3335 
       38.99        24.69        37.38        23.21        48.82        21.86 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       31.07        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       82.32        51.25        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ 
       53.29        55.76        18.64        28.31        65.52        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 
       22.65         0.10         0.10        11.18        10.62        73.08 
TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       66.31        68.61        48.36        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 
       22.45        38.40        31.27        28.04         1.41         2.53 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        7.82         2.14         3.16         3.25        20.25        46.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 
        5.52        45.07        16.77        14.93        54.48        10.09 
TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 
       78.44        27.42        53.88         6.71        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 
       25.32        18.51        15.95        90.87        90.48        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       21.44        14.76        79.17        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 
       46.68        56.78        84.92        90.12        35.57        39.55 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      120.59        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
       35.90        12.30        21.30        31.30        10.36        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       16.67         9.57         1.25         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 
       16.80        27.16        27.55        25.05        24.66        23.01 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 
       23.74         0.85        24.23         6.38        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
       27.29         1.74         8.42        17.36        16.27       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 
        0.43        77.03        61.78        97.45         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68        37.25        15.16        18.48        52.24 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 
       54.77        49.08        44.94        12.23        31.89        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       72.59        77.98        44.15        71.80        48.07        13.15 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4789 
       61.97        60.59        13.51        56.91        11.64        48.95 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
       36.95         6.94        87.45        63.62        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       61.51        57.40        58.98        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 
       47.11        53.65        14.93        36.07        33.34        36.95 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45         5.82        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 
       27.62        37.48        35.21        48.10         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5201 
       22.78        33.24        23.47        13.41        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 
        0.95        59.84        75.88        65.69        58.95        11.05 
TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 
       49.25        75.06        77.36        64.27        71.87        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 
       69.86        64.18        30.64        63.98        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       27.65        59.44        50.24        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 
       49.28        50.33        45.14        72.00        79.89        18.87 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
       83.77        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       73.18        78.18        35.34       105.93       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        0.59        58.75        60.59        63.39        93.04        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       56.94        55.33        47.01        10.22        21.76        47.54 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 
        2.40        12.69        80.19        12.26        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       45.96        11.67        56.84        66.02        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MW-A4EC TCGA-AL-3473 TCGA-BQ-5892 
       10.85        25.08        11.97 

$subtype4
TCGA-6D-AA2E TCGA-A3-3363 TCGA-AK-3456 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5697 
       12.16        10.49        37.58        52.08        30.48        60.33 
TCGA-B0-5707 TCGA-B2-4098 TCGA-B4-5835 TCGA-B8-4621 TCGA-B8-A54E TCGA-BP-4756 
       92.98         1.68         0.53        25.91        29.88        12.30 
TCGA-CJ-4638 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       14.17         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
       56.91         4.57        67.30        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        35.67        26.43        30.71        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       18.21        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       16.64        30.48        29.46        25.64        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
        9.63        58.45        76.64        13.55        30.35        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       47.80        21.63        26.04        30.28        26.04        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.66         0.95       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        13.08         2.40         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
       25.97        15.48        99.78        87.22        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W 
       14.07        47.90        47.44        33.04        28.80        26.89 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  151.96   109.91   120.59   194.79 
subtype1 subtype2 subtype3 subtype4 
   47.24    28.87    37.38    21.65 
[1] "0.2 - 152.0 (47.2)" "0.1 - 109.9 (28.9)" "0.1 - 120.6 (37.4)"
[4] "0.1 - 194.8 (21.6)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      56       33        19       10
  subtype2      57       20        70       48
  subtype3     173       31        61       33
  subtype4     168       19        39       10
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         56       57      173      168
  STAGE II        33       20       31       19
  STAGE III       19       70       61       39
  STAGE IV        10       48       33       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        T1  T2  T3  T4
  subtype1  56  33  27   2
  subtype2  62  24  99  10
  subtype3 174  38  84   2
  subtype4 176  28  41   1
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       56       62      174      176
  T2       33       24       38       28
  T3       27       99       84       41
  T4        2       10        2        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  60   5   3
  subtype2  85  20   1
  subtype3 130   2   0
  subtype4  48  15   2
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       60       85      130       48
  N1        5       20        2       15
  N2        3        1        0        2
[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"
D5V6, binary
          cls
clus         0   1
  subtype1  72   7
  subtype2 139  44
  subtype3 248  32
  subtype4  88   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    7
  subtype2  139   44
  subtype3  248   32
  subtype4   88    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       72      139      248       88
  1        7       44       32        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"
D5V7, binary
          cls
clus         0   1
  subtype1  47  71
  subtype2  51 145
  subtype3 122 176
  subtype4  66 187
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   71
  subtype2   51  145
  subtype3  122  176
  subtype4   66  187
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       47       51      122       66
  MALE         71      145      176      187
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 64                                38
  subtype2                  2                               182
  subtype3                  0                               296
  subtype4                  0                                13
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    16
  subtype2                                    12
  subtype3                                     2
  subtype4                                   240
D5V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          64        2        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           38      182      296       13
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       16       12        2      240
[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"
D5V10, continuous
D5V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        19
  subtype2                                0     4                        13
  subtype3                                0     2                        27
  subtype4                                2     6                        57
          vv
clus       WHITE
  subtype1    93
  subtype2   176
  subtype3   264
  subtype4   175
D5V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        2
  ASIAN                                   3        4        2        6
  BLACK OR AFRICAN AMERICAN              19       13       27       57
  WHITE                                  93      176      264      175
[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"
D5V13, binary
          cls
clus         0   1
  subtype1   4  76
  subtype2   7 125
  subtype3  19 192
  subtype4  12 210
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   76
  subtype2    7  125
  subtype3   19  192
  subtype4   12  210
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        7       19       12
  NOT HISPANIC OR LATINO       76      125      192      210
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  75  12
  subtype2  97  37
  subtype3 163  45
  subtype4  82  76
  subtype5  81  29
  subtype6 140  12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      87      134      208      158      110      152 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12       37       45       76       29       12 
$subtype1
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3328 TCGA-A3-3374 TCGA-AK-3427 
       57.17        61.58        63.95        45.53        43.20        84.36 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 
       72.07        57.37        46.78        40.01        45.93        12.13 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-5083 TCGA-B0-5117 TCGA-B2-3923 
       40.70         3.62        68.71        34.36        17.59        32.61 
TCGA-B8-4619 TCGA-BP-4334 TCGA-BP-4994 TCGA-BP-4995 TCGA-2Z-A9JN TCGA-A4-8312 
       17.19        21.21        43.00        45.07        24.33        23.28 
TCGA-BQ-5883 TCGA-BQ-7055 TCGA-MH-A857 
       40.83        26.27        21.44 

$subtype2
TCGA-KN-8427 TCGA-KO-8404 TCGA-6D-AA2E TCGA-A3-3313 TCGA-AK-3456 TCGA-B0-4688 
        0.99        10.68        12.16        24.16        37.58         3.32 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 
       28.47         1.38         7.30        52.08        62.89        30.48 
TCGA-B0-5109 TCGA-B0-5702 TCGA-B2-4098 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 
       19.30        52.77         1.68        30.21         5.75         0.53 
TCGA-B8-5546 TCGA-B8-A54E TCGA-B8-A54K TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4760 
       16.60        29.88        15.42        54.90        12.30        77.62 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4795 TCGA-CJ-4642 TCGA-CJ-5681 
       61.68        10.82        60.95        20.38        53.52        18.15 
TCGA-CW-5591 TCGA-CW-6087 TCGA-DV-5567 TCGA-DV-5576 TCGA-2Z-A9J2 TCGA-2Z-A9J8 
       74.66         1.35        65.88        23.90        59.01        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JO TCGA-4A-A93X 
       75.42        34.85        51.52        35.67        31.20        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
       11.57        19.63        61.05        35.18         0.23        29.46 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 
       19.73        12.46         8.48         8.28        12.99         9.63 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 
       49.25        19.56        16.77         0.46        10.09        34.49 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61         2.10         6.81         0.16        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
       93.34        44.84        61.28        49.84        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
        7.17        79.86        80.88        10.68        13.08         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
        0.43         4.01        11.05        13.68        17.33        16.90 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A9DE TCGA-HE-A5NK 
      194.79        12.92         3.68         1.05         4.60        73.25 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A855 
       19.99         2.04        22.26         0.13        30.38        12.13 
TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       25.97        99.78        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM 
       52.27        50.60        78.90        12.85        14.07        11.93 
TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A896 
       38.63        18.02        21.93        86.27        29.00        18.64 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
        6.74        13.28 

$subtype3
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 
       12.66        36.82        47.21        39.16        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3335 TCGA-A3-3343 
       38.99        24.69        37.38        23.21        21.86        31.07 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 
       29.92        18.44        51.25        28.70        74.63        24.16 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NN TCGA-A3-A8OV 
       55.76        18.64        28.31        20.28         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3434 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
       10.62        73.08        68.61        28.73        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
       28.04         1.41         2.14         3.25        20.25        46.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4841 TCGA-B0-4845 
        5.52        45.07        14.93        10.09         6.71        65.29 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5106 TCGA-B0-5115 
       26.07         2.27        43.30        18.51        52.54        26.20 
TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5694 
       21.60        18.21        21.44        14.76       112.80        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 
       46.68        56.78        84.92        90.12        35.57        56.94 
TCGA-B0-5703 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       39.55        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5834 TCGA-B4-5843 TCGA-B8-4153 TCGA-B8-4622 
       21.57        16.67         1.25         0.36        25.05        23.01 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-A54J TCGA-BP-4158 
        0.85        24.23        17.16         6.38        17.36       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4329 
       85.51        94.72        90.28        62.24        61.78        27.78 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4353 TCGA-BP-4758 
       80.68        37.25        49.08        44.94        12.33        72.59 
TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4777 
       77.98        44.15        71.80        13.15        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 
       68.38        11.64        48.95        36.53        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        6.94        63.62        60.30        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
       14.24        45.50        47.11        53.65        14.93        33.34 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       46.45        16.47         5.82        30.64        41.62        18.51 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5173 
       37.02        27.62        37.48        35.21        48.10         1.78 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 
       74.40        38.30        42.44        37.25        37.22        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 
       27.02        33.24        23.47        13.41        24.62        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4870 TCGA-CJ-4871 
       31.27         0.95        46.55        65.69        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4894 
       47.18        77.36        64.27        69.86        30.64        27.65 
TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5672 TCGA-CJ-5675 
       50.24        51.29        49.28        50.33        72.00        79.89 
TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CW-5580 
       18.87        61.91        62.10        73.35        53.26        64.57 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-6088 
       92.02         5.39        85.78        78.18        35.34       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 
      103.43        25.45        14.66        60.59        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       63.42         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5470 
       55.33        47.01        10.85        21.76        22.52        12.69 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-A4W0 
       45.96        12.16        11.67        37.15        66.28        66.02 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-MM-A563 
        6.77         4.18        10.29        19.43 

$subtype4
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 
        0.53        49.08        49.02        37.15         4.50        52.93 
TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3431 
       88.37        20.71        18.87       109.91        29.10        60.92 
TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3451 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       67.20        42.08        48.69         1.41         4.57         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 
       19.00        65.10         5.98        19.73        43.96         6.64 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 
       15.72         0.59        52.21        33.50         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       36.53        29.10        40.70        45.30        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5092 
       10.29        29.03        20.94        11.24        11.90        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5400 
       10.95         8.05         2.24        21.86        29.95        37.22 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 
       79.36       102.48         0.23         5.46        23.31        25.55 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D 
       20.91         1.18        27.02        14.27         0.53        27.29 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
       17.06         1.74         4.93        93.34         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 
       23.05        64.27        53.42         0.07        93.99        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 
       62.86        49.84        11.31        33.99         5.98        41.75 
TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4804 
        5.33        15.78        36.39        10.98        37.25        47.97 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-4983 TCGA-BP-4985 
       87.45        71.41        58.68        48.89        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 
       25.81        27.22         3.88        36.23        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5196 
       79.30        74.20        30.64        62.86        31.79        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4641 
       19.82        44.55        63.25        73.22        14.17        54.61 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       21.24        83.97        74.27        66.21        61.91        57.83 
TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 
       51.52        68.55        26.93        39.45        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 
       49.97        54.48         3.06        18.81        63.88        84.66 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       25.71        22.32        25.25        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 
       62.66         7.36        66.31        83.90        18.77        46.16 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 
       47.08        69.21         6.77        61.41        58.82        56.28 
TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
       10.22        57.21         1.94        31.10        67.96         3.91 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A564 TCGA-MM-A84U TCGA-2Z-A9JK TCGA-AL-3473 
        7.96        70.13        19.96        15.25        38.99        25.08 
TCGA-BQ-5892 TCGA-WN-A9G9 
       11.97        26.01 

$subtype5
TCGA-A3-3320 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3370 
       49.58        48.82        45.53        42.97        82.32        74.76 
TCGA-A3-3373 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-AK-3429 
       53.29        65.52        15.39        22.65         0.10        66.31 
TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 
       48.36        58.49        22.45         2.53         7.82         3.16 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4846 
       16.77        54.48        78.44        27.42        53.88        39.45 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       36.85        70.52        25.32        15.95        90.87        90.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5690 TCGA-B0-5692 
       35.90        11.80         1.94        16.21        79.17        48.89 
TCGA-B0-5693 TCGA-B0-5705 TCGA-B0-5712 TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5844 
      101.13       120.59        89.49         9.57         4.64         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5552 
       16.80        27.16        27.55        24.66        23.74        34.39 
TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4162 TCGA-BP-4164 
       14.30         8.42        16.27        14.17       101.06        32.61 
TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4335 
       99.85        77.03        97.45         3.58        62.07        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 
       18.48        52.24        54.77        12.23        31.89        31.33 
TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4972 
       48.07        61.97        60.59        61.22        58.98        49.38 
TCGA-BP-4974 TCGA-BP-4981 TCGA-BP-4987 TCGA-BP-5001 TCGA-BP-5176 TCGA-BP-5177 
        7.23        36.07        36.95        38.70        52.27         9.63 
TCGA-BP-5181 TCGA-BP-5186 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       49.15        22.78        59.84        75.88        58.95        11.05 
TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 
       75.06        71.87        64.18        63.98        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5686 
       59.44        58.92        49.18        45.14         4.57        67.00 
TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5587 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 
       83.77        81.83        73.18         0.59        58.75        63.39 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-DV-5575 TCGA-EU-5904 TCGA-G6-A8L8 
       47.54         2.40        80.19        56.84        18.12        35.87 
TCGA-GK-A6C7 TCGA-MW-A4EC 
        2.01        10.85 

$subtype6
TCGA-A3-3363 TCGA-B0-5697 TCGA-B0-5707 TCGA-B8-4621 TCGA-2K-A9WE TCGA-2Z-A9J1 
       10.49        60.33        92.98        25.91         7.04        75.55 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       58.22       100.27        56.91         4.57        56.81        54.64 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       26.43        30.71        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
       22.49         0.13        18.21         0.10        19.13         0.89 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       16.64        30.48        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       19.63        14.33        16.96        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU 
       58.45        76.64        13.55        30.35        44.61         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A657 
        7.33        21.67        24.56        16.87         3.55         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
       19.23        17.49        47.80        48.26        96.92        50.40 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       19.00        24.89         2.40        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       34.82        25.15        25.84         6.38        17.98        80.65 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
       27.65        12.43        17.95         0.89        11.21        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83S 
       13.41        11.84        56.75         5.49        16.80        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       88.24        67.17        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
       29.10        11.41        34.29        27.78        27.65        20.25 
TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71R 
        0.36        15.48        87.22        16.01        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN 
       47.44        33.04        28.80        26.89        27.06        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       14.83         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       27.39        12.99        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    2.50     0.13     0.10     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  151.96   194.79   112.80   109.91   120.59   129.86 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  52.270   19.595   35.735   32.630   46.535   23.640 
[1] "2.5 - 152.0 (52.3)" "0.1 - 194.8 (19.6)" "0.1 - 112.8 (35.7)"
[4] "0.1 - 109.9 (32.6)" "0.1 - 120.6 (46.5)" "0.1 - 129.9 (23.6)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      38       30        15        5
  subtype2      59        8        42       21
  subtype3     122       21        40       25
  subtype4      39       20        61       39
  subtype5      72        9        22        8
  subtype6     124       15         9        3
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         38       59      122       39       72      124
  STAGE II        30        8       21       20        9       15
  STAGE III       15       42       40       61       22        9
  STAGE IV         5       21       25       39        8        3
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  38  30  19   1
  subtype2  64  12  50   7
  subtype3 123  27  56   2
  subtype4  43  24  87   5
  subtype5  72  10  29   0
  subtype6 128  20  10   0
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       38       64      123       43       72      128
  T2       30       12       27       24       10       20
  T3       19       50       56       87       29       10
  T4        1        7        2        5        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 51  2  2
  subtype2 33 26  3
  subtype3 77  2  0
  subtype4 76 11  0
  subtype5 59  1  0
  subtype6 27  0  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       51       33       77       76       59       27
  N1        2       26        2       11        1        0
  N2        2        3        0        0        0        1
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1  55   3
  subtype2  62  14
  subtype3 177  24
  subtype4 109  40
  subtype5  93   8
  subtype6  51   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    3
  subtype2   62   14
  subtype3  177   24
  subtype4  109   40
  subtype5   93    8
  subtype6   51    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       55       62      177      109       93       51
  1        3       14       24       40        8        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  33  55
  subtype2  56  82
  subtype3  12 196
  subtype4  48 111
  subtype5 108   3
  subtype6  29 132
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   55
  subtype2   56   82
  subtype3   12  196
  subtype4   48  111
  subtype5  108    3
  subtype6   29  132
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       33       56       12       48      108       29
  MALE         55       82      196      111        3      132
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 64                                19
  subtype2                  2                                32
  subtype3                  0                               208
  subtype4                  0                               155
  subtype5                  0                               111
  subtype6                  0                                 4
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     5
  subtype2                                   104
  subtype3                                     0
  subtype4                                     4
  subtype5                                     0
  subtype6                                   157
D6V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          64        2        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           19       32      208      155
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        5      104        0        4
                                       clus
vv                                      subtype5 subtype6
  KIDNEY CHROMOPHOBE                           0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA          111        4
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        0      157
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12       24        6        7        2       41 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype6" "subtype4" "subtype3" "subtype2"
[19] "subtype4" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
[25] "subtype2" "subtype6" "subtype6" "subtype2" "subtype2" "subtype2"
[31] "subtype4" "subtype6" "subtype1" "subtype2" "subtype6" "subtype6"
[37] "subtype2" "subtype6" "subtype2" "subtype2" "subtype2" "subtype2"
[43] "subtype6" "subtype6" "subtype6" "subtype6" "subtype6" "subtype6"
[49] "subtype2" "subtype2" "subtype6" "subtype6" "subtype6" "subtype2"
[55] "subtype2" "subtype6" "subtype2" "subtype6" "subtype2" "subtype6"
[61] "subtype6" "subtype6" "subtype6" "subtype2" "subtype6" "subtype6"
[67] "subtype6" "subtype6" "subtype2" "subtype6" "subtype2" "subtype6"
[73] "subtype2" "subtype6" "subtype6" "subtype6" "subtype6" "subtype2"
[79] "subtype6" "subtype6" "subtype6" "subtype6" "subtype6" "subtype6"
[85] "subtype6" "subtype4" "subtype6" "subtype2" "subtype6" "subtype2"
D6V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                        10
  subtype2                                0     5                        36
  subtype3                                0     3                        14
  subtype4                                0     2                        11
  subtype5                                0     1                        12
  subtype6                                2     2                        33
          vv
clus       WHITE
  subtype1    74
  subtype2    92
  subtype3   186
  subtype4   145
  subtype5    97
  subtype6   114
D6V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   2        5        3        2        1
  BLACK OR AFRICAN AMERICAN              10       36       14       11       12
  WHITE                                  74       92      186      145       97
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        2
  ASIAN                                   2
  BLACK OR AFRICAN AMERICAN              33
  WHITE                                 114
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
          cls
clus         0   1
  subtype1   4  51
  subtype2   8 105
  subtype3   9 131
  subtype4   5 110
  subtype5  11  67
  subtype6   5 139
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   51
  subtype2    8  105
  subtype3    9  131
  subtype4    5  110
  subtype5   11   67
  subtype6    5  139
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            4        8        9        5       11        5
  NOT HISPANIC OR LATINO       51      105      131      110       67      139
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 265  38
  subtype2 120  66
  subtype3 239 105
subtype1 subtype2 subtype3 
     303      186      344 
subtype1 subtype2 subtype3 
      38       66      105 
$subtype1
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       73.91        71.41        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       11.21        59.08       115.00        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3363 TCGA-A3-3374 
       77.85        57.17        61.58        63.95        10.49        43.20 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 
       72.07        57.37        46.78        40.01        45.93        37.58 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5117 
       40.70         3.62         7.30        52.08        30.48        17.59 
TCGA-B0-5707 TCGA-B2-4098 TCGA-B4-5835 TCGA-B8-4621 TCGA-B8-A54D TCGA-B8-A54E 
       92.98         1.68         0.53        25.91        27.29        29.88 
TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4994 TCGA-CJ-4873 TCGA-CJ-4900 TCGA-2K-A9WE 
       21.21         5.98        43.00        74.27        56.35         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       35.67        26.43        30.71        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 
       16.18        22.49         0.13        12.82        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
        0.10        35.18        19.13         0.89        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ 
       58.45        76.64        13.55        30.35        25.08        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
        3.55        16.77         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        86.76        19.27        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       21.63        26.04        30.28        26.04        13.25         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        96.92        61.28 
TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       50.40        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7Q0 
       51.19        61.02        54.90        34.19        19.00        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         0.43        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R 
       17.33        16.90       194.79        12.92        27.65        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 
        2.04        85.78        88.24        67.17        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       92.58        52.27        50.60        78.90        12.85        17.75 
TCGA-PJ-A8JU TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W 
       12.49        47.90        47.44        33.04        28.80        26.89 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       48.30        43.76        18.02        60.03        14.83         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       25.28         6.74         6.02 

$subtype2
TCGA-KL-8333 TCGA-KL-8344 TCGA-KM-8441 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 
       98.33        28.80        28.80         0.99       100.87        10.68 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       12.66        12.16         0.53        24.16        49.08        49.02 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3387 TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-AK-3425 
       52.93        45.53        20.28         0.10         0.10       109.91 
TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3451 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 
       29.10        60.92        48.69        12.13         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 
        4.57         3.48        19.00         1.38        65.10         5.98 
TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-4827 TCGA-B0-4843 
       43.96        46.59         0.59         6.02        29.10        11.64 
TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5095 TCGA-B0-5096 
       70.52        11.24        11.90        34.36         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5120 TCGA-B0-5400 
       21.86        62.89        29.95        19.30        16.21        37.22 
TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-5635 
      112.80        52.77       102.48        97.41        32.61        10.36 
TCGA-B2-5636 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5162 TCGA-B8-5163 
       30.21         5.46        23.31        17.19         1.18        27.02 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A54H 
       17.16        14.27         0.53        34.39        17.06         8.42 
TCGA-B8-A54I TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4167 
        4.93        15.42        16.27        14.17        94.72        89.36 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4337 
       23.05        62.24        54.90        80.68        37.25         0.07 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       52.24        62.86        49.84        11.31        12.33        33.99 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4787 
       77.62        44.15        71.80        61.68        10.82        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       48.95        36.53        20.38        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4982 TCGA-BP-4983 
       63.62        58.68        14.24        48.89        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 
       31.30        25.81        27.22         3.88        30.64        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
       28.87         6.35         9.63        38.30        37.25        22.78 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4881 TCGA-CJ-4882 
       33.47        19.82        59.84        63.25        66.21        61.91 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       63.98        68.55        39.45        49.18        49.28        50.33 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5677 TCGA-CJ-5689 TCGA-CJ-6031 
        3.06        18.81        63.88        25.71        53.26        62.66 
TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 
        7.36        66.31         1.35        83.90        18.77        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5988 TCGA-DV-5574 TCGA-DV-5576 
       69.21         6.77        56.28        22.78        66.28        23.90 
TCGA-DV-A4W0 TCGA-EU-5905 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
       66.02         3.91        70.13        35.87        19.43        15.25 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7915 
       38.99        24.33        31.20        11.57        19.63         0.23 
TCGA-AL-7173 TCGA-B1-A656 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
       44.61         0.46         8.88        22.92        40.83        25.35 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 
       10.88         2.76        93.34        44.84        49.84        20.12 
TCGA-DW-7834 TCGA-DZ-6132 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 
      129.86        80.88        24.89        10.68         4.01        11.05 
TCGA-G7-A8LE TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-KV-A6GD TCGA-MH-A857 
       80.65         3.68         1.05        22.26        11.97        21.44 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       16.01        14.07        11.93        21.93        86.27        13.28 

$subtype3
TCGA-KN-8436 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       42.35        47.21        39.16        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3351 
       36.36        38.99        37.38        48.82         4.50        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        42.97        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8OV TCGA-A3-A8OW 
       28.31        65.52        15.39        22.65        11.18        10.62 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 
       84.36        73.08        66.31        15.78        68.61        67.20 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 
       48.36        42.08        58.49        28.73        22.45        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4701 TCGA-B0-4706 
       31.27        28.04         2.53        28.47         7.82         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       19.73         3.16         6.64         3.25        20.25        15.72 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 
        5.52        52.21        45.07        33.50        16.77        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       36.53        14.93        54.48        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       36.85        20.94        43.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5110 
       10.95        15.95        90.87        90.48        52.54        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
       11.80        26.20        21.60         1.94        18.21        21.44 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76        79.17        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 
       56.78        60.33        84.92        90.12        35.57        56.94 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       39.55       120.59        79.36        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       61.32        35.90        12.30        21.30        31.30        11.77 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        1.25         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       27.55        25.05        24.66        25.55        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5553 
       23.74         0.85        24.23        16.60         6.38        14.30 
TCGA-B8-A54G TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        1.74        17.36       111.02        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
       93.34        32.61        99.85         0.43        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 
       97.45        53.42         3.58        27.78        62.07        15.16 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        74.17        54.77        49.08        44.94 
TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       31.89        31.33        12.30        72.59        77.98        41.75 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       48.07        13.15         5.33        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       68.38        11.64        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        6.71        87.45        60.30        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       58.98        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       14.93        36.07        36.95        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5009 
       45.07        18.51        38.70        37.02        37.48        36.23 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 
       62.86        74.40        49.15        42.44        37.22        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4637 
       44.55        34.95        31.27         0.95        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4875 
       11.05        83.97        49.25        79.66        47.18        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       64.27        71.87        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
       51.52        26.93        50.01        24.66        27.65        59.44 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4912 
       50.24        47.67        49.97        51.29        58.92        54.48 
TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
       45.14         4.57        72.00        79.89        84.66        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CW-5580 
       67.00        60.99        53.42        75.58        83.77        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
       35.34        74.66       105.93       103.43        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        14.63        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
       12.16        11.67        37.15        56.84        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        4.18         7.96        10.29         2.01        19.96        10.85 
TCGA-BQ-5892 TCGA-WN-A9G9 
       11.97        26.01 

subtype1 subtype2 subtype3 
    0.10     0.07     0.23 
subtype1 subtype2 subtype3 
  194.79   129.86   120.59 
subtype1 subtype2 subtype3 
  26.430   26.415   37.235 
[1] "0.1 - 194.8 (26.4)" "0.1 - 129.9 (26.4)" "0.2 - 120.6 (37.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     183       47        55       15
  subtype2      85       17        51       33
  subtype3     173       37        83       52
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        183       85      173
  STAGE II        47       17       37
  STAGE III       55       51       83
  STAGE IV        15       33       52
[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        T1  T2  T3  T4
  subtype1 191  56  59   4
  subtype2  87  18  72   9
  subtype3 177  47 119   2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      191       87      177
  T2       56       18       47
  T3       59       72      119
  T4        4        9        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  88  20   3
  subtype2  73  16   3
  subtype3 150   7   0
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       88       73      150
  N1       20       16        7
  N2        3        3        0
[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"
D7V6, binary
          cls
clus         0   1
  subtype1 128  11
  subtype2 123  26
  subtype3 280  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  128   11
  subtype2  123   26
  subtype3  280   52
   clus
vv  subtype1 subtype2 subtype3
  0      128      123      280
  1       11       26       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  92 224
  subtype2  67 121
  subtype3 121 224
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  224
  subtype2   67  121
  subtype3  121  224
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       92       67      121
  MALE        224      121      224
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 59                                25
  subtype2                  6                               145
  subtype3                  1                               342
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   232
  subtype2                                    37
  subtype3                                     2
D7V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          59        6        1
  KIDNEY CLEAR CELL RENAL CARCINOMA           25      145      342
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      232       37        2
[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"
D7V10, continuous
D7V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                        58
  subtype2                                0     3                        37
  subtype3                                0     4                        21
          vv
clus       WHITE
  subtype1   233
  subtype2   145
  subtype3   314
D7V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   8        3        4
  BLACK OR AFRICAN AMERICAN              58       37       21
  WHITE                                 233      145      314
[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"
D7V13, binary
          cls
clus         0   1
  subtype1  14 241
  subtype2   7 124
  subtype3  19 229
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  241
  subtype2    7  124
  subtype3   19  229
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        7       19
  NOT HISPANIC OR LATINO      241      124      229
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  64  12
  subtype2 387 183
  subtype3 173  14
subtype1 subtype2 subtype3 
      76      570      187 
subtype1 subtype2 subtype3 
      12      183       14 
$subtype1
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
      151.96        44.91        47.24        49.97       123.12        51.06 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
       11.21        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3374 
       86.10        77.85        57.17        61.58        63.95        43.20 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3465 
       84.36        72.07        57.37        46.78        40.01        12.13 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-5083 TCGA-B0-5117 TCGA-B2-3923 
       40.70         3.62        68.71        34.36        17.59        32.61 
TCGA-B8-4619 TCGA-BP-4334 TCGA-BP-4994 TCGA-BQ-7055 
       17.19        21.21        43.00        26.27 

$subtype2
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 
       23.28        28.80        31.33         0.99       100.87        10.68 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        12.16        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       38.99        37.38        48.82         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
       29.92        88.37        42.97        51.25        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4688 
       22.45        37.58        38.40        31.27        28.04         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 
       46.68        56.78        60.33        84.92        90.12        35.57 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       47.97        96.36        89.49        61.32        97.41        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 
       12.30        21.30        31.30        11.77        10.36        30.21 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.55        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
        3.58        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.84        49.08        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4776 
       13.15        61.68        10.82         5.33        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       45.07        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        49.28        50.33        54.48        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       35.34        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       19.96        15.25        10.85        59.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7287 
       35.67        38.99        24.33        31.20        11.57        19.63 
TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A5Y1 
       35.18         0.23        29.46        23.28        19.73        12.99 
TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-A656 TCGA-B3-4104 
        9.63        25.08        44.61        49.25         0.46        34.49 
TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5883 
       14.86        19.27         8.88        22.92        43.20        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       11.97         7.92         2.76        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-7834 
       49.84        20.12        11.28         7.17        11.61       129.86 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY 
       79.86        80.88        61.02        24.89        10.68         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
        0.43         4.01        11.05        13.68        16.90         3.68 
TCGA-GL-A4EM TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-A5E8 
        1.05        22.26         0.13        11.97        21.44        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM 
        6.61        92.58        16.01        12.85        14.07        11.93 
TCGA-SX-A7SO TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A8S1 
       38.63        21.93        86.27        26.01        29.00        13.28 

$subtype3
TCGA-A3-3363 TCGA-B0-5707 TCGA-B2-4098 TCGA-B8-4621 TCGA-G6-A8L7 TCGA-2K-A9WE 
       10.49        92.98         1.68        25.91        70.13         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       75.55        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP 
       56.81        54.64        51.52        26.43        30.71        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
       18.21        61.05         0.10        19.13         0.89        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       30.48        25.64        23.97        23.31         0.76        19.63 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46        58.45        76.64        13.55        30.35 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
        3.55        16.77         6.58        33.83        10.09        30.58 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81         0.16        17.49        12.30        86.76 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7044 
       63.72        47.80        21.63        26.04        13.25       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       48.26        96.92        50.40         7.63         7.04         3.81 
TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       14.63         3.02        40.77        51.19        54.90        34.19 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       19.00        13.08         2.40        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       34.82        25.15        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       80.65       194.79        12.92        27.65        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       85.78        88.24        67.17        21.34        16.34        12.36 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25         0.36        12.13        25.97        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
       87.22        84.95        52.27        50.60        78.90        17.75 
TCGA-PJ-A8JU TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W 
       12.49        47.90        47.44        33.04        28.80        26.89 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        18.02        60.03        14.83         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       52.11        30.67        25.68        27.39        12.99        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 
        6.02 

subtype1 subtype2 subtype3 
    2.50     0.07     0.10 
subtype1 subtype2 subtype3 
  151.96   129.86   194.79 
subtype1 subtype2 subtype3 
   60.33    32.25    21.34 
[1] "2.5 - 152.0 (60.3)" "0.1 - 129.9 (32.2)" "0.1 - 194.8 (21.3)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      28       29        15        5
  subtype2     273       55       153       91
  subtype3     140       17        21        4
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         28      273      140
  STAGE II        29       55       17
  STAGE III       15      153       21
  STAGE IV         5       91        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  28  29  19   1
  subtype2 280  68 211  13
  subtype3 147  24  20   1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       28      280      147
  T2       29       68       24
  T3       19      211       20
  T4        1       13        1
[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
  subtype1  49   2   2
  subtype2 228  36   4
  subtype3  34   5   0
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49      228       34
  N1        2       36        5
  N2        2        4        0
[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"
D8V6, binary
          cls
clus         0   1
  subtype1  50   3
  subtype2 421  84
  subtype3  60   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    3
  subtype2  421   84
  subtype3   60    2
   clus
vv  subtype1 subtype2 subtype3
  0       50      421       60
  1        3       84        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  28  49
  subtype2 208 366
  subtype3  44 154
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   49
  subtype2  208  366
  subtype3   44  154
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28      208       44
  MALE         49      366      154
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 60                                16
  subtype2                  6                               491
  subtype3                  0                                 5
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     1
  subtype2                                    77
  subtype3                                   193
D8V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          60        6        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           16      491        5
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        1       77      193
[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"
D8V10, continuous
D8V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         6
  subtype2                                0    10                        65
  subtype3                                2     3                        45
          vv
clus       WHITE
  subtype1    67
  subtype2   489
  subtype3   136
D8V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        2
  ASIAN                                   2       10        3
  BLACK OR AFRICAN AMERICAN               6       65       45
  WHITE                                  67      489      136
[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"
D8V13, binary
          cls
clus         0   1
  subtype1   4  41
  subtype2  29 386
  subtype3   7 167
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   41
  subtype2   29  386
  subtype3    7  167
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4       29        7
  NOT HISPANIC OR LATINO       41      386      167
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 125  13
  subtype2  57   9
  subtype3  37  20
  subtype4  87  38
subtype1 subtype2 subtype3 subtype4 
     138       66       57      125 
subtype1 subtype2 subtype3 subtype4 
      13        9       20       38 
$subtype1
TCGA-B8-4621 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       25.91         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9JD TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.91        34.85        54.64        51.52        26.43        30.71 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       29.36        25.58         5.29        22.49         0.13        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       18.21        61.05         0.89        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A57E 
       25.64        23.31         0.76        19.63        14.33         8.48 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       15.75         8.28        30.35         2.20        19.56        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 
       16.87         3.55         6.58        33.83        26.40         0.46 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       15.12        43.99         2.10         0.16        17.49        12.30 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
       63.72        47.80        26.04        13.25         7.66         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 
      123.62        48.26        96.92        61.28        50.40        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
       35.93        37.55        24.46        13.78         3.75         3.02 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6790 
       51.19        54.90        19.00        10.68        13.08        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       48.62        39.25        34.82        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NJ TCGA-IA-A40U 
       17.95         0.89        11.21         4.60        56.75        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A854 TCGA-MH-A855 
       21.34        12.36        29.10        11.41         0.36        12.13 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVM 
       25.97        15.48        99.78        87.22        52.27        50.60 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        26.89        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        38.63        16.31        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
       43.76        60.03         0.53        38.86        30.67        25.68 
TCGA-UZ-A9PX TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       27.39        18.05        15.62        25.28         6.74         6.02 

$subtype2
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8332 
       38.07       141.73       137.06       102.81        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 
       98.33        96.95        92.55        30.25        86.56        28.11 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8639 TCGA-KN-8418 
      151.96        23.28        28.80        47.24        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 
       23.47        25.48        25.91        65.19         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 
       87.12        19.33         2.50        11.21        59.08        42.35 
TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      100.87        74.93        16.67        80.38        87.78        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 
       57.17        61.58        63.95        57.37        12.13        32.61 
TCGA-B8-A54K TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-A4-8312 
       15.42        75.42        35.67        24.33        31.20        23.28 
TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5893 TCGA-BQ-7048 
       22.92        40.83        26.04        25.35         7.92        93.34 
TCGA-BQ-7055 TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-7501 TCGA-MH-A857 TCGA-WN-AB4C 
       26.27        79.86         1.18        13.68        21.44        29.00 

$subtype3
TCGA-KN-8427 TCGA-KO-8404 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-B0-4698 TCGA-B0-5702 
        0.99        10.68        12.66        12.16         1.38        52.77 
TCGA-B8-A8YJ TCGA-BP-4173 TCGA-BP-4770 TCGA-BP-4804 TCGA-BP-4985 TCGA-CJ-4881 
       14.17        62.24        10.82        47.97        31.30        66.21 
TCGA-CJ-4890 TCGA-CW-6087 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-G6-A8L7 TCGA-MM-A84U 
       68.55         1.35        47.08         6.77        70.13        15.25 
TCGA-2Z-A9JK TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8518 
       38.99        11.57        19.63        35.18         0.23        19.73 
TCGA-AL-3466 TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 
        9.63        44.61         0.46        34.49        12.46        19.27 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-BQ-7053 
        8.88        43.20        10.88         2.76        44.84        49.84 
TCGA-BQ-7056 TCGA-DW-7834 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
       20.12       129.86        80.88        61.02        34.19        24.89 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM TCGA-J7-8537 
        0.43         4.01        11.05         3.68         1.05         0.13 
TCGA-KV-A6GD TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       11.97        42.94         6.61        16.01        12.85        14.07 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       21.93        86.27        13.28 

$subtype4
TCGA-A3-3317 TCGA-A3-3358 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       49.02        42.97        20.28        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3458 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4710 
       11.18        10.62        38.40        65.10         2.14         3.16 
TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4836 TCGA-B0-4837 
       43.96        15.72        46.59        40.44        40.70        45.30 
TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5399 TCGA-B0-5691 
       36.85        11.24        25.32        18.51        21.44       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 
       48.89       101.13        15.78        46.68        56.78        90.12 
TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5709 TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5635 
       35.57       120.59       102.48        35.90        11.77        10.36 
TCGA-B2-5636 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-5545 TCGA-B8-5550 
       30.21        32.98         9.57         4.64        17.16        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
        0.53        34.39        14.30         8.42         4.93        17.36 
TCGA-B8-A7U6 TCGA-BP-4340 TCGA-BP-4761 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       16.27        18.48         5.98        15.78        48.95        36.53 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        6.94        87.45        63.62         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4988 
       14.24         7.23        53.65        36.07        33.34        27.22 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5008 
        3.88        16.47        45.07        30.64        38.70        35.21 
TCGA-BP-5009 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4887 
       36.23        49.25        77.36        64.27        71.87        30.64 
TCGA-CJ-4889 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
       63.98        39.45        56.35        63.88        79.89        84.66 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5585 
       18.15        62.10        67.00        62.66        83.77        85.78 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4864 TCGA-CZ-5453 
       78.18       105.93        46.16        69.21        93.04         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       23.74        18.44        55.33        55.33        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5989 
       57.21        22.52         2.40        31.10        12.69        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-G6-A5PC 
       43.69        45.96        11.67        37.15        18.12         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-A4-A5Y1 
       10.29        35.87         2.01        19.43        19.96        12.99 
TCGA-AL-3473 TCGA-B9-A69E TCGA-BQ-5882 TCGA-BQ-5892 TCGA-WN-A9G9 
       25.08        14.86        21.63        11.97        26.01 

subtype1 subtype2 subtype3 subtype4 
    0.13     1.18     0.13     0.10 
subtype1 subtype2 subtype3 subtype4 
  194.79   151.96   129.86   120.59 
subtype1 subtype2 subtype3 subtype4 
   22.90    41.59    15.25    32.98 
[1] "0.1 - 194.8 (22.9)" "1.2 - 152.0 (41.6)" "0.1 - 129.9 (15.2)"
[4] "0.1 - 120.6 (33.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     102       11        19        4
  subtype2      27       17        18        6
  subtype3      23        4        15       15
  subtype4      63       16        27       20
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I        102       27       23       63
  STAGE II        11       17        4       16
  STAGE III       19       18       15       27
  STAGE IV         4        6       15       20
[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        T1  T2  T3  T4
  subtype1 106  13  20   1
  subtype2  27  17  23   1
  subtype3  24   5  23   5
  subtype4  66  18  40   2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1      106       27       24       66
  T2       13       17        5       18
  T3       20       23       23       40
  T4        1        1        5        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
  subtype1 26  6  1
  subtype2 33  6  2
  subtype3 13 12  3
  subtype4 50  5  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       26       33       13       50
  N1        6        6       12        5
  N2        1        2        3        0
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 45  2
  subtype2 36  4
  subtype3 25  8
  subtype4 89 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    2
  subtype2   36    4
  subtype3   25    8
  subtype4   89   19
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       45       36       25       89
  1        2        4        8       19
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  31 114
  subtype2  32  36
  subtype3  23  36
  subtype4  42  84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31  114
  subtype2   32   36
  subtype3   23   36
  subtype4   42   84
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       31       32       23       42
  MALE        114       36       36       84
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                  0                                 1
  subtype2                 46                                 4
  subtype3                  2                                17
  subtype4                  0                               120
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   144
  subtype2                                    18
  subtype3                                    40
  subtype4                                     6
D9V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                           0       46        2        0
  KIDNEY CLEAR CELL RENAL CARCINOMA            1        4       17      120
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      144       18       40        6
[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"
D9V10, continuous
D9V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     2                        24
  subtype2                                0     2                        11
  subtype3                                0     2                        14
  subtype4                                0     3                        19
          vv
clus       WHITE
  subtype1   112
  subtype2    52
  subtype3    41
  subtype4   100
D9V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0
  ASIAN                                   2        2        2        3
  BLACK OR AFRICAN AMERICAN              24       11       14       19
  WHITE                                 112       52       41      100
[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"
D9V13, binary
          cls
clus         0   1
  subtype1   7 123
  subtype2   4  34
  subtype3   3  43
  subtype4   6  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  123
  subtype2    4   34
  subtype3    3   43
  subtype4    6   89
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7        4        3        6
  NOT HISPANIC OR LATINO      123       34       43       89
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 44  4
  subtype2 74  4
  subtype3 57 28
  subtype4 93 37
  subtype5 38  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      48       78       85      130       45 
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        4       28       37        7 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-A4-7734 TCGA-AL-3472 TCGA-AT-A5NU 
        7.04        25.58         0.13         0.89        30.35         2.20 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-8121 TCGA-B9-5155 
       24.56        16.87         3.55         6.58        12.46        15.12 
TCGA-B9-A5W9 TCGA-BQ-5888 TCGA-BQ-7045 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        0.16        13.25        48.26        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM 
       35.93        24.46         3.02        34.82        25.84         6.38 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DD TCGA-HE-A5NJ 
       80.65       194.79        12.92        27.65        11.21        56.75 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IZ-8196 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       85.78        88.24        21.34         0.36        25.97        15.48 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71S TCGA-SX-A71W TCGA-SX-A7SP TCGA-SX-A7SU 
       87.22        17.75        47.44        26.89        16.31        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PX TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       60.03        27.39        18.05        15.62        25.28         6.02 

$subtype2
TCGA-B8-4621 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JD 
       25.91        75.55        58.22       100.27        56.91        34.85 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        51.52        26.43        30.71        29.36         5.29 
TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 
       22.49        12.82        18.21        61.05        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       29.46        25.64        23.31         0.76        19.63        14.33 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 
       15.75         8.28        19.56        33.83        26.40         0.46 
TCGA-B9-5156 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5886 TCGA-BQ-5890 
       43.99        17.49        12.30        63.72        26.04         7.66 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
      123.62        96.92        50.40         7.63         7.04         3.81 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 
       37.55        13.78         3.75        51.19        54.90        19.00 
TCGA-F9-A7Q0 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-A8LB TCGA-G7-A8LC 
       13.08        51.78        48.62        39.25        17.98        17.33 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DE TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       17.95         0.89         4.60        16.80        19.99         2.04 
TCGA-IA-A83W TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A855 TCGA-P4-A5E6 
       67.17        12.36        29.10        11.41        12.13        99.78 
TCGA-P4-AAVM TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR 
       50.60        47.90        33.04        27.06        19.00        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-Y8-A8RZ 
       48.30         0.53        38.86        30.67        25.68         6.74 

$subtype3
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 
       23.28        28.80        31.33         0.99       100.87        10.68 
TCGA-6D-AA2E TCGA-B0-4698 TCGA-B2-5636 TCGA-B8-A54K TCGA-BP-4770 TCGA-BP-4804 
       12.16         1.38        30.21        15.42        10.82        47.97 
TCGA-BP-4985 TCGA-CJ-5681 TCGA-CW-6087 TCGA-G6-A8L7 TCGA-2Z-A9J2 TCGA-2Z-A9J9 
       31.30        18.15         1.35        70.13        59.01        75.42 
TCGA-2Z-A9JJ TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7585 
       35.67        24.33        31.20        11.57        19.63        35.18 
TCGA-A4-7915 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 
        0.23        23.28        19.73         8.48        12.99         9.63 
TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-4104 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5876 
       44.61         0.46        34.49         2.10        14.86        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       26.04        25.35        10.88         0.95         7.92         2.76 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
       93.34        44.84        61.28        49.84        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
        7.17        79.86        80.88        61.02        34.19        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 
       10.68         1.18         0.43         4.01        11.05        13.68 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD 
       16.90         3.68         1.05        22.26         0.13        11.97 
TCGA-MH-A857 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 
       21.44        42.94         6.61        52.27        16.01        12.85 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C 
       14.07        11.93        38.63        21.93        86.27        29.00 
TCGA-Y8-A8S1 
       13.28 

$subtype4
TCGA-3Z-A93Z TCGA-A3-3317 TCGA-A3-3358 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       12.66        49.02        42.97        20.28        15.39        22.65 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3458 TCGA-B0-4700 TCGA-B0-4706 
        0.10        11.18        10.62        38.40        65.10         2.14 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4836 
        3.16        43.96        15.72        46.59        40.44        40.70 
TCGA-B0-4837 TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5399 
       45.30        36.85        11.24        25.32        18.51        21.44 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B2-3924 
       90.12        35.57        52.77       120.59       102.48        35.90 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-5545 
       11.77        10.36        32.98         9.57         4.64        17.16 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54I 
       14.27         0.53        34.39        14.30         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4173 TCGA-BP-4340 TCGA-BP-4761 
       17.36        16.27        14.17        62.24        18.48         5.98 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       15.78        48.95        36.53         6.94        87.45        63.62 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4976 
        6.74        57.40        58.98        14.24         7.23        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4995 
       36.07        33.34        27.22         3.88        16.47        45.07 
TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5008 TCGA-BP-5009 TCGA-CJ-4870 TCGA-CJ-4875 
       30.64        38.70        35.21        36.23        49.25        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 
       64.27        71.87        66.21        30.64        63.98        68.55 
TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5683 
       39.45        56.35        63.88        79.89        84.66        62.10 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 
       67.00        62.66        83.77        85.78        78.18       105.93 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4864 TCGA-CZ-5453 
       46.16        47.08        69.21         6.77        93.04         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       23.74        18.44        55.33        55.33        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5989 
       57.21        22.52         2.40        31.10        12.69        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-G6-A5PC 
       43.69        45.96        11.67        37.15        18.12         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        35.87         2.01        19.43        19.96        15.25 
TCGA-2Z-A9JK TCGA-AL-3473 TCGA-BQ-5892 TCGA-WN-A9G9 
       38.99        25.08        11.97        26.01 

$subtype5
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8332 
       38.07       141.73       137.06       102.81        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 
       98.33        96.95        92.55        30.25        86.56        28.11 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
      151.96        47.24       129.37        23.47        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 
       11.21        59.08        42.35        74.93        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-AK-3440 
       87.78        86.10        57.17        61.58        63.95        57.37 
TCGA-AK-3465 TCGA-B2-3923 TCGA-BQ-7055 
       12.13        32.61        26.27 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.46     0.13     0.10     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 
  194.79   123.62   100.87   120.59   151.96 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.695   25.795   19.730   35.390   59.080 
[1] "0.1 - 194.8 (19.7)" "0.5 - 123.6 (25.8)" "0.1 - 100.9 (19.7)"
[4] "0.1 - 120.6 (35.4)" "2.5 - 152.0 (59.1)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      43        3         2        1
  subtype2      56        7        12        1
  subtype3      37        4        27       17
  subtype4      66       17        26       22
  subtype5      13       17        12        4
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         43       56       37       66       13
  STAGE II         3        7        4       17       17
  STAGE III        2       12       27       26       12
  STAGE IV         1        1       17       22        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 44  2  2  1
  subtype2 59  9 12  0
  subtype3 39  6 35  5
  subtype4 68 19 41  3
  subtype5 13 17 16  0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       44       59       39       68       13
  T2        2        9        6       19       17
  T3        2       12       35       41       16
  T4        1        0        5        3        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 10  1  0
  subtype2 13  3  0
  subtype3 16 19  4
  subtype4 54  4  0
  subtype5 29  2  2
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10       13       16       54       29
  N1        1        3       19        4        2
  N2        0        0        4        0        2
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 16  0
  subtype2 23  0
  subtype3 37 10
  subtype4 91 21
  subtype5 28  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    0
  subtype2   23    0
  subtype3   37   10
  subtype4   91   21
  subtype5   28    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       16       23       37       91       28
  1        0        0       10       21        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 13 38
  subtype2 14 68
  subtype3 38 50
  subtype4 43 88
  subtype5 20 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   38
  subtype2   14   68
  subtype3   38   50
  subtype4   43   88
  subtype5   20   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       14       38       43       20
  MALE         38       68       50       88       26
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                  0                                 0
  subtype2                  0                                 1
  subtype3                  6                                11
  subtype4                  0                               127
  subtype5                 42                                 3
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    51
  subtype2                                    81
  subtype3                                    71
  subtype4                                     4
  subtype5                                     1
D10V9, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                           0        0        6        0
  KIDNEY CLEAR CELL RENAL CARCINOMA            0        1       11      127
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       51       81       71        4
                                       clus
vv                                      subtype5
  KIDNEY CHROMOPHOBE                          42
  KIDNEY CLEAR CELL RENAL CARCINOMA            3
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        1
[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"
D10V10, continuous
D10V11, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         7
  subtype2                                2     1                        15
  subtype3                                0     3                        22
  subtype4                                0     3                        22
  subtype5                                0     1                         2
          vv
clus       WHITE
  subtype1    41
  subtype2    61
  subtype3    59
  subtype4   103
  subtype5    41
D10V12, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        2        0        0        0
  ASIAN                                   1        1        3        3        1
  BLACK OR AFRICAN AMERICAN               7       15       22       22        2
  WHITE                                  41       61       59      103       41
[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"
D10V13, binary
          cls
clus        0  1
  subtype1  4 44
  subtype2  1 70
  subtype3  5 65
  subtype4  6 92
  subtype5  4 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   44
  subtype2    1   70
  subtype3    5   65
  subtype4    6   92
  subtype5    4   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        1        5        6        4
  NOT HISPANIC OR LATINO       44       70       65       92       18
[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"
