[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/22506733/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/22570984/KIPAN-TP.mergedcluster.txt"

nPatients in clinical file=941, in cluster file=894, common to both=894
[1]  12 894
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
32 25 14 17 
 1  2  3  4 
32 25 14 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 
328 200 354 
  1   2   3 
328 200 354 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
104 123 172  71 190 
  1   2   3   4   5 
104 123 172  71 190 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
185 185 189 197 
  1   2   3   4 
185 185 189 197 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
200  65 116 149  60  71  95 
  1   2   3   4   5   6   7 
200  65 116 149  60  71  95 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
125 200 288 276 
  1   2   3   4 
125 200 288 276 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7   8   9 
 90  62 151  84 122  38 111  59 172 
  1   2   3   4   5   6   7   8   9 
 90  62 151  84 122  38 111  59 172 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
346 197 330 
  1   2   3 
346 197 330 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 77 350 234 212 
  1   2   3   4 
 77 350 234 212 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
158  69  65 124 
  1   2   3   4 
158  69  65 124 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
92 84 50 20 46 78 46 
 1  2  3  4  5  6  7 
92 84 50 20 46 78 46 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 894 columns.

[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=215,	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=594,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 894 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
490 127 260  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
490 127 260  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
490 127 260  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
490 127 260  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
330  44   6 
[1] "table(vv)"
vv
 N0  N1  N2 
330  44   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
330  44   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
330  44   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=40, 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 27  5
  subtype2 17  8
  subtype3 13  1
  subtype4 12  5
subtype1 subtype2 subtype3 subtype4 
      32       25       14       17 
subtype1 subtype2 subtype3 subtype4 
       5        8        1        5 
$subtype1
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3455 
       47.21        38.47        53.39        31.07        82.32        22.45 
TCGA-BP-4164 TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 
       32.61        36.82        49.58        48.59        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3372 TCGA-A3-3380 
       48.82        45.53        18.44        51.25        24.16        18.64 
TCGA-A3-3383 TCGA-AK-3444 TCGA-AS-3778 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 
       28.31        48.36         1.41        35.90        31.96        31.30 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4634 TCGA-CJ-4639 
       42.71        45.37        17.19       101.06       115.00       106.16 
TCGA-CJ-4643 TCGA-CJ-4644 
       58.95        11.05 

$subtype2
TCGA-CJ-4636 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       63.25         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3374 
       36.36        62.01         4.50        52.93        29.92        43.20 
TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3426 TCGA-B8-4143 TCGA-B8-4620 TCGA-BP-4161 
       20.71        18.87        29.10        23.31        25.55        90.28 
TCGA-BP-4163 TCGA-BP-4167 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       93.34        89.36        73.22        14.17       114.41        54.61 
TCGA-AL-3473 
       62.66 

$subtype3
TCGA-A3-3328 TCGA-A3-3336 TCGA-A3-3313 TCGA-A3-3365 TCGA-AK-3427 TCGA-AK-3440 
       45.53        34.29        24.16        28.70       117.80        94.19 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 
       46.78        40.01        83.21        12.13        40.70        32.61 
TCGA-B8-4148 TCGA-B3-4104 
       49.97        34.49 

$subtype4
TCGA-AL-3468 TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 TCGA-AL-3466 TCGA-AL-3467 
       76.64        10.49        37.58         1.68         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 
       49.32        66.71        33.83        29.03        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 
  115.00   114.41   117.80    76.64 
subtype1 subtype2 subtype3 subtype4 
  38.730   43.200   40.355   29.030 
[1] "1.4 - 115.0 (38.7)"  "0.5 - 114.4 (43.2)"  "12.1 - 117.8 (40.4)"
[4] "0.5 - 76.6 (29.0)"  
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      22        3         6        1
  subtype2       8        5         8        4
  subtype3       9        5         0        0
  subtype4       6        3         1        1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         22        8        9        6
  STAGE II         3        5        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 22  3  7
  subtype2  9  6 10
  subtype3  9  5  0
  subtype4  8  7  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       22        9        9        8
  T2        3        6        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 17  0
  subtype2 12  3
  subtype3  5  0
  subtype4  3  1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       17       12        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 31  1
  subtype2 21  4
  subtype3 14  0
  subtype4 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    1
  subtype2   21    4
  subtype3   14    0
  subtype4   11    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       31       21       14       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 17
  subtype2  9 16
  subtype3  4 10
  subtype4  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   17
  subtype2    9   16
  subtype3    4   10
  subtype4    5   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       15        9        4        5
  MALE         17       16       10       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, binary
          cls
clus        0
  subtype1 12
  subtype2  5
  subtype3  6
  subtype4  7
[1] "NOT AVAILABLE: table only has an event [0]"
D1V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype2 subtype4 
       2        1 
character(0)
          vv
clus       KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                                32
  subtype2                                24
  subtype3                                13
  subtype4                                 3
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     0
  subtype2                                     1
  subtype3                                     1
  subtype4                                    14
D1V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CLEAR CELL RENAL CARCINOMA           32       24       13        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"
D1V11, continuous
D1V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    30
  subtype2     0                         1    22
  subtype3     0                         2    12
  subtype4     1                         9     7
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        1        2        9
  WHITE                           30       22       12        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"
D1V14, binary
          cls
clus        0  1
  subtype1  4 19
  subtype2  3 11
  subtype3  0 12
  subtype4  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   19
  subtype2    3   11
  subtype3    0   12
  subtype4    0   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        3        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 19  2
  subtype2 16  8
  subtype3 12  6
  subtype4 10  3
  subtype5 12  0
subtype1 subtype2 subtype3 subtype4 subtype5 
      21       24       18       13       12 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        8        6        3        0 
$subtype1
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3306 TCGA-A3-3322 
       47.21        38.47        53.39        31.07        36.82        48.59 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 
       38.99        37.38        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 
       31.96        31.30       115.00 

$subtype2
TCGA-CJ-4636 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       63.25         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3378 
       36.36        62.01         4.50        52.93        43.20        20.71 
TCGA-A3-3382 TCGA-AK-3426 TCGA-B8-4143 TCGA-B8-4620 TCGA-BP-4161 TCGA-BP-4163 
       18.87        29.10        23.31        25.55        90.28        93.34 
TCGA-BP-4167 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-AL-3473 
       89.36        73.22        14.17       114.41        54.61        62.66 

$subtype3
TCGA-AL-3468 TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 TCGA-AL-3466 
       76.64        24.16        10.49        37.58         1.68         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       70.19        49.32        66.71        33.83        29.03        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-A3-3359 TCGA-AK-3455 TCGA-BP-4164 TCGA-A3-3320 TCGA-A3-3331 TCGA-AK-3444 
       82.32        22.45        32.61        49.58        48.82        48.36 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4639 TCGA-CJ-4643 
       42.71        45.37        17.19       101.06       106.16        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       117.80        94.19        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 TCGA-B3-4104 
       83.21        12.13        40.70        32.61        49.97        34.49 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.41     0.53     0.46    11.05    12.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
  115.00   114.41    76.64   106.16   117.80 
subtype1 subtype2 subtype3 subtype4 subtype5 
  35.900   46.110   28.605   48.360   43.115 
[1] "1.4 - 115.0 (35.9)"  "0.5 - 114.4 (46.1)"  "0.5 - 76.6 (28.6)"  
[4] "11.1 - 106.2 (48.4)" "12.1 - 117.8 (43.1)"
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, binary
          cls
clus       0
  subtype1 7
  subtype2 5
  subtype3 7
  subtype4 5
  subtype5 6
[1] "NOT AVAILABLE: table only has an event [0]"
D2V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       2        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
D2V10, 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"
D2V11, continuous
D2V12, continuous
          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
D2V13, 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"
D2V14, 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 266  58
  subtype2 160  38
  subtype3 222 132
subtype1 subtype2 subtype3 
     324      198      354 
subtype1 subtype2 subtype3 
      58       38      132 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B8-4621 TCGA-BP-4760 
      102.81        28.11        47.24       130.13        25.91        77.62 
TCGA-CZ-4862 TCGA-G6-A8L7 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
      107.54        70.13        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       10.16        21.86        19.23        26.04        13.25        96.92 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       19.73        17.75        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
       15.62        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       49.97       123.12       129.37        23.47        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
       65.19        52.27        87.12        19.33        11.21        59.08 
TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       103.10        99.88        90.48        92.55 
TCGA-A3-3313 TCGA-A3-3363 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 
       24.16        10.49        43.20       117.80       112.08        94.19 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4696 
       83.21        37.58        12.13        40.70         3.32        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-5080 TCGA-B0-5081 
        1.38         3.62        68.71        53.88        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5106 TCGA-B0-5117 TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5838 
        7.30        52.54        52.87        32.61         1.68         5.46 
TCGA-B8-4619 TCGA-B8-A54E TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4337 TCGA-BP-4756 
       17.19        29.88        54.90        21.21         0.07        12.30 
TCGA-BP-4770 TCGA-BP-4994 TCGA-CJ-4889 TCGA-CJ-4907 TCGA-CJ-5681 TCGA-CW-6087 
       10.82        43.00        63.98        49.28        18.15         1.35 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JO TCGA-2Z-A9JP 
        4.57        91.73        56.81        30.71        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        12.82       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
        0.10        35.18        19.13         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        25.64        23.97        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU 
        8.28        12.46        49.32        66.71        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 
       41.13        37.51        36.49        20.25        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       29.03        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
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-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       47.80        26.04        30.28        10.82         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        93.34        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        1.18        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       25.15        25.84        25.25        17.98        80.65       194.79 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
       27.65         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       16.80        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 

$subtype2
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3455 TCGA-B0-5088 
       23.28        28.80        31.07        82.32        22.45        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B8-5162 TCGA-B8-A54K 
      112.80       133.94        70.68       126.05         1.18        15.42 
TCGA-BP-4762 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4999 
       44.15        20.38         6.94        61.51        53.65        41.62 
TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4894 TCGA-CW-6093 
       27.62        48.10        49.15        44.55        27.65       103.43 
TCGA-CZ-4856 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-2Z-A9J9 TCGA-BQ-7049 
        0.59        65.88        11.67        23.90        75.42        44.84 
TCGA-BQ-7055 TCGA-MH-A857 TCGA-SX-A7SO TCGA-KL-8333 TCGA-KM-8477 TCGA-KM-8639 
       26.27        29.26        41.33        98.33        51.06        31.33 
TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8437 TCGA-KO-8414 TCGA-6D-AA2E 
       87.91       104.52         2.50       100.87       105.60        11.90 
TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3362 
        0.53        37.38        48.82        45.53        29.92        51.25 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       28.70        74.63        74.76        53.29        55.76        20.71 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NN TCGA-A3-A8OV 
       28.31        65.52        33.47        15.39         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3447 TCGA-AS-3778 
       10.62       122.56        73.68        46.78        40.01         1.41 
TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4818 
        2.53        19.00         3.25        58.45        45.07        16.77 
TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-5085 TCGA-B0-5100 
       14.93        29.10        39.45        26.07        25.32        62.89 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5120 TCGA-B0-5121 
       90.48        30.48        58.59        66.05        38.43        48.82 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      111.52       129.67       126.28        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B2-3924 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-A4SR 
      130.65        79.89        35.90        21.30        31.30        16.67 
TCGA-B4-5378 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 
        5.75         4.64         0.23        16.80        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       45.37        50.14        24.23        50.14        16.60        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4165 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       14.30        85.51        99.85        27.78        62.07        37.25 
TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4759 TCGA-BP-4765 
       52.24        12.23        33.99        31.33        77.98        71.80 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       61.68        61.97        13.51        60.95        48.95        36.53 
TCGA-BP-4801 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 
       36.95        63.62        61.22        57.40        14.24        49.38 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5001 
       47.11        36.07        33.34        46.45        30.64        38.70 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
       37.48        35.21        28.87        38.30        37.25        22.78 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5202 TCGA-CJ-4870 TCGA-CJ-4878 
       33.24        23.47        13.41         0.95        49.25        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       57.83       113.46        50.24        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5680 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 
       45.14         3.06        25.25        67.00        62.66        92.02 
TCGA-CW-5583 TCGA-CW-5589 TCGA-CZ-4861 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       81.83        78.18        14.66        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       91.69        55.33        22.78        12.00        18.12         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-T7-A92I TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-4A-A93Y 
        7.96        10.29        11.70        38.99        24.33        11.57 
TCGA-A4-7828 TCGA-A4-8312 TCGA-AL-3467 TCGA-B1-A655 TCGA-B3-4104 TCGA-B9-A69E 
        7.82        23.28        70.19        16.77        34.49        14.86 
TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-7050 TCGA-DZ-6135 TCGA-F9-A97G 
       12.30        63.72        40.83        61.28        74.60         0.43 
TCGA-GL-7773 TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A856 TCGA-P4-A5ED TCGA-Y8-A8S1 
       12.92        16.31        19.99        31.13        92.58        13.28 

$subtype3
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 
       47.21        38.47        34.29        42.97       109.91        58.49 
TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 
       28.73        19.73        43.96        52.21        15.78       119.38 
TCGA-B2-5635 TCGA-B8-A54H TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
       24.82         8.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4782 
       80.68        74.17        54.77        12.33        60.59        11.64 
TCGA-BP-4799 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5009 
       37.25        25.81        27.22         5.82        45.07        35.90 
TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       62.86        27.02        31.79        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 
       26.93       108.56        53.26       118.85        75.58        46.16 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        37.15        66.28 
TCGA-DV-5575 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5892 
       56.84        81.21        23.01        12.99        11.87        11.97 
TCGA-Y8-A8RZ TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8436 TCGA-KO-8415 TCGA-3Z-A93Z 
        6.74         3.55         0.99        42.35        96.62        12.66 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       48.59        36.36        38.99        62.01         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 
       18.44        88.37        24.16        18.64        18.87        20.28 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 
       22.65         0.10        29.10       109.41        15.78        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 
      109.51        48.36        78.64        94.29        38.40        82.45 
TCGA-AK-3461 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4700 TCGA-B0-4701 
       72.89         1.41         4.57         3.48        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 
        5.98         2.14        57.70         6.64        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        0.59         5.52        33.50         6.02        40.44        36.53 
TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       54.48        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 
        6.71        56.68        10.52        10.29        65.29        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5092 
        2.27        36.85        70.52        20.94        43.30        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       90.87        19.30        38.63        52.73        41.88        51.02 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 
       46.39        56.98        42.41        85.78        86.47        80.91 
TCGA-B0-5702 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4099 TCGA-B2-5633 
       71.41       131.15        89.49        91.46        31.96        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       32.98        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
        0.36        23.31        49.97        25.55        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D 
       27.02         0.85         6.38        48.53         0.53        27.29 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        97.45        53.42 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       15.62        93.99        18.48        62.86        49.08        44.94 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 
       31.89        11.31        72.59         5.98        41.75        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 
       13.15         5.33        56.91        68.38        15.78        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
       10.98         6.71        47.97        87.45        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4974 
       60.30         6.74        58.98        48.89        45.50         6.94 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 
       14.93        46.45        31.30        36.95         3.88        16.47 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       18.51        37.02         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 
       30.64        52.27         9.63        74.40        42.44        37.22 
TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 
       13.35        24.62        33.47        19.82        34.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06       116.84        64.27        66.21        61.91 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        51.52       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        56.35        47.67        49.97        51.29 
TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       54.48         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        25.71        18.87        22.32       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
       73.35        53.42       119.64         7.36        64.57         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
       85.78        73.18        66.31        74.66       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04       107.41        63.42        58.82        79.53 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       79.63        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        14.63        62.63 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
       53.46         3.91         4.18        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9K9 TCGA-A4-A57E 
       19.96        16.37        54.64        51.52        19.36         8.48 
TCGA-AL-3466 TCGA-AL-3473 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5890 
        9.63        62.66         8.88        21.63        25.35         7.66 
TCGA-BQ-5891 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
        0.95        79.86         4.01        20.52        23.08        16.90 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 
        3.68         2.04        10.55        14.07        86.27        26.01 

subtype1 subtype2 subtype3 
    0.07     0.10     0.10 
subtype1 subtype2 subtype3 
  194.79   149.16   133.71 
subtype1 subtype2 subtype3 
  29.230   37.430   38.435 
[1] "0.1 - 194.8 (29.2)" "0.1 - 149.2 (37.4)" "0.1 - 133.7 (38.4)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     182       43        52       24
  subtype2     127       21        37       14
  subtype3     145       39       101       66
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        182      127      145
  STAGE II        43       21       39
  STAGE III       52       37      101
  STAGE IV        24       14       66
[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 200  53  66   7
  subtype2 130  24  45   1
  subtype3 150  50 147   7
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      200      130      150
  T2       53       24       50
  T3       66       45      147
  T4        7        1        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        N0  N1  N2
  subtype1  92  19   4
  subtype2  74   3   0
  subtype3 157  22   2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       92       74      157
  N1       19        3       22
  N2        4        0        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"
D3V6, binary
          cls
clus         0   1
  subtype1 136  13
  subtype2 155  13
  subtype3 255  63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  136   13
  subtype2  155   13
  subtype3  255   63
   clus
vv  subtype1 subtype2 subtype3
  0      136      155      255
  1       13       13       63
[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  93 235
  subtype2  82 118
  subtype3 117 237
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93  235
  subtype2   82  118
  subtype3  117  237
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       93       82      117
  MALE        235      118      237
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1 234   1
  subtype2  80   0
  subtype3  94   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  234    1
  subtype2   80    0
  subtype3   94    2
     clus
vv    subtype1 subtype2 subtype3
  NO       234       80       94
  YES        1        0        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"
D3V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 52                                40
  subtype2                 10                               164
  subtype3                  4                               324
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   236
  subtype2                                    26
  subtype3                                    26
D3V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          52       10        4
  KIDNEY CLEAR CELL RENAL CARCINOMA           40      164      324
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      236       26       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"
D3V11, continuous
D3V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     8                        59
  subtype2                                0     4                        32
  subtype3                                0     4                        30
          vv
clus       WHITE
  subtype1   244
  subtype2   163
  subtype3   312
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   8        4        4
  BLACK OR AFRICAN AMERICAN              59       32       30
  WHITE                                 244      163      312
[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"
D3V14, binary
          cls
clus         0   1
  subtype1  14 254
  subtype2   7 138
  subtype3  21 230
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  254
  subtype2    7  138
  subtype3   21  230
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        7       21
  NOT HISPANIC OR LATINO      254      138      230
[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  87  16
  subtype2  74  46
  subtype3 132  39
  subtype4  34  37
  subtype5 173  16
subtype1 subtype2 subtype3 subtype4 subtype5 
     103      120      171       71      189 
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       46       39       37       16 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-DV-5567 TCGA-DV-5576 TCGA-2Z-A9J9 
       15.42        77.62        20.38        65.88        23.90        75.42 
TCGA-BQ-7055 TCGA-MH-A857 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       26.27        29.26        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        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-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        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-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-AK-3433 
       99.88       105.60        96.62        90.48        92.55       112.08 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-5083 TCGA-B0-5098 TCGA-B0-5100 
       94.19        83.21         3.62        34.36        52.08        62.89 
TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-5636 TCGA-B4-5378 TCGA-BP-4177 TCGA-CJ-5681 
       52.87        71.41        30.21         5.75        54.90        18.15 
TCGA-DV-A4VZ TCGA-T7-A92I TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-5P-A9K8 TCGA-5P-A9KH 
       12.00        11.70        24.33        31.20        43.04        67.43 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8312 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-7048 
        7.82         0.23        23.28        22.92        40.83        93.34 
TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-6793 TCGA-GL-7966 TCGA-HE-7130 TCGA-J7-A8I2 
       79.86         1.18        11.05         3.68        58.19        10.09 
TCGA-P4-A5ED 
       92.58 

$subtype2
TCGA-AK-3425 TCGA-B0-4815 TCGA-B8-5162 TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-6030 
      109.91        52.21         1.18        27.02        31.79        75.58 
TCGA-CZ-4865 TCGA-DV-5568 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-B1-A47O 
        5.46        12.16        66.28        70.13        23.01        27.68 
TCGA-BQ-5888 TCGA-BQ-7049 TCGA-DW-7838 TCGA-HE-A5NF TCGA-PJ-A5Z8 TCGA-KN-8427 
       13.25        44.84        24.46        84.89        19.73         0.99 
TCGA-KO-8404 TCGA-6D-AA2E TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       10.68        11.90         3.32         1.41         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4713 
       19.00         1.38        65.10         7.82         5.98         6.64 
TCGA-B0-4810 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4827 
       15.72        45.07        33.50         6.02        36.53        29.10 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4848 TCGA-B0-5080 TCGA-B0-5092 TCGA-B0-5095 
       56.68        10.52        29.03        11.24        15.09         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5400 
        2.24        21.86        52.54        58.59        19.30        56.98 
TCGA-B0-5697 TCGA-B0-5706 TCGA-B0-5709 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 
       86.47       105.37       130.65        21.57         5.10         0.53 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54E 
       40.04        27.02         0.85        48.53         0.53        29.88 
TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4770 TCGA-BP-5010 TCGA-BP-5169 
        1.74         4.93        14.17        10.82        28.87         6.35 
TCGA-BP-5175 TCGA-BP-5182 TCGA-BP-5196 TCGA-CJ-4869 TCGA-CJ-4882 TCGA-CJ-4901 
       30.64        38.30        33.47        83.97        61.91        47.67 
TCGA-CJ-4902 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5686 
       49.97        45.14         3.06        18.81       131.08        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4863 TCGA-CZ-5452 
       53.42        62.66         1.35        18.77        63.39        58.82 
TCGA-CZ-5458 TCGA-CZ-5462 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-2K-A9WE 
       91.69        10.22        22.52         1.94        67.96         7.04 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-4A-A93Y TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7585 
       51.52        38.99        11.57        12.39        19.63        35.18 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5880 
       41.13        20.32        12.46        17.23        14.86        43.20 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7059 TCGA-DZ-6132 
       26.04        25.35        10.82         2.76         7.63        80.88 
TCGA-F9-A97G TCGA-G7-6796 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-HE-A5NK TCGA-J7-8537 
        0.43        71.44         1.05        11.21        73.25        10.55 
TCGA-KV-A6GD TCGA-P4-A5EA TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.41         6.61        26.01        39.06        18.64        13.28 

$subtype3
TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       42.97        58.49        28.73       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-A54H TCGA-BP-4782 
       70.68       119.38       126.05        24.82         8.42        11.64 
TCGA-BP-4993 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4904 
        5.82        48.10        49.15        44.55        31.27       108.56 
TCGA-CJ-5689 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 
       53.26       103.43         0.59        43.69        45.96        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-5P-A9JV TCGA-BQ-5892 TCGA-3Z-A93Z TCGA-A3-3370 
       37.15        56.84        67.17        11.97        12.66        74.76 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       53.29        55.76        65.52        20.28        33.47        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       122.56 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4693 
       73.68        68.61        38.40        82.45        72.89         2.53 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4818 
        2.14        57.70         3.25        46.59         5.52        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       14.93        54.48         6.71        65.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
        2.27        36.85        70.52        15.95        90.87        90.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        38.63        52.73        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5700 
       46.39       111.52       129.67        85.78       126.28        58.85 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3924 
       73.84       149.16        79.89       131.15        91.46        35.90 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 
       21.30        31.66        32.98        16.67        12.00         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-5159 
        4.64         0.36         0.23        16.80        25.05        23.74 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       24.23        50.14         6.38        34.39        14.30        27.29 
TCGA-B8-A54F TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4801 TCGA-BP-5170 TCGA-BP-5173 
       17.06        17.36        16.27        36.95        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 
       74.20        52.27         9.63        74.40        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4905 
       24.62        34.95         0.95       109.84        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5680 
       49.28        50.33        38.56         4.57        72.00        25.25 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.10        73.35       119.64        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 
       85.78        73.18        66.31        78.18       105.93        25.45 
TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       58.75        93.04        63.42        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5982 
       90.54        55.33        21.76        69.96         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       12.26        22.78        62.63        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-MW-A4EC TCGA-B1-A655 TCGA-BQ-5876 
       16.37        16.77        19.27 

$subtype4
TCGA-B0-4707 TCGA-B0-4712 TCGA-BP-5178 TCGA-CJ-6027 TCGA-DV-A4W0 TCGA-5P-A9JU 
       19.73        43.96        62.86       118.85        81.21        12.26 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-7056 TCGA-BQ-7058 TCGA-A3-3357 
       12.99        49.25        11.87        20.12        11.28        88.37 
TCGA-A3-3367 TCGA-AK-3445 TCGA-B0-4691 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4821 
       74.63        78.64         4.57        58.45         0.59        40.44 
TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5094 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5402 
       10.09        10.29        10.95        30.48        41.88        42.41 
TCGA-B0-5701 TCGA-B0-5712 TCGA-B4-5838 TCGA-B8-4622 TCGA-BP-5198 TCGA-CJ-4912 
       80.91        89.49         5.46        50.14        19.82        54.48 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 
      129.40       133.71        25.71        18.87        22.32       122.83 
TCGA-CJ-6033 TCGA-CW-5584 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4866 
        7.36         5.39        35.34        74.66        83.90       107.41 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
       79.63        94.45        10.85        84.30        31.10        12.69 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-MM-A564 TCGA-4A-A93X TCGA-5P-A9K3 
       65.65        14.63        53.46        19.96        12.82        15.48 
TCGA-5P-A9K9 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-5891 
       19.36        86.76         8.88        21.63         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7061 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LD 
        7.92         7.17        10.68         4.01        20.52        16.90 
TCGA-GL-A9DE TCGA-IA-A40Y TCGA-P4-A5E8 TCGA-SX-A7SM TCGA-UZ-A9PQ 
       16.31         2.04        42.94        11.93        86.27 

$subtype5
TCGA-B8-4621 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       25.91        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-B1-A47M TCGA-B1-A657 
       22.49        61.05        21.37         0.89        21.67        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-5560 
       10.16        21.86        19.23        26.04        96.92        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        67.17        16.34 
TCGA-MH-A855 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-B0-5707 
       86.37        21.60        15.91        15.62         6.74       123.09 
TCGA-B8-5546 TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       16.60        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-2Z-A9JP 
        4.57        91.73        56.81        54.64        30.71        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        5.29         0.13       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KF 
       78.64        71.80        62.93        12.99        27.09        27.78 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       18.21         0.10        19.13        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.31         0.76        19.63        19.73 
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-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N 
        8.28        12.46        67.73         2.20        37.51        36.49 
TCGA-B1-A654 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       20.25        43.99        22.06         0.16        17.49        12.30 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5885 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 
       63.72        47.80        30.28       123.62        48.26        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 
       50.40        49.84         7.04         3.81        40.77        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       74.60        34.19        19.00        24.89        13.08         2.40 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        90.90        39.25        25.15        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        23.08        80.65       194.79        12.92        27.65 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        12.89        81.93        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V 
       22.26        21.34        12.36        12.76        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK 
       31.13        15.48        99.78        87.09        99.12        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       44.61        28.80        27.06        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A894 
       47.47        65.13       110.73        51.35        31.73        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.05        25.28         6.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.43     0.10     0.59     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  153.73   131.08   149.16   133.71   194.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
   54.90    22.19    37.25    21.63    27.06 
[1] "0.2 - 153.7 (54.9)" "0.4 - 131.1 (22.2)" "0.1 - 149.2 (37.2)"
[4] "0.6 - 133.7 (21.6)" "0.1 - 194.8 (27.1)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      46       28        20        8
  subtype2      47        8        45       21
  subtype3     108       16        27       19
  subtype4       7        8        28       26
  subtype5     136       14        18        5
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         46       47      108        7      136
  STAGE II        28        8       16        8       14
  STAGE III       20       45       27       28       18
  STAGE IV         8       21       19       26        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  47  28  27   2
  subtype2  51   9  56   7
  subtype3 110  20  41   1
  subtype4   9  16  45   1
  subtype5 150  19  18   1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       47       51      110        9      150
  T2       28        9       20       16       19
  T3       27       56       41       45       18
  T4        2        7        1        1        1
[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 51  5  3
  subtype2 46 13  0
  subtype3 69  0  0
  subtype4 24 12  2
  subtype5 31  4  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       51       46       69       24       31
  N1        5       13        0       12        4
  N2        3        0        0        2        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"
D4V6, binary
          cls
clus         0   1
  subtype1  57   5
  subtype2  76  17
  subtype3 135  18
  subtype4  34  21
  subtype5  51   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57    5
  subtype2   76   17
  subtype3  135   18
  subtype4   34   21
  subtype5   51    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       57       76      135       34       51
  1        5       17       18       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"
D4V7, binary
          cls
clus         0   1
  subtype1  46  58
  subtype2  38  85
  subtype3  71 101
  subtype4  18  53
  subtype5  41 149
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   58
  subtype2   38   85
  subtype3   71  101
  subtype4   18   53
  subtype5   41  149
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       46       38       71       18       41
  MALE         58       85      101       53      149
[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"
D4V8, binary
          cls
clus         0   1
  subtype1  86   0
  subtype2  47   0
  subtype3  71   1
  subtype4  29   1
  subtype5 150   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86    0
  subtype2   47    0
  subtype3   71    1
  subtype4   29    1
  subtype5  150    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        86       47       71       29      150
  YES        0        0        1        1        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"
D4V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 64                                20
  subtype2                  2                                82
  subtype3                  0                               168
  subtype4                  0                                46
  subtype5                  0                                 3
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    20
  subtype2                                    39
  subtype3                                     4
  subtype4                                    25
  subtype5                                   187
D4V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          64        2        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           20       82      168       46
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       20       39        4       25
                                       clus
vv                                      subtype5
  KIDNEY CHROMOPHOBE                           0
  KIDNEY CLEAR CELL RENAL CARCINOMA            3
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      187
[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"
D4V11, continuous
D4V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        20
  subtype2                                0     2                        14
  subtype3                                0     0                        24
  subtype4                                0     1                        12
  subtype5                                2     2                        37
          vv
clus       WHITE
  subtype1    77
  subtype2   101
  subtype3   148
  subtype4    55
  subtype5   141
D4V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        2
  ASIAN                                   4        2        0        1        2
  BLACK OR AFRICAN AMERICAN              20       14       24       12       37
  WHITE                                  77      101      148       55      141
[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"
D4V14, binary
          cls
clus         0   1
  subtype1   5  64
  subtype2   3 100
  subtype3   6 133
  subtype4   2  59
  subtype5  10 163
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   64
  subtype2    3  100
  subtype3    6  133
  subtype4    2   59
  subtype5   10  163
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        3        6        2       10
  NOT HISPANIC OR LATINO       64      100      133       59      163
[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(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 113  72
  subtype2 149  36
  subtype3 165  22
  subtype4 121  76
subtype1 subtype2 subtype3 subtype4 
     185      185      187      197 
subtype1 subtype2 subtype3 subtype4 
      72       36       22       76 
$subtype1
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
       43.96        52.21        18.51         1.18         8.42        15.42 
TCGA-BP-4353 TCGA-BP-4762 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 
       12.33        44.15       105.37        27.65        53.26        75.58 
TCGA-CZ-4856 TCGA-DV-5567 TCGA-DV-5574 TCGA-DV-5576 TCGA-AL-A5DJ TCGA-B9-A44B 
        0.59        65.88        66.28        23.90        49.25        11.87 
TCGA-BQ-5888 TCGA-BQ-7049 TCGA-DW-7840 TCGA-PJ-A5Z8 TCGA-Y8-A895 TCGA-KL-8324 
       13.25        44.84         3.75        19.73        15.91       153.73 
TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8338 
       90.48        98.96        84.89        96.95        92.55        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       66.54        73.91        62.37       151.96        44.91        49.97 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8433 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3323 
       52.27        87.12        11.21       105.60        12.66        36.36 
TCGA-A3-3349 TCGA-A3-3376 TCGA-A3-3387 TCGA-AK-3451 TCGA-B0-4688 TCGA-B0-4697 
       45.53        55.76        20.28        94.29         3.32        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4810 TCGA-B0-4813 
       65.10         7.82         5.98        57.70        15.72         0.59 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4844 
        6.02        40.44        14.93        40.70        45.30        10.29 
TCGA-B0-5080 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 
       11.24         8.05         2.24        21.86        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5706 
       52.54        58.59        19.30        38.63        52.73       105.37 
TCGA-B0-5707 TCGA-B0-5710 TCGA-B2-5633 TCGA-B2-5636 TCGA-B2-A4SR TCGA-B4-5834 
      123.09        79.89        31.66        30.21        16.67         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B8-4143 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5551 
        0.53         4.64        23.31        27.02        50.14         0.53 
TCGA-B8-A54D TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4326 TCGA-BP-4332 TCGA-BP-4334 
       27.29        23.05        77.03        53.42        37.25        21.21 
TCGA-BP-4337 TCGA-BP-4345 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4763 TCGA-BP-4765 
        0.07        49.84        12.23        31.33        41.75        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 
       61.68        10.82         5.33        60.95        15.78        36.53 
TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4974 
       47.97        63.62        58.68        14.24        48.89         6.94 
TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5182 
       30.64        35.21        28.87        79.30         9.63        38.30 
TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4882 TCGA-CJ-4885 
       33.47        34.95        21.24        47.18        61.91       113.46 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98       115.69        50.01        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 
       49.97        49.18        50.33         3.06        18.81       131.08 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6033 
      133.71        18.15       122.83        73.35        67.00         7.36 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4860 TCGA-CZ-5454 TCGA-CZ-5466 
      105.93        83.90        18.77         6.77        23.74        22.52 
TCGA-DV-A4VZ TCGA-GK-A6C7 TCGA-AL-3473 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5877 
       12.00         2.01        62.66        67.73        12.46         8.88 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       22.92        21.63        30.28        10.82         7.92         2.76 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-F9-A97G 
       80.88        74.60        10.68        13.08         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A8LD TCGA-GL-A59R 
        4.01        11.05        39.25        71.44        16.90        12.43 
TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A55Z 
       56.75        16.80        96.69        22.26        10.55        27.78 
TCGA-P4-A5E6 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-SX-A7SM TCGA-SX-A7SN 
       99.78         6.61        92.58        16.01        11.93        19.00 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PQ TCGA-Y8-A897 
       26.47        53.10       103.63        86.27        18.05 

$subtype2
TCGA-KM-8442 TCGA-A3-3329 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5698 TCGA-B2-5635 
       47.24        53.39       133.94        15.78       119.38        24.82 
TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4760 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4999 
       32.61        80.68        77.62        53.65        25.81        41.62 
TCGA-BP-5009 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-CW-6093 TCGA-CZ-4862 
       35.90        49.15        27.02        44.55       103.43       107.54 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-2Z-A9J9 
       43.69        45.96        12.16        37.15        81.21        75.42 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-A4-7734 TCGA-B9-5155 TCGA-DW-5561 
       39.88        33.07        25.58         0.89        21.86        13.61 
TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7842 TCGA-UZ-A9PR TCGA-KL-8325 TCGA-KL-8333 
      129.86        13.78         3.02        86.37        23.84        98.33 
TCGA-KL-8336 TCGA-KL-8343 TCGA-KL-8345 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 
       30.25        71.41        54.74       129.37        25.91        65.19 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8409 
       19.33         2.50       105.47       100.47       103.40       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
      103.10        99.88         0.53        39.16        49.08        49.02 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3383 TCGA-B0-4846 
       29.92        18.44        74.63        24.16        28.31        39.45 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5110 
        2.27        36.85        11.90        15.95        90.87        66.05 
TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5705 
       51.02        46.39        42.41       129.67        86.47       149.16 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4101 TCGA-B2-5639 TCGA-B4-5377 
      131.15        89.49        91.46        21.30        32.98        12.00 
TCGA-B4-5378 TCGA-B4-5843 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5552 
        5.75         0.36        23.74         0.85        48.53        34.39 
TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4330 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 
       14.30        17.36        62.07        62.86        44.94        31.89 
TCGA-BP-4768 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4973 
       13.15        36.39         6.71        60.30        57.40        45.50 
TCGA-BP-4975 TCGA-BP-4982 TCGA-BP-5007 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5183 
       47.11        33.34        37.48         2.04        74.20        42.44 
TCGA-BP-5184 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 TCGA-CJ-4640 TCGA-CJ-4884 
       37.25        33.24        23.47        24.62       114.41        57.83 
TCGA-CJ-4888 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-6032 
       51.52        24.66       109.84        49.28         4.57       119.64 
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-6096 TCGA-CZ-4864 
       66.31        78.18        35.34        74.66        88.80        93.04 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       18.44        91.69        10.85        84.30         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 
       12.26        22.78        62.63         4.18        10.29        35.87 
TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J7 TCGA-5P-A9KF TCGA-A4-7915 TCGA-A4-7996 
       19.43        16.37         4.57        27.78         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-AL-3472 TCGA-B1-A654 
       30.48        23.97         0.76        14.33        66.71        20.25 
TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5878 TCGA-BQ-7050 TCGA-BQ-7062 TCGA-DZ-6133 
       22.06        17.49        63.72        61.28         3.81        51.19 
TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       34.19        19.00        90.90        25.15        20.52        25.84 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-7129 TCGA-HE-A5NH TCGA-IZ-8196 
       80.65       194.79         3.68        81.93        26.01        21.34 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E7 TCGA-SX-A7SQ 
       12.76        10.09        29.10        11.41        87.09        41.62 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
       18.02        26.20       117.40        37.35        98.96        71.24 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-V9-A7HT TCGA-Y8-A894 TCGA-Y8-A8S0 
       47.47        65.13        31.73        18.64         6.02 

$subtype3
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-B0-5691 TCGA-B8-4621 
       28.11        23.28        28.80       130.13       112.80        25.91 
TCGA-BP-4344 TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4988 
       54.77        60.59        37.25         6.94        61.51        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5006 TCGA-BP-5168 TCGA-CJ-4904 TCGA-CZ-4865 
        5.82        45.07        27.62        48.10       108.56         5.46 
TCGA-DV-5569 TCGA-DV-5575 TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       11.67        56.84        34.85        22.49        61.05        21.37 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5892 
       21.67        27.68        21.07        10.16        19.23        11.97 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DZ-6134 TCGA-HE-A5NF 
       96.92        26.27        20.12        11.28        61.02        84.89 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO 
       16.34        12.13        17.75        12.49        41.33        62.83 
TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8337 TCGA-KL-8344 
        6.74       109.22       137.06       108.62        44.84        28.80 
TCGA-KM-8476 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8434 TCGA-KN-8435 
      123.12        31.33        23.47        87.91        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8407 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E 
       42.35       100.87        92.71        90.48        92.55        11.90 
TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3357 
       24.16        48.59        38.99        48.82         4.50        88.37 
TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 
       51.25        28.70        74.76        53.29        43.20        18.64 
TCGA-A3-3382 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3444 TCGA-AK-3456 TCGA-B0-4714 
       18.87       117.80       122.56        48.36        37.58         3.25 
TCGA-B0-4817 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-4945 TCGA-B0-5116 TCGA-B0-5120 
       33.50        68.71        53.88        70.52        41.88        38.43 
TCGA-B0-5700 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       58.85        71.41        32.61        35.90         1.68        31.96 
TCGA-B2-4102 TCGA-B2-5641 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5165 TCGA-B8-5549 
       31.30        21.57        16.80        25.55        24.23         6.38 
TCGA-B8-A54E TCGA-B8-A54I TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4165 TCGA-BP-4174 
       29.88         4.93        16.27        14.17        99.85        61.78 
TCGA-BP-4341 TCGA-BP-4756 TCGA-BP-4766 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 
       52.24        12.30        48.07        56.91        68.38        48.95 
TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4972 
       36.95        87.45        61.22         6.74        58.98        49.38 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5185 TCGA-BP-5186 
       36.95         3.88        43.00        37.02        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5194 TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4874 
       13.35        13.41        19.82         0.95       115.00        75.06 
TCGA-CJ-4886 TCGA-CJ-4903 TCGA-CJ-5672 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CZ-5453 
       64.18        51.29        72.00        53.42        62.66        79.53 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-EU-5904 TCGA-EU-5905 
       90.54        55.33        10.22        21.76        18.12         3.91 
TCGA-EU-5906 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI 
        6.77         7.04        75.55       100.27        56.91        51.52 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9KE TCGA-A4-7585 
       31.20        29.36        12.82        11.57        27.09        35.18 
TCGA-A4-8098 TCGA-A4-8517 TCGA-B1-5398 TCGA-B1-7332 TCGA-B9-A69E TCGA-B9-A8YI 
       29.46        19.63        41.13        37.51        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5890 
       86.76        43.20        47.80        40.83        25.35         7.66 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
      123.62        93.34        49.84         7.63         7.04         7.17 
TCGA-DW-7963 TCGA-G7-6790 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       40.77        51.78         1.05        12.89        11.21        16.31 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-KV-A6GD TCGA-MH-A560 TCGA-P4-A5EB TCGA-P4-AAVK 
       19.99         2.04        18.41        30.38        99.12        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-UZ-A9Q1 
       50.60        78.90        14.07        16.31       125.29        51.35 
TCGA-Y8-A8S1 
       13.28 

$subtype4
TCGA-KL-8328 TCGA-A3-3336 TCGA-B0-4707 TCGA-B0-5695 TCGA-B0-5812 TCGA-BP-4158 
      102.81        34.29        19.73        70.68       126.05       111.02 
TCGA-BP-4327 TCGA-BP-4342 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4891 
        3.58        74.17        62.86        31.79        31.27        26.93 
TCGA-CJ-6027 TCGA-CZ-4854 TCGA-G6-A8L7 TCGA-5P-A9JU TCGA-DW-5560 TCGA-DW-7837 
      118.85        46.16        70.13        12.26        48.85        37.55 
TCGA-DW-7838 TCGA-DW-7841 TCGA-IA-A83W TCGA-UZ-A9PZ TCGA-KL-8341 TCGA-KN-8425 
       24.46        14.63        67.17        21.60        24.79       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8415 TCGA-A3-3306 
        3.55         0.99        10.68        16.67        96.62        36.82 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3363 
       37.15        49.58        37.38        62.01        52.93        10.49 
TCGA-A3-3378 TCGA-A3-3385 TCGA-AK-3434 TCGA-AK-3436 TCGA-B0-4690 TCGA-B0-4691 
       20.71        65.52        68.61       109.51         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4706 
        2.53         3.48        28.47         1.38         3.62         2.14 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 
        6.64        58.45        46.59         5.52        45.07        16.77 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4838 
       36.53        54.48        29.10        10.09        78.44        27.42 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 
        6.71        56.68        10.52        65.29        26.07        29.03 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       20.94        43.30         7.30        25.32        15.09        10.95 
TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5690 
       52.08        30.48        52.87        48.82        56.98       111.52 
TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5709 TCGA-B4-5832 
       85.78       126.28        80.91        73.84       130.65         5.10 
TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5546 
        5.46         0.23        25.05        50.14        40.04        16.60 
TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4161 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4329 
       17.06         1.74        90.28        62.24        97.45        27.78 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4758 
       15.62        93.99        49.08        11.31        33.99        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4798 TCGA-BP-4960 
       77.98         5.98        61.97        13.51        10.98        71.41 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4991 TCGA-BP-4992 
       14.93        36.07        46.45        31.30        46.45        16.47 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 
       18.51        38.70         6.35        30.64        52.27        74.40 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 
       46.55        14.17        83.97        49.25        79.66        74.27 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4901 
      116.84        64.27        71.87        66.21        30.64        47.67 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
       54.48        38.56        45.14       129.40        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5683 TCGA-CW-6087 TCGA-CZ-4853 TCGA-CZ-4857 
       22.32        25.25        62.10         1.35        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 
       58.82        79.63        94.45        69.96         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-G6-A5PC 
       12.69        67.96        65.65        14.63        53.46         7.96 
TCGA-MM-A564 TCGA-2Z-A9J3 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-4A-A93W TCGA-5P-A9JY 
       19.96        58.22        91.73        56.81         0.13        49.58 
TCGA-A4-7583 TCGA-A4-A57E TCGA-B1-A47N TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.10         8.48        36.49        43.99        17.23         0.16 
TCGA-BQ-5891 TCGA-BQ-7051 TCGA-DZ-6131 TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-A4TM 
        0.95        50.40        79.86        24.89         2.40        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-8500 TCGA-HE-7130 TCGA-HE-A5NI 
       17.98        23.08        12.92        27.65        58.19        11.84 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-MH-A562 TCGA-P4-A5E8 TCGA-SX-A71R TCGA-SX-A71U 
       73.25        25.22        20.25        42.94        47.90        44.61 
TCGA-UZ-A9PU TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A896 TCGA-Y8-A8RY 
       30.67       110.73        26.01        18.64        25.28 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.23     0.95     0.10 
subtype1 subtype2 subtype3 subtype4 
  153.73   194.79   137.06   130.65 
subtype1 subtype2 subtype3 subtype4 
   35.21    37.35    36.95    36.53 
[1] "0.1 - 153.7 (35.2)" "0.2 - 194.8 (37.4)" "0.9 - 137.1 (37.0)"
[4] "0.1 - 130.7 (36.5)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      75       22        50       37
  subtype2     102       23        41       16
  subtype3     128       20        33        6
  subtype4      77       26        48       42
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         75      102      128       77
  STAGE II        22       23       20       26
  STAGE III       50       41       33       48
  STAGE IV        37       16        6       42
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  78  25  76   6
  subtype2 105  27  51   2
  subtype3 131  20  38   0
  subtype4  82  37  71   7
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       78      105      131       82
  T2       25       27       20       37
  T3       76       51       38       71
  T4        6        2        0        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 84 17  3
  subtype2 66  5  1
  subtype3 67  5  0
  subtype4 83 12  1
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       84       66       67       83
  N1       17        5        5       12
  N2        3        1        0        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus         0   1
  subtype1 116  33
  subtype2 121  12
  subtype3 122   5
  subtype4 128  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  116   33
  subtype2  121   12
  subtype3  122    5
  subtype4  128   36
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      116      121      122      128
  1       33       12        5       36
[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  64 121
  subtype2  63 122
  subtype3  62 127
  subtype4  54 143
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64  121
  subtype2   63  122
  subtype3   62  127
  subtype4   54  143
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       64       63       62       54
  MALE        121      122      127      143
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 76  1
  subtype2 89  2
  subtype3 99  0
  subtype4 67  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76    1
  subtype2   89    2
  subtype3   99    0
  subtype4   67    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        76       89       99       67
  YES        1        2        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 17                               122
  subtype2                 17                               112
  subtype3                 21                                96
  subtype4                  8                               148
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    46
  subtype2                                    56
  subtype3                                    72
  subtype4                                    41
D5V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          17       17       21        8
  KIDNEY CLEAR CELL RENAL CARCINOMA          122      112       96      148
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       46       56       72       41
[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"
D5V11, continuous
D5V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     9                        24
  subtype2                                0     2                        23
  subtype3                                1     2                        30
  subtype4                                0     3                        16
          vv
clus       WHITE
  subtype1   146
  subtype2   153
  subtype3   153
  subtype4   173
D5V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   9        2        2        3
  BLACK OR AFRICAN AMERICAN              24       23       30       16
  WHITE                                 146      153      153      173
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   7 125
  subtype2  12 136
  subtype3   6 125
  subtype4   7 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  125
  subtype2   12  136
  subtype3    6  125
  subtype4    7  137
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7       12        6        7
  NOT HISPANIC OR LATINO      125      136      125      137
[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 = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 153  47
  subtype2  61   3
  subtype3  60  56
  subtype4 119  29
  subtype5  37  23
  subtype6  63   8
  subtype7  55  40
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     200       64      116      148       60       71       95 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      47        3       56       29       23        8       40 
$subtype1
TCGA-KL-8328 TCGA-KM-8442 TCGA-A3-3336 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
      102.81        47.24        34.29       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4164 
       70.68       119.38       126.05        24.82       111.02        32.61 
TCGA-BP-4327 TCGA-BP-5009 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CZ-4862 
        3.58        35.90        27.02        31.79        31.27       107.54 
TCGA-DV-5565 TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-B9-5155 TCGA-DW-5560 TCGA-DW-5561 
       43.69        25.58        12.26        21.86        48.85        13.61 
TCGA-DW-7839 TCGA-DW-7842 TCGA-UZ-A9PR TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8345 
       13.78         3.02        86.37       153.73        23.84        54.74 
TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8432 
      129.37        25.91        65.19       104.52         3.55         2.50 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      105.47       100.47       103.40        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 
       99.88       105.60        36.82        39.16        49.02        37.15 
TCGA-A3-3335 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3434 
       62.01        18.44        74.63        28.31        65.52        68.61 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4841 
        2.14        58.45        46.59        54.48        29.10         6.71 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 
       65.29        39.45        26.07         2.27        36.85        20.94 
TCGA-B0-5077 TCGA-B0-5102 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5399 
       43.30        90.87        30.48        41.88        51.02        46.39 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5705 
      111.52       129.67        85.78       126.28        80.91       149.16 
TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 
      130.65       131.15        91.46        21.30        31.30        32.98 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4153 
       21.57        12.00         4.64         0.36         0.23        25.05 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-A54G TCGA-BP-4161 
       50.14        23.74         0.85        16.60         1.74        90.28 
TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4346 
       62.24        97.45        27.78        62.07        15.62        49.08 
TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4973 
       31.89        13.15        13.51        60.30        57.40        45.50 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5174 TCGA-BP-5180 
       14.93        36.07        16.47        18.51        74.20        74.40 
TCGA-BP-5183 TCGA-BP-5190 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4887 
       42.44        33.24        46.55       114.41        64.27        30.64 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5683 TCGA-CW-5580 
      129.40        25.71        18.87        25.25        62.10        64.57 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6096 
       92.02         5.39        85.78        35.34        74.66        88.80 
TCGA-CZ-4853 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5455 
       25.45        63.39       107.41        63.42        58.82        18.44 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       55.33        94.45        12.69        67.96        65.65        14.63 
TCGA-CZ-5989 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-MM-A564 TCGA-2Z-A9J3 
       62.63         4.18        10.29        35.87        19.96        58.22 
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9KF TCGA-A4-7996 
        4.57        56.81         0.13        49.58        27.78        16.64 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 
       30.48        23.97         0.76        14.33         8.48        66.71 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5891 
       37.51        36.49        20.25        22.06         0.16         0.95 
TCGA-BQ-7051 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 
       50.40        19.00         2.40        90.90        25.15        20.52 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 
       25.25        17.98        23.08        80.65       194.79        27.65 
TCGA-HE-7129 TCGA-HE-A5NI TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z 
       81.93        11.84        12.76        29.10        11.41        27.78 
TCGA-MH-A562 TCGA-P4-AAVL TCGA-SX-A71R TCGA-SX-A7SQ TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       20.25        16.01        47.90        41.62        18.02        26.20 
TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       98.96        30.67        47.47        65.13       110.73        18.64 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$subtype2
TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-2Z-A9JD TCGA-2Z-A9JT TCGA-A4-7288 
       23.28        28.80       130.13        34.85        22.49        61.05 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-HE-A5NF TCGA-IZ-A6M8 
       96.92        26.27        20.12        11.28        84.89        16.34 
TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-KL-8326 TCGA-KL-8327 
       12.13        12.49        41.33        62.83       109.22       137.06 
TCGA-KL-8330 TCGA-KL-8344 TCGA-KM-8476 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8431 
      108.62        28.80       123.12        31.33        23.47        19.33 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8407 TCGA-KO-8416 TCGA-KO-8417 
      115.00        42.35       100.87        92.71        90.48        92.55 
TCGA-B8-A54E TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9KE 
       29.88        31.20        29.36        12.82        11.57        27.09 
TCGA-A4-7585 TCGA-A4-8098 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       35.18        29.46        41.13        14.86        12.30        86.76 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 
       43.20        47.80        40.83         7.66       123.62        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 TCGA-G7-6790 
       61.28        49.84         7.04         7.17        40.77        51.78 
TCGA-GL-A4EM TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A560 TCGA-P4-AAVK TCGA-P4-AAVM 
        1.05        16.31        19.99        30.38        52.27        50.60 
TCGA-P4-AAVO TCGA-UZ-A9PM TCGA-UZ-A9Q1 TCGA-Y8-A8S1 
       78.90       125.29        51.35        13.28 

$subtype3
TCGA-KL-8339 TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4799 TCGA-BP-4988 
       28.11        19.73        43.96        25.91        37.25        27.22 
TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CZ-4854 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-DW-7840 
       26.93        53.26        46.16        49.25        11.87         3.75 
TCGA-IA-A83W TCGA-Y8-A895 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 
       67.17        15.91        90.48        98.96        84.89        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8346 
       92.55        44.84        86.56        66.54        73.91        62.37 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KN-8421 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       44.91        49.97        87.91         0.99        52.27        87.12 
TCGA-KN-8433 TCGA-KO-8404 TCGA-A3-3313 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3378 
       11.21        10.68        24.16         4.50        43.20        20.71 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3436 TCGA-AK-3456 TCGA-B0-4688 TCGA-B0-4690 
      117.80       122.56       109.51        37.58         3.32         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4713 
        3.48        28.47         1.38         3.62        65.10         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4828 
        3.25        15.72         0.59         5.52        33.50        10.09 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 
       68.71        45.30        56.68         7.30        10.95         8.05 
TCGA-B0-5098 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5703 TCGA-B2-3923 
       52.08        19.30        52.87        56.98        73.84        32.61 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5551 TCGA-BP-4334 TCGA-BP-4337 TCGA-BP-4338 
        5.46        25.55         0.53        21.21         0.07        93.99 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4771 
       11.31        33.99        12.30         5.98        10.82         5.33 
TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-5169 
       15.78        10.98        58.68        46.45        43.00         6.35 
TCGA-CJ-4638 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4895 
       14.17        61.91       113.46        51.52        50.01        39.45 
TCGA-CJ-4913 TCGA-CJ-6031 TCGA-CW-6087 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 
       38.56        62.66         1.35        69.21         6.77        14.66 
TCGA-CZ-5464 TCGA-AL-3473 TCGA-B9-A5W8 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5889 
       69.96        62.66        17.23        21.63        25.35        10.82 
TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-A59R 
       79.86        13.08         0.43        39.25        71.44        12.43 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A83V TCGA-P4-A5EA TCGA-P4-A5ED TCGA-SX-A7SN 
       56.75        73.25        96.69         6.61        92.58        19.00 
TCGA-SX-A7SR TCGA-UZ-A9PL 
       26.47       103.63 

$subtype4
TCGA-A3-3329 TCGA-B0-5088 TCGA-B8-A54K TCGA-BP-4331 TCGA-BP-4760 TCGA-BP-4965 
       53.39        18.51        15.42        80.68        77.62        61.51 
TCGA-BP-4976 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 
       53.65        45.07        41.62        27.62        48.10        49.15 
TCGA-BP-5199 TCGA-CJ-4904 TCGA-CW-6093 TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 
       44.55       108.56       103.43         5.46        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-2Z-A9J9 TCGA-2Z-A9JJ 
       12.16        56.84        23.90        81.21        75.42        39.88 
TCGA-2Z-A9JL TCGA-A4-7734 TCGA-B3-A6W5 TCGA-DW-7834 TCGA-DW-7838 TCGA-KL-8333 
       33.07         0.89        10.16       129.86        24.46        98.33 
TCGA-KL-8336 TCGA-KL-8343 TCGA-KO-8415 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3320 
       30.25        71.41        96.62         0.53        49.08        49.58 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3372 
       37.38        48.82        29.92        88.37        51.25        24.16 
TCGA-AK-3444 TCGA-B0-4693 TCGA-B0-4710 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4833 
       48.36         2.53        57.70        45.07        16.77        78.44 
TCGA-B0-4839 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5110 TCGA-B0-5121 
       53.88        25.32        15.95        62.89        66.05        48.82 
TCGA-B0-5402 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-4098 TCGA-B2-4099 TCGA-B4-5378 
       42.41        79.89        89.49         1.68        31.96         5.75 
TCGA-B8-4146 TCGA-B8-5158 TCGA-B8-5165 TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4165 
       16.80        40.04        24.23        17.36        16.27        99.85 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4326 TCGA-BP-4341 TCGA-BP-4345 TCGA-BP-4347 
       77.03        61.78        53.42        52.24        49.84        44.94 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       72.59        77.98        48.07        61.97        56.91        68.38 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4969 TCGA-BP-4975 
       48.95        36.39        87.45        63.62        58.98        47.11 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       33.34        36.95        46.45        38.70        37.02        37.48 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5184 TCGA-BP-5185 
       79.30         2.04        30.64        52.27        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4870 TCGA-CJ-4871 
       22.78        23.47         0.95       115.00        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4886 TCGA-CJ-4893 TCGA-CJ-4897 
       47.18        75.06        71.87        64.18        24.66       109.84 
TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-6032 TCGA-CW-5583 
       49.28        45.14         4.57        18.81       119.64        81.83 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5453 TCGA-CZ-5457 
       73.18        78.18        58.75        93.04        79.53        90.54 
TCGA-CZ-5458 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 
       91.69        21.76        84.30         2.40        80.19        12.26 
TCGA-CZ-5988 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-MW-A4EC TCGA-2K-A9WE 
       22.78         3.91         6.77         7.96        16.37         7.04 
TCGA-A4-7583 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5901 
        0.10         7.63         3.81        80.88        51.19        34.19 
TCGA-G7-7502 TCGA-GL-A9DC TCGA-HE-A5NH TCGA-IZ-8196 TCGA-KV-A6GD TCGA-P4-A5E7 
       25.84        12.89        26.01        21.34        18.41        87.09 
TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-V9-A7HT TCGA-WN-A9G9 
      117.40        71.24        31.73        26.01 

$subtype5
TCGA-B8-A54H TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4986 TCGA-BP-5178 TCGA-CJ-6027 
        8.42        74.17        12.33        25.81        62.86       118.85 
TCGA-G6-A8L7 TCGA-Y8-A8RZ TCGA-KL-8341 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3347 
       70.13         6.74        24.79        48.59        36.36        52.93 
TCGA-A3-3382 TCGA-A3-3387 TCGA-B0-4691 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4843 
       18.87        20.28         4.57        40.44        36.53        10.52 
TCGA-B0-4844 TCGA-B0-5081 TCGA-B0-5092 TCGA-B0-5700 TCGA-B4-5832 TCGA-B8-5163 
       10.29        11.90        15.09        58.85         5.10        27.02 
TCGA-B8-5553 TCGA-B8-A54F TCGA-BP-4343 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4967 
       14.30        17.06        62.86         6.71        71.41         6.74 
TCGA-BP-4985 TCGA-BP-5187 TCGA-BP-5195 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4875 
       31.30        13.35        24.62        83.97        74.27       116.84 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4912 TCGA-CJ-5679 
       66.21        57.83        47.67        51.29        54.48        22.32 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-5456 TCGA-CZ-5462 
       67.00        53.42        66.31        47.08        79.63        10.22 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-A4VX TCGA-2Z-A9J8 TCGA-BQ-5878 TCGA-BQ-5885 
        1.94        31.10        53.46        91.73        63.72        30.28 
TCGA-HE-7130 TCGA-IA-A40U TCGA-J7-A8I2 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Y8-A896 
       58.19        16.80        10.09        99.78        99.12        18.64 

$subtype6
TCGA-B8-5162 TCGA-BP-4344 TCGA-BP-4775 TCGA-BP-4807 TCGA-BP-4993 TCGA-CJ-4642 
        1.18        54.77        60.59         6.94         5.82       105.37 
TCGA-CZ-4856 TCGA-DV-5569 TCGA-A4-7584 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.59        11.67        21.37        21.67        27.68        21.07 
TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-DW-7837 TCGA-DW-7841 TCGA-DZ-6134 TCGA-PJ-A5Z9 
       19.23        13.25        37.55        14.63        61.02        17.75 
TCGA-UZ-A9PZ TCGA-KM-8438 TCGA-3Z-A93Z TCGA-A3-3324 TCGA-A3-3373 TCGA-B0-5096 
       21.60       151.96        12.66        38.99        53.29         2.24 
TCGA-B0-5097 TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5120 TCGA-B0-5702 TCGA-B0-5706 
       21.86        52.54        38.63        38.43        71.41       105.37 
TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-A4SR TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54D 
       35.90        31.66        16.67         6.38        34.39        27.29 
TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4332 TCGA-BP-4355 TCGA-BP-4765 TCGA-BP-4801 
        4.93        14.17        37.25        31.33        71.80        36.95 
TCGA-BP-4964 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4989 TCGA-BP-5194 TCGA-BP-5198 
       61.22        49.38         6.94         3.88        13.41        19.82 
TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4899 TCGA-CJ-5684 TCGA-CJ-6033 TCGA-CZ-5454 
       34.95        21.24        50.24        73.35         7.36        23.74 
TCGA-EU-5904 TCGA-GK-A6C7 TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI 
       18.12         2.01        75.55       100.27        56.91        51.52 
TCGA-A4-8517 TCGA-B9-5156 TCGA-B9-A8YH TCGA-EV-5903 TCGA-GL-7773 TCGA-GL-A9DD 
       19.63        43.99        17.49        24.89        12.92        11.21 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IZ-8195 TCGA-SX-A71U TCGA-SX-A7SP 
       25.22         2.04        22.26        44.61        16.31 

$subtype7
TCGA-B0-4815 TCGA-BP-4762 TCGA-CJ-4894 TCGA-CJ-6030 TCGA-DV-5573 TCGA-DV-5574 
       52.21        44.15        27.65        75.58        37.15        66.28 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-PJ-A5Z8 TCGA-KN-8434 TCGA-6D-AA2E TCGA-A3-3349 
       11.97        44.84        19.73        59.08        11.90        45.53 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3376 TCGA-A3-3380 TCGA-AK-3451 
       10.49        28.70        74.76        55.76        18.64        94.29 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4836 
       19.00         7.82         5.98         6.02        14.93        40.70 
TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5104 TCGA-B0-5108 
       27.42        29.03        70.52        11.24        90.48        58.59 
TCGA-B0-5115 TCGA-B0-5697 TCGA-B0-5707 TCGA-B2-5636 TCGA-B4-5834 TCGA-B4-5835 
       52.73        86.47       123.09        30.21         1.25         0.53 
TCGA-B8-4143 TCGA-B8-5545 TCGA-B8-5550 TCGA-BP-4169 TCGA-BP-4349 TCGA-BP-4763 
       23.31        50.14        48.53        23.05        12.23        41.75 
TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4970 TCGA-BP-4971 
       61.68        60.95        36.53        47.97        14.24        48.89 
TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5196 
       30.64        35.21        28.87         9.63        38.30        33.47 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       63.98       115.69        56.35        49.97        49.18        50.33 
TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        3.06       131.08        72.00       133.71        18.15       122.83 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-5461 TCGA-CZ-5466 TCGA-DV-A4VZ 
      105.93        83.90        18.77        10.85        22.52        12.00 
TCGA-MM-A563 TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5877 TCGA-BQ-5879 
       19.43         0.23        67.73        12.46         8.88        22.92 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6135 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 
        7.92         2.76        74.60        10.68         1.18         4.01 
TCGA-G7-6793 TCGA-G7-A8LD TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5E8 TCGA-Q2-A5QZ 
       11.05        16.90         3.68        10.55        42.94        14.07 
TCGA-SX-A7SM TCGA-SX-A7SS TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A897 
       11.93        53.10        37.35        86.27        18.05 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.13     1.05     0.07     0.10     1.94     0.59     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  194.79   137.06   122.56   129.86   118.85   151.96   133.71 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  36.280   37.975   33.055   47.145   36.445   23.740   30.640 
[1] "0.1 - 194.8 (36.3)" "1.1 - 137.1 (38.0)" "0.1 - 122.6 (33.1)"
[4] "0.1 - 129.9 (47.1)" "1.9 - 118.8 (36.4)" "0.6 - 152.0 (23.7)"
[7] "0.2 - 133.7 (30.6)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     101       28        41       27
  subtype2      38        9        15        1
  subtype3      32       17        35       29
  subtype4     101       17        24        7
  subtype5      20        7        22       11
  subtype6      44        8        14        4
  subtype7      46        5        21       22
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I        101       38       32      101       20       44       46
  STAGE II        28        9       17       17        7        8        5
  STAGE III       41       15       35       24       22       14       21
  STAGE IV        27        1       29        7       11        4       22
[1] 4 7
[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 103  37  59   1
  subtype2  40   9  16   0
  subtype3  34  19  52  11
  subtype4 102  18  28   1
  subtype5  24   9  27   0
  subtype6  45   9  17   0
  subtype7  48   8  37   2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1      103       40       34      102       24       45       48
  T2       37        9       19       18        9        9        8
  T3       59       16       52       28       27       17       37
  T4        1        0       11        1        0        0        2
[1] 4 7
[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 87  4  0
  subtype2 19  3  0
  subtype3 60 12  0
  subtype4 46  1  1
  subtype5 28  4  1
  subtype6 25  2  0
  subtype7 35 13  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       87       19       60       46       28       25       35
  N1        4        3       12        1        4        2       13
  N2        0        0        0        1        1        0        3
[1] 3 7
[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 125  24
  subtype2  28   0
  subtype3  71  25
  subtype4 121   5
  subtype5  41   9
  subtype6  41   4
  subtype7  60  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125   24
  subtype2   28    0
  subtype3   71   25
  subtype4  121    5
  subtype5   41    9
  subtype6   41    4
  subtype7   60   19
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0      125       28       71      121       41       41       60
  1       24        0       25        5        9        4       19
[1] 2 7
[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  59 141
  subtype2  20  45
  subtype3  27  89
  subtype4  63  86
  subtype5  15  45
  subtype6  23  48
  subtype7  36  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59  141
  subtype2   20   45
  subtype3   27   89
  subtype4   63   86
  subtype5   15   45
  subtype6   23   48
  subtype7   36   59
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       59       20       27       63       15       23       36
  MALE        141       45       89       86       45       48       59
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1 104   2
  subtype2  48   0
  subtype3  45   0
  subtype4  43   0
  subtype5  18   0
  subtype6  38   0
  subtype7  35   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104    2
  subtype2   48    0
  subtype3   45    0
  subtype4   43    0
  subtype5   18    0
  subtype6   38    0
  subtype7   35    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO       104       48       45       43       18       38       35
  YES        2        0        0        0        0        0        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 19                               122
  subtype2                 18                                 1
  subtype3                 19                                73
  subtype4                  4                               120
  subtype5                  1                                49
  subtype6                  1                                44
  subtype7                  1                                69
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    59
  subtype2                                    46
  subtype3                                    24
  subtype4                                    25
  subtype5                                    10
  subtype6                                    26
  subtype7                                    25
D6V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          19       18       19        4
  KIDNEY CLEAR CELL RENAL CARCINOMA          122        1       73      120
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       59       46       24       25
                                       clus
vv                                      subtype5 subtype6 subtype7
  KIDNEY CHROMOPHOBE                           1        1        1
  KIDNEY CLEAR CELL RENAL CARCINOMA           49       44       69
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       10       26       25
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        18
  subtype2                                1     0                        14
  subtype3                                0     5                        12
  subtype4                                0     1                        20
  subtype5                                0     3                         5
  subtype6                                0     1                        12
  subtype7                                0     5                        12
          vv
clus       WHITE
  subtype1   175
  subtype2    48
  subtype3    96
  subtype4   124
  subtype5    51
  subtype6    57
  subtype7    74
D6V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   1        0        5        1        3
  BLACK OR AFRICAN AMERICAN              18       14       12       20        5
  WHITE                                 175       48       96      124       51
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   1        5
  BLACK OR AFRICAN AMERICAN              12       12
  WHITE                                  57       74
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
          cls
clus         0   1
  subtype1  10 151
  subtype2   5  49
  subtype3   2  75
  subtype4   8  90
  subtype5   3  39
  subtype6   0  50
  subtype7   4  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  151
  subtype2    5   49
  subtype3    2   75
  subtype4    8   90
  subtype5    3   39
  subtype6    0   50
  subtype7    4   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO           10        5        2        8        3        0
  NOT HISPANIC OR LATINO      151       49       75       90       39       50
                        clus
vv                       subtype7
  HISPANIC OR LATINO            4
  NOT HISPANIC OR LATINO       69
[1] 2 7
[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 = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 101  22
  subtype2 104  96
  subtype3 219  68
  subtype4 231  42
subtype1 subtype2 subtype3 subtype4 
     123      200      287      273 
subtype1 subtype2 subtype3 subtype4 
      22       96       68       42 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3328 TCGA-B0-5691 TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-BP-4995 
       45.53       112.80        15.42        77.62        20.38        45.07 
TCGA-CJ-4642 TCGA-CJ-5689 TCGA-DV-5567 TCGA-DV-5573 TCGA-DV-5576 TCGA-2Z-A9J9 
      105.37        53.26        65.88        37.15        23.90        75.42 
TCGA-BQ-7055 TCGA-MH-A857 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       26.27        29.26        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        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-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        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-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 
       99.88       105.60        96.62        90.48        92.55        24.16 
TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       43.20       117.80       112.08        94.19        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4834 
       83.21        12.13        40.70         3.62         2.14        68.71 
TCGA-B0-4841 TCGA-B0-5083 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5636 
        6.71        34.36        52.87        71.41        32.61        30.21 
TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-5546 TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4769 
        5.75        17.19        16.60        54.90        21.21        61.68 
TCGA-BP-4784 TCGA-BP-4994 TCGA-CJ-5681 TCGA-CW-5591 TCGA-DV-A4VZ TCGA-2Z-A9JN 
       60.95        43.00        18.15        74.66        12.00        24.33 
TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8312 TCGA-B3-4104 
       43.04        67.43        19.63         0.23        23.28        34.49 
TCGA-BQ-5883 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-6793 
       40.83        10.82         7.92        79.86         1.18        11.05 
TCGA-GL-7966 TCGA-HE-7130 TCGA-J7-A8I2 
        3.68        58.19        10.09 

$subtype2
TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B8-5162 TCGA-BP-4342 
      109.91        19.73        43.96        52.21         1.18        74.17 
TCGA-BP-4353 TCGA-BP-4799 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-5009 TCGA-BP-5178 
       12.33        37.25        25.81        27.22        35.90        62.86 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-6027 
       27.02        31.79        44.55        63.25        26.93       118.85 
TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5568 TCGA-DV-5574 
       75.58        46.16       107.54         5.46        12.16        66.28 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-BQ-7049 TCGA-KN-8427 TCGA-KO-8404 TCGA-A3-3308 
       70.13        23.01        44.84         0.99        10.68         0.53 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3346 
       49.08        49.02        37.15        36.36        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3426 TCGA-AK-3431 
       52.93        20.71        18.87        20.28        29.10        73.68 
TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
      109.51        78.64         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4713 
       28.47        19.00         1.38        65.10         5.98         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 
       58.45        15.72         0.59        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        10.52 
TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5092 TCGA-B0-5094 
       10.29        29.03        11.24        11.90        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        58.59 
TCGA-B0-5109 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5701 TCGA-B0-5706 
       19.30        41.88        38.43        56.98        80.91       105.37 
TCGA-B0-5709 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 
      130.65        31.66        21.57         5.10         5.46        23.31 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 
       25.55        40.04        27.02        50.14        48.53         0.53 
TCGA-B8-A54F TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4169 
       17.06         4.93        14.17        93.34        89.36        23.05 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 
       62.24        64.27        53.42         0.07        93.99        62.86 
TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4770 
       49.84        11.31        33.99         5.98        41.75        10.82 
TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
        5.33        68.38        15.78        36.53        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4967 TCGA-BP-4970 
        6.71        47.97        71.41        58.68         6.74        14.24 
TCGA-BP-4971 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 
       48.89        46.45        31.30         3.88        16.47        30.64 
TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5180 
       18.51        28.87         6.35        79.30        30.64        74.40 
TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
       38.30        13.35        24.62        33.47        19.82        46.55 
TCGA-CJ-4637 TCGA-CJ-4641 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
       73.22        54.61        21.24        83.97        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 
       74.27        66.21        61.91        51.52       115.69        39.45 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-4920 
       56.35        47.67        49.97        54.48         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 
       18.81       131.08       133.71        25.71        22.32        53.42 
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-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5456 TCGA-CZ-5461 
       47.08        69.21         6.77        14.66        79.63        10.85 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 
       69.96        22.52         1.94        31.10        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-EU-5905 TCGA-MM-A564 TCGA-2Z-A9JK TCGA-4A-A93Y 
       14.63        22.78         3.91        19.96        38.99        11.57 
TCGA-A4-7828 TCGA-BQ-5879 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-G7-6789 
        7.82        22.92        25.35         2.76        10.68         4.01 
TCGA-P4-A5E8 TCGA-P4-A5EA 
       42.94         6.61 

$subtype3
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        53.39        31.07        42.97        82.32 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 
       58.49        28.73        22.45        18.51       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-A54H TCGA-BP-4158 
       70.68       119.38       126.05        24.82         8.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4762 
       94.72        32.61         3.58        80.68        54.77        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4993 
       60.59        11.64         6.94        61.51        53.65         5.82 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5201 TCGA-CJ-4894 
       41.62        27.62        48.10        49.15        31.27        27.65 
TCGA-CJ-4904 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 
      108.56       103.43         0.59        43.69        45.96        11.67 
TCGA-DV-5575 TCGA-DV-A4W0 TCGA-5P-A9JV TCGA-BQ-5892 TCGA-3Z-A93Z TCGA-A3-3306 
       56.84        81.21        67.17        11.97        12.66        36.82 
TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.58        48.59        38.99        37.38        48.82 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 
       45.53        29.92        18.44        88.37        51.25        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        24.16        53.29        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 
        0.10        11.18        10.62       122.56       109.41        68.61 
TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       48.36        94.29        38.40        82.45        72.89         1.41 
TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 
        2.53         7.82        57.70         3.25        46.59         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
       45.07        16.77        14.93        54.48        10.09        78.44 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       27.42        53.88        65.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 
       36.85        70.52        20.94        43.30        25.32        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 
       90.87        90.48        66.05        38.63        52.73        51.02 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        42.41       111.52       129.67        85.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 
      126.28        58.85        73.84       149.16        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       89.49        91.46        35.90        31.96        21.30        31.30 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       32.98        16.67        12.00         1.25         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5552 
       50.14        23.74         0.85        24.23         6.38        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4159 
       14.30        27.29         1.74        17.36        16.27        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4170 TCGA-BP-4174 
       90.28       101.06        99.85         0.43        77.03        61.78 
TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4340 
       97.45        27.78        62.07        37.25        15.62        18.48 
TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 
       52.24        49.08        44.94        12.23        31.89        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 
       72.59        77.98        71.80        48.07        13.15        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 
       13.51        56.91        48.95        36.95        87.45        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 
       60.30        61.22        57.40        58.98        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 
        6.94        47.11        14.93        36.07        33.34        36.95 
TCGA-BP-4991 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5173 
       46.45        38.70        37.02        37.48        35.21         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.20        52.27         9.63        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 
       22.78        33.24        23.47        13.41        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 
      115.00       106.16       114.41        58.95        11.05        49.25 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
       75.06       116.84        64.27        71.87        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 
       64.18        30.64        63.98        50.01        24.66       109.84 
TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 
       50.24        51.29        49.18        49.28        50.33        45.14 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 
       72.00       129.40        18.87        25.25       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       73.35        67.00       119.64        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-6088 
        5.39        85.78        73.18        78.18        35.34       105.93 
TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       25.45        58.75        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 
       55.33        94.45        21.76        84.30         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       80.19        12.26        62.63        18.12         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        16.37 

$subtype4
TCGA-B8-4621 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       25.91        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       22.49        12.26        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       19.73        17.75        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-6D-AA2E TCGA-A3-3363 
       21.60        15.91        15.62         6.74        11.90        10.49 
TCGA-AK-3456 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5697 TCGA-B0-5707 
       37.58         7.30        52.08        30.48        86.47       123.09 
TCGA-B2-4098 TCGA-B4-5835 TCGA-B8-A54E TCGA-BP-4756 TCGA-CJ-4638 TCGA-CZ-5462 
        1.68         0.53        29.88        12.30        14.17        10.22 
TCGA-DV-A4VX TCGA-G6-A5PC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       53.46         7.96        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        51.52        30.71        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        12.82       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        27.78        18.21         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
       19.13        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        29.03        30.58        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 
       21.63        26.04        30.28         7.66         0.95       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       74.60        34.19        19.00        24.89        13.08         2.40 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        0.43        51.78        90.90        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.09        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  153.73   133.71   149.16   194.79 
subtype1 subtype2 subtype3 subtype4 
   49.97    31.20    45.53    25.64 
[1] "0.2 - 153.7 (50.0)" "0.1 - 133.7 (31.2)" "0.1 - 149.2 (45.5)"
[4] "0.1 - 194.8 (25.6)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      59       33        19       12
  subtype2      61       21        70       47
  subtype3     169       29        57       31
  subtype4     171       20        43       15
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         59       61      169      171
  STAGE II        33       21       29       20
  STAGE III       19       70       57       43
  STAGE IV        12       47       31       15
[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  60  34  29   2
  subtype2  65  26  99  10
  subtype3 170  35  81   2
  subtype4 192  32  49   1
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       60       65      170      192
  T2       34       26       35       32
  T3       29       99       81       49
  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  61   6   3
  subtype2  89  18   1
  subtype3 126   1   0
  subtype4  54  18   2
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       61       89      126       54
  N1        6       18        1       18
  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"
D7V6, binary
          cls
clus         0   1
  subtype1  75   9
  subtype2 146  42
  subtype3 239  29
  subtype4  91  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75    9
  subtype2  146   42
  subtype3  239   29
  subtype4   91   10
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       75      146      239       91
  1        9       42       29       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  48  77
  subtype2  52 148
  subtype3 120 168
  subtype4  71 205
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   77
  subtype2   52  148
  subtype3  120  168
  subtype4   71  205
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       48       52      120       71
  MALE         77      148      168      205
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1  88   0
  subtype2  39   0
  subtype3  87   2
  subtype4 201   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   88    0
  subtype2   39    0
  subtype3   87    2
  subtype4  201    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        88       39       87      201
  YES        0        0        2        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 64                                42
  subtype2                  2                               187
  subtype3                  0                               286
  subtype4                  0                                18
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    19
  subtype2                                    11
  subtype3                                     2
  subtype4                                   258
D7V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          64        2        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           42      187      286       18
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       19       11        2      258
[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"
D7V11, continuous
D7V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        20
  subtype2                                0     4                        13
  subtype3                                0     2                        27
  subtype4                                2     6                        61
          vv
clus       WHITE
  subtype1    98
  subtype2   180
  subtype3   254
  subtype4   194
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        2
  ASIAN                                   4        4        2        6
  BLACK OR AFRICAN AMERICAN              20       13       27       61
  WHITE                                  98      180      254      194
[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"
D7V14, binary
          cls
clus         0   1
  subtype1   5  82
  subtype2   7 128
  subtype3  18 186
  subtype4  12 233
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   82
  subtype2    7  128
  subtype3   18  186
  subtype4   12  233
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        7       18       12
  NOT HISPANIC OR LATINO       82      128      186      233
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  77  12
  subtype2  37  24
  subtype3 117  34
  subtype4  66  18
  subtype5  56  66
  subtype6  24  13
  subtype7  80  30
  subtype8  45  14
  subtype9 153  17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      89       61      151       84      122       37      110       59 
subtype9 
     170 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12       24       34       18       66       13       30       14 
subtype9 
      17 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3328 TCGA-BP-4995 TCGA-BQ-7055 TCGA-MH-A857 TCGA-KL-8323 TCGA-KL-8324 
       45.53        45.07        26.27        29.26        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
       92.55        43.20       117.80       112.08        94.19        46.78 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4834 
       40.01        83.21        12.13        40.70         3.62        68.71 
TCGA-B0-5083 TCGA-B0-5117 TCGA-B2-3923 TCGA-B8-4619 TCGA-BP-4334 TCGA-BP-4994 
       34.36        52.87        32.61        17.19        21.21        43.00 
TCGA-2Z-A9JN TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-8312 TCGA-BQ-5883 
       24.33        43.04        67.43        23.28        40.83 

$subtype2
TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-CJ-4642 TCGA-DV-5567 TCGA-DV-5576 
       15.42        77.62        20.38       105.37        65.88        23.90 
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-BQ-5888 TCGA-BQ-7049 TCGA-PJ-A5Z8 TCGA-KN-8427 
       75.42        39.88        13.25        44.84        19.73         0.99 
TCGA-KO-8404 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-5084 TCGA-B0-5098 
       10.68         3.32        28.47         1.38         7.30        52.08 
TCGA-B0-5100 TCGA-B0-5109 TCGA-B0-5702 TCGA-B2-5636 TCGA-B4-5378 TCGA-BP-4177 
       62.89        19.30        71.41        30.21         5.75        54.90 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4784 TCGA-CW-5591 TCGA-CW-6087 TCGA-DV-A4VZ 
       61.68        10.82        60.95        74.66         1.35        12.00 
TCGA-A4-7287 TCGA-A4-7828 TCGA-A4-7915 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
       19.63         7.82         0.23        29.03        34.49        20.61 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6132 
        8.88        22.92        10.82         7.92         2.76        80.88 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LC 
       10.68        13.08         1.18         4.01        11.05        23.08 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-A8I2 
       16.90        12.92         3.68        58.19         2.04        10.09 
TCGA-MH-A856 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-UN-AAZ9 TCGA-UZ-A9PN 
       31.13        42.94         6.61        92.58        18.02        37.35 
TCGA-Y8-A896 
       18.64 

$subtype3
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-AK-3454 TCGA-B0-5691 
       47.21        38.47        53.39        31.07        28.73       112.80 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 
       70.68       119.38       126.05       111.02        94.72        80.68 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 
       61.51        53.65         5.82        41.62        27.62        48.10 
TCGA-BP-5201 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CW-6093 TCGA-DV-5565 TCGA-DV-5566 
       31.27        27.65        53.26       103.43        43.69        45.96 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 
       11.67        37.15        66.28        12.66        36.82        39.16 
TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3365 
       48.59        38.99        37.38        18.44        51.25        28.70 
TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NN 
       74.63        24.16        55.76        18.64        28.31         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3434 TCGA-AK-3458 TCGA-AK-3460 
       11.18        10.62       122.56        68.61        38.40        82.45 
TCGA-AK-3461 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 
       72.89         2.14         3.25        58.45        46.59         5.52 
TCGA-B0-4828 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-5115 
       10.09         6.71        65.29        26.07         2.27        52.73 
TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5699 
       41.88        48.82        46.39        42.41        85.78       126.28 
TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3924 
       58.85        73.84        79.89       131.15        91.46        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5834 
       31.96        21.30        31.30        32.98        16.67         1.25 
TCGA-B4-5843 TCGA-B8-4153 TCGA-B8-4622 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-A54J 
        0.36        25.05        50.14         0.85        24.23        17.36 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4347 
       85.51        90.28        61.78        27.78        37.25        44.94 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4777 
       72.59        77.98        71.80        13.15        13.51        56.91 
TCGA-BP-4789 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4982 
       48.95        63.62        60.30        45.50        47.11        33.34 
TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5190 
       37.02         2.04        42.44        37.25        37.22        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4640 TCGA-CJ-4870 
       23.47        13.41        34.95         0.95       114.41        49.25 
TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4899 
       47.18       116.84        64.27       113.46        30.64        50.24 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 
       51.29        49.28        50.33        72.00       129.40        18.87 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 
      122.83        62.10        73.35        92.02         5.39        85.78 
TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4861 TCGA-CZ-4864 
       78.18        35.34       105.93        25.45        14.66        93.04 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5460 
       63.42        79.53        23.74        18.44        90.54        94.45 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5906 
       10.85        21.76        12.69        12.26        62.63         6.77 
TCGA-G6-A8L6 
       10.29 

$subtype4
TCGA-2Z-A9JD TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B 
       34.85        12.26        61.05        12.99        49.25        11.87 
TCGA-BQ-5886 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-MH-A855 TCGA-SX-A7SO TCGA-Y8-A8RZ 
       26.04        20.12        11.28        12.13        41.33         6.74 
TCGA-6D-AA2E TCGA-A3-3313 TCGA-AK-3456 TCGA-B0-5107 TCGA-B2-4098 TCGA-B4-5835 
       11.90        24.16        37.58        30.48         1.68         0.53 
TCGA-B8-5546 TCGA-B8-A54E TCGA-BP-4756 TCGA-CJ-5681 TCGA-T7-A92I TCGA-2Z-A9J2 
       16.60        29.88        12.30        18.15        11.70        59.01 
TCGA-2Z-A9J8 TCGA-2Z-A9JI TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       91.73        51.52        31.20        12.82        11.57       106.55 
TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8518 
       15.48        19.36        12.39        35.18        29.46        19.73 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-B1-5398 TCGA-B1-A655 
       12.46         8.48         8.28         9.63        41.13        16.77 
TCGA-B1-A656 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.32        17.23         0.16        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 
       19.27        63.72        43.20        21.63        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
       25.35         7.66         0.95       123.62        93.34        61.28 
TCGA-BQ-7053 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-7501 TCGA-GL-6846 
       49.84         7.17        79.86         0.43        20.52       194.79 
TCGA-GL-A4EM TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 
        1.05        16.31        73.25        19.99        22.26        10.55 
TCGA-MH-A560 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       30.38        99.78        99.12        52.27        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-AB4C TCGA-Y8-A8S1 
       14.07        11.93        86.27        51.35        39.06        13.28 

$subtype5
TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B8-5162 TCGA-BP-4342 
      109.91        19.73        43.96        52.21         1.18        74.17 
TCGA-BP-4799 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5191 
       37.25        25.81        27.22        35.90        62.86        31.79 
TCGA-BP-5199 TCGA-CJ-4891 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-G6-A8L7 
       44.55        26.93       118.85        75.58        46.16        70.13 
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3378 
        0.53        49.08        37.15         4.50        52.93        20.71 
TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4690 
       18.87        29.10        73.68       109.51        78.64         1.41 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4813 
        3.48        19.00        65.10         5.98        15.72         0.59 
TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 
       33.50         6.02        40.44        36.53        29.10        40.70 
TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5080 
       45.30        56.68        10.52        10.29        29.03        11.24 
TCGA-B0-5081 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5108 
       11.90        10.95         8.05         2.24        21.86        58.59 
TCGA-B0-5400 TCGA-B0-5706 TCGA-B4-5832 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5158 
       56.98       105.37         5.10        23.31        25.55        40.04 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4167 
       27.02         0.53        17.06         4.93         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4345 
       23.05        64.27        53.42        93.99        62.86        49.84 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4787 TCGA-BP-4798 
       11.31        33.99         5.98        41.75        15.78        10.98 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5010 
       47.97        71.41        46.45        31.30         3.88        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4637 
        6.35        79.30        30.64        33.47        19.82        73.22 
TCGA-CJ-4868 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4890 
       21.24        74.27        66.21        61.91        51.52       115.69 
TCGA-CJ-4895 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-4923 
       39.45        47.67        49.97        54.48         3.06        18.81 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 
      131.08       133.71        22.32        53.42        62.66         7.36 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 
       66.31        83.90        47.08        69.21         6.77        79.63 
TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX 
       10.22        69.96         1.94        31.10        67.96        53.46 
TCGA-EU-5905 TCGA-MM-A564 
        3.91        19.96 

$subtype6
TCGA-CJ-4636 TCGA-MM-A84U TCGA-BQ-5892 TCGA-A3-3317 TCGA-A3-3357 TCGA-AK-3451 
       63.25        23.01        11.97        49.02        88.37        94.29 
TCGA-B0-4691 TCGA-B0-4713 TCGA-B0-5075 TCGA-B0-5092 TCGA-B0-5709 TCGA-B4-5838 
        4.57         6.64        20.94        15.09       130.65         5.46 
TCGA-B8-5550 TCGA-B8-A54D TCGA-B8-A54G TCGA-BP-4163 TCGA-BP-4337 TCGA-BP-4771 
       48.53        27.29         1.74        93.34         0.07         5.33 
TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-5174 TCGA-CJ-4638 
       36.39        87.45        58.68        48.89        74.20        14.17 
TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4884 TCGA-CJ-4900 TCGA-CJ-5677 TCGA-CJ-5680 
       54.61        83.97        57.83        56.35        25.71        25.25 
TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-G6-A5PC TCGA-2Z-A9JK TCGA-AL-3473 
       18.77       107.41        58.82         7.96        38.99        62.66 
TCGA-WN-A9G9 
       26.01 

$subtype7
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-5693 TCGA-B8-A54H 
       42.97        82.32        58.49        22.45       133.94         8.42 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4344 TCGA-BP-4775 TCGA-BP-5181 TCGA-CJ-4904 
       32.61         3.58        54.77        60.59        49.15       108.56 
TCGA-CZ-4856 TCGA-DV-5575 TCGA-A3-3320 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3370 
        0.59        56.84        49.58        48.82        45.53        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       109.41 
TCGA-AK-3444 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4818 TCGA-B0-4824 
       48.36         2.53         7.82        57.70        16.77        54.48 
TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-4945 
       78.44        27.42        53.88        39.45        36.85        70.52 
TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 
       25.32        15.95        90.87        90.48        66.05        38.63 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5705 TCGA-B0-5712 
       51.02        38.43       111.52       129.67       149.16        89.49 
TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
       12.00         4.64         0.23        16.80        49.97        42.71 
TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A7U6 TCGA-B8-A8YJ 
       45.37        23.74        34.39        14.30        16.27        14.17 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4335 
      101.06        99.85        77.03        97.45        62.07        15.62 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4766 
       18.48        52.24        12.23        31.89        31.33        48.07 
TCGA-BP-4774 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4981 
       61.97        61.22        58.98        49.38         6.94        36.07 
TCGA-BP-4987 TCGA-BP-5001 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5186 TCGA-CJ-4634 
       36.95        38.70        52.27         9.63        22.78       115.00 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4886 
      106.16        58.95        11.05        75.06        71.87        64.18 
TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4916 
       63.98        50.01        24.66       109.84        49.18        45.14 
TCGA-CJ-4920 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5587 TCGA-CZ-4859 
        4.57        67.00       119.64        81.83        73.18        58.75 
TCGA-CZ-4863 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-EU-5904 TCGA-G6-A8L8 
       63.39        84.30         2.40        80.19        18.12        35.87 
TCGA-GK-A6C7 TCGA-MW-A4EC 
        2.01        16.37 

$subtype8
TCGA-B0-5088 TCGA-B0-5694 TCGA-B2-5635 TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4782 
       18.51        15.78        24.82        12.33        44.15        11.64 
TCGA-BP-4807 TCGA-BP-5189 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5568 TCGA-DV-A4W0 
        6.94        27.02       107.54         5.46        12.16        81.21 
TCGA-5P-A9JV TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3351 TCGA-A3-3387 TCGA-A3-A6NI 
       67.17        36.36        62.01        29.92        20.28        33.47 
TCGA-AS-3778 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-5077 TCGA-B0-5106 TCGA-B0-5701 
        1.41        45.07        14.93        43.30        52.54        80.91 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B8-5545 TCGA-B8-5549 TCGA-BP-4173 TCGA-BP-4346 
       31.66        21.57        50.14         6.38        62.24        49.08 
TCGA-BP-4781 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4967 TCGA-BP-4968 
       68.38        36.53        36.95         6.71         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4977 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       14.24        14.93        46.45        16.47        30.64        18.51 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5195 
       37.48        35.21        74.40        38.30        13.35        24.62 
TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CW-5580 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5466 
       46.55        79.66        64.57        91.69        55.33        22.52 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-EU-5907 TCGA-MM-A563 
       65.65        14.63        22.78         4.18        19.43 

$subtype9
TCGA-B8-4621 TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7584 
       25.91        33.07        25.58        16.18        22.49        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
        0.89        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       21.86        19.23        96.92        48.85        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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        35.38        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-A3-3363 TCGA-B0-5697 TCGA-B0-5707 TCGA-2K-A9WE TCGA-2Z-A9J1 
       15.62        10.49        86.47       123.09         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-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ 
       30.71        29.36         5.29         0.13        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KE 
       22.26        78.64        71.80        62.93        12.99        27.09 
TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 
       27.78        18.21         0.10        19.13        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       25.64        23.97        23.31         0.76        19.63        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.96        16.31        15.75        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       66.71        67.73         2.20        37.51        36.49        20.25 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       33.83        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 
        0.46         1.15        43.99        22.06        17.49        47.80 
TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 
       48.26        50.40         7.63         7.04         3.81        40.77 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       51.19        74.60        34.19        19.00        24.89         2.40 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       51.78        90.90        39.25        71.44        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC 
       25.25        17.98        80.65        27.65        12.43        12.89 
TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       11.21        81.93        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 
       16.80        85.78        88.24        96.69        21.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL 
       27.65        20.25        17.62        15.48        87.09        16.01 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        27.06        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      117.40       103.63       125.29        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-Y8-A894 TCGA-Y8-A897 
       47.47        65.13       110.73        31.73        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    2.50     0.23     0.10     0.16     0.43     0.07     0.10     1.41 
subtype9 
    0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  153.73   105.37   131.15   194.79   133.71   130.65   149.16   107.54 
subtype9 
  129.86 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  54.740   19.300   44.940   20.420   34.945   38.990   49.165   31.660 
subtype9 
  26.435 
[1] "2.5 - 153.7 (54.7)" "0.2 - 105.4 (19.3)" "0.1 - 131.2 (44.9)"
[4] "0.2 - 194.8 (20.4)" "0.4 - 133.7 (34.9)" "0.1 - 130.7 (39.0)"
[7] "0.1 - 149.2 (49.2)" "1.4 - 107.5 (31.7)" "0.1 - 129.9 (26.4)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      38       30        15        5
  subtype2      29        3        14       15
  subtype3      84       15        29       23
  subtype4      36        5        30        7
  subtype5      31       14        45       31
  subtype6       8        6        14       10
  subtype7      72        9        22        8
  subtype8      38        6        10        3
  subtype9     124       15        10        3
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         38       29       84       36       31        8       72
  STAGE II        30        3       15        5       14        6        9
  STAGE III       15       14       29       30       45       14       22
  STAGE IV         5       15       23        7       31       10        8
           clus
vv          subtype8 subtype9
  STAGE I         38      124
  STAGE II         6       15
  STAGE III       10       10
  STAGE IV         3        3
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  39  30  20   1
  subtype2  29   5  22   6
  subtype3  85  21  43   2
  subtype4  42   9  32   1
  subtype5  33  16  69   4
  subtype6  10   8  19   1
  subtype7  72  10  29   0
  subtype8  40   6  13   0
  subtype9 137  22  11   0
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1       39       29       85       42       33       10       72       40
  T2       30        5       21        9       16        8       10        6
  T3       20       22       43       32       69       19       29       13
  T4        1        6        2        1        4        1        0        0
    clus
vv   subtype9
  T1      137
  T2       22
  T3       11
  T4        0
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 51  2  2
  subtype2 11 16  2
  subtype3 54  1  0
  subtype4 25 12  1
  subtype5 60  7  0
  subtype6 17  4  0
  subtype7 60  0  0
  subtype8 23  1  0
  subtype9 29  0  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       51       11       54       25       60       17       60       23
  N1        2       16        1       12        7        4        0        1
  N2        2        2        0        1        0        0        0        0
    clus
vv   subtype9
  N0       29
  N1        0
  N2        1
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1  55   3
  subtype2  30   9
  subtype3 125  21
  subtype4  35   5
  subtype5  86  31
  subtype6  23   9
  subtype7  93   8
  subtype8  52   3
  subtype9  52   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    3
  subtype2   30    9
  subtype3  125   21
  subtype4   35    5
  subtype5   86   31
  subtype6   23    9
  subtype7   93    8
  subtype8   52    3
  subtype9   52    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       55       30      125       35       86       23       93       52
  1        3        9       21        5       31        9        8        3
   clus
vv  subtype9
  0       52
  1        1
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  34  56
  subtype2  26  36
  subtype3   9 142
  subtype4  33  51
  subtype5  31  91
  subtype6  17  21
  subtype7 108   3
  subtype8   3  56
  subtype9  30 142
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   56
  subtype2   26   36
  subtype3    9  142
  subtype4   33   51
  subtype5   31   91
  subtype6   17   21
  subtype7  108    3
  subtype8    3   56
  subtype9   30  142
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       34       26        9       33       31       17      108
  MALE         56       36      142       51       91       21        3
        clus
vv       subtype8 subtype9
  FEMALE        3       30
  MALE         56      142
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus         0   1
  subtype1  77   0
  subtype2  29   0
  subtype3  45   2
  subtype4  54   0
  subtype5  19   0
  subtype6  12   0
  subtype7  36   0
  subtype8  11   0
  subtype9 132   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77    0
  subtype2   29    0
  subtype3   45    2
  subtype4   54    0
  subtype5   19    0
  subtype6   12    0
  subtype7   36    0
  subtype8   11    0
  subtype9  132    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        77       29       45       54       19       12       36       11
  YES        0        0        2        0        0        0        0        0
     clus
vv    subtype9
  NO       132
  YES        1
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      15       11       15       17       13        2       13        5 
subtype9 
      52 
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype5" "subtype7"
  [7] "subtype8" "subtype3" "subtype3" "subtype2" "subtype8" "subtype3"
 [13] "subtype3" "subtype3" "subtype7" "subtype2" "subtype8" "subtype5"
 [19] "subtype9" "subtype9" "subtype4" "subtype9" "subtype9" "subtype9"
 [25] "subtype9" "subtype9" "subtype9" "subtype9" "subtype9" "subtype9"
 [31] "subtype9" "subtype9" "subtype4" "subtype9" "subtype1" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [43] "subtype1" "subtype3" "subtype7" "subtype7" "subtype7" "subtype5"
 [49] "subtype3" "subtype7" "subtype3" "subtype7" "subtype2" "subtype5"
 [55] "subtype3" "subtype4" "subtype7" "subtype3" "subtype7" "subtype5"
 [61] "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype3"
 [67] "subtype5" "subtype3" "subtype8" "subtype7" "subtype5" "subtype7"
 [73] "subtype5" "subtype2" "subtype7" "subtype5" "subtype3" "subtype8"
 [79] "subtype3" "subtype7" "subtype4" "subtype9" "subtype1" "subtype9"
 [85] "subtype4" "subtype4" "subtype9" "subtype2" "subtype4" "subtype9"
 [91] "subtype9" "subtype1" "subtype9" "subtype4" "subtype9" "subtype4"
 [97] "subtype9" "subtype4" "subtype9" "subtype9" "subtype9" "subtype4"
[103] "subtype9" "subtype9" "subtype9" "subtype9" "subtype2" "subtype2"
[109] "subtype9" "subtype9" "subtype2" "subtype9" "subtype9" "subtype9"
[115] "subtype4" "subtype9" "subtype9" "subtype9" "subtype2" "subtype2"
[121] "subtype9" "subtype9" "subtype4" "subtype2" "subtype4" "subtype4"
[127] "subtype4" "subtype9" "subtype9" "subtype9" "subtype9" "subtype9"
[133] "subtype4" "subtype9" "subtype9" "subtype9" "subtype9" "subtype9"
[139] "subtype9" "subtype9" "subtype9"
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 64                                19
  subtype2                  2                                23
  subtype3                  0                               151
  subtype4                  0                                11
  subtype5                  0                               122
  subtype6                  0                                34
  subtype7                  0                               111
  subtype8                  0                                58
  subtype9                  0                                 4
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     7
  subtype2                                    37
  subtype3                                     0
  subtype4                                    73
  subtype5                                     0
  subtype6                                     4
  subtype7                                     0
  subtype8                                     1
  subtype9                                   168
D8V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          64        2        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           19       23      151       11
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        7       37        0       73
                                       clus
vv                                      subtype5 subtype6 subtype7 subtype8
  KIDNEY CHROMOPHOBE                           0        0        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA          122       34      111       58
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        0        4        0        1
                                       clus
vv                                      subtype9
  KIDNEY CHROMOPHOBE                           0
  KIDNEY CLEAR CELL RENAL CARCINOMA            4
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      168
[1] 3 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
[1] "Remove cluster labels:" "subtype8"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12        5        4       23        5        6        3        2 
subtype9 
      47 
  [1] "subtype9" "subtype5" "subtype4" "subtype9" "subtype4" "subtype4"
  [7] "subtype9" "subtype9" "subtype9" "subtype9" "subtype9" "subtype9"
 [13] "subtype9" "subtype9" "subtype9" "subtype4" "subtype1" "subtype1"
 [19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [25] "subtype1" "subtype1" "subtype1" "subtype7" "subtype3" "subtype3"
 [31] "subtype5" "subtype6" "subtype3" "subtype7" "subtype5" "subtype3"
 [37] "subtype6" "subtype4" "subtype5" "subtype6" "subtype7" "subtype5"
 [43] "subtype6" "subtype4" "subtype4" "subtype9" "subtype9" "subtype4"
 [49] "subtype4" "subtype6" "subtype9" "subtype1" "subtype4" "subtype9"
 [55] "subtype4" "subtype4" "subtype9" "subtype9" "subtype4" "subtype4"
 [61] "subtype4" "subtype4" "subtype9" "subtype9" "subtype9" "subtype9"
 [67] "subtype9" "subtype9" "subtype9" "subtype4" "subtype9" "subtype4"
 [73] "subtype9" "subtype2" "subtype9" "subtype4" "subtype9" "subtype2"
 [79] "subtype9" "subtype2" "subtype9" "subtype9" "subtype9" "subtype4"
 [85] "subtype9" "subtype9" "subtype9" "subtype9" "subtype2" "subtype9"
 [91] "subtype4" "subtype4" "subtype9" "subtype9" "subtype9" "subtype4"
 [97] "subtype9" "subtype9" "subtype9" "subtype9" "subtype9" "subtype6"
[103] "subtype9" "subtype2" "subtype9"
D8V12, continuous
[1] "Remove cluster labels:" "subtype8"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype8 subtype9 
       9        5        3       18        3        4        2       31 
 [1] "subtype5" "subtype6" "subtype4" "subtype9" "subtype9" "subtype9"
 [7] "subtype9" "subtype9" "subtype4" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype5" "subtype6" "subtype3" "subtype5" "subtype6"
[25] "subtype4" "subtype9" "subtype9" "subtype4" "subtype4" "subtype1"
[31] "subtype4" "subtype9" "subtype4" "subtype4" "subtype4" "subtype4"
[37] "subtype9" "subtype9" "subtype9" "subtype9" "subtype9" "subtype4"
[43] "subtype9" "subtype4" "subtype2" "subtype9" "subtype4" "subtype9"
[49] "subtype2" "subtype9" "subtype2" "subtype9" "subtype9" "subtype9"
[55] "subtype9" "subtype2" "subtype4" "subtype4" "subtype4" "subtype9"
[61] "subtype9" "subtype9" "subtype4" "subtype9" "subtype9" "subtype9"
[67] "subtype9" "subtype9" "subtype6" "subtype4" "subtype9" "subtype2"
[73] "subtype9"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                        10
  subtype2                                0     3                        14
  subtype3                                0     1                        11
  subtype4                                0     3                        24
  subtype5                                0     2                         7
  subtype6                                0     0                         5
  subtype7                                0     1                        12
  subtype8                                0     2                         4
  subtype9                                2     2                        34
          vv
clus       WHITE
  subtype1    76
  subtype2    42
  subtype3   135
  subtype4    55
  subtype5   113
  subtype6    32
  subtype7    97
  subtype8    52
  subtype9   124
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   2        3        1        3        2
  BLACK OR AFRICAN AMERICAN              10       14       11       24        7
  WHITE                                  76       42      135       55      113
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        2
  ASIAN                                   0        1        2        2
  BLACK OR AFRICAN AMERICAN               5       12        4       34
  WHITE                                  32       97       52      124
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
          cls
clus         0   1
  subtype1   4  53
  subtype2   3  48
  subtype3   7 102
  subtype4   5  66
  subtype5   4  81
  subtype6   1  30
  subtype7  11  67
  subtype8   2  32
  subtype9   5 150
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   53
  subtype2    3   48
  subtype3    7  102
  subtype4    5   66
  subtype5    4   81
  subtype6    1   30
  subtype7   11   67
  subtype8    2   32
  subtype9    5  150
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            4        3        7        5        4        1
  NOT HISPANIC OR LATINO       53       48      102       66       81       30
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO           11        2        5
  NOT HISPANIC OR LATINO       67       32      150
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 292  50
  subtype2 128  68
  subtype3 222 107
subtype1 subtype2 subtype3 
     342      196      329 
subtype1 subtype2 subtype3 
      50       68      107 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8442 TCGA-KO-8411 TCGA-B8-4621 
      102.81        28.11        23.28        47.24       130.13        25.91 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       22.49        12.26        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       26.27        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 
       19.33         2.50        11.21        59.08       115.00       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3357 
       99.88       105.60        96.62        90.48        92.55        88.37 
TCGA-A3-3363 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       10.49        43.20       112.08        94.19        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5084 TCGA-B0-5098 
       83.21        37.58        40.70         3.62         7.30        52.08 
TCGA-B0-5117 TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5835 TCGA-B8-A54D 
       52.87       123.09        32.61         1.68         0.53        27.29 
TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4994 
       29.88         4.93        21.21        11.31         5.98        43.00 
TCGA-CJ-4873 TCGA-CJ-4900 TCGA-G6-A5PC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       74.27        56.35         7.96         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        51.52        30.71        24.33        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        12.82       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KF TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.39        27.09        27.78        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
       35.18        19.13        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
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-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       62.66         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       17.49        12.30        86.76        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 
       47.80        21.63        26.04        30.28         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 
        7.92       123.62        48.26        61.28        50.40         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        79.86        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       74.60        34.19        19.00        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         0.43        51.78        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC 
       16.90       194.79        12.92        27.65        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        10.09        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       92.58        52.27        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      117.40       103.63       125.29        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 

$subtype2
TCGA-KM-8441 TCGA-AK-3425 TCGA-B0-4712 TCGA-B0-5691 TCGA-B0-5812 TCGA-B8-5162 
       28.80       109.91        43.96       112.80       126.05         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4353 TCGA-BP-4760 
        8.42        15.42        94.72        80.68        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4986 TCGA-BP-4988 TCGA-CJ-4636 
       44.15        20.38         6.94        25.81        27.22        63.25 
TCGA-CJ-5689 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       53.26        37.15        66.28        56.84        23.90        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-5P-A9JV TCGA-BQ-7049 TCGA-BQ-7056 TCGA-KL-8333 
       70.13        23.01        67.17        44.84        20.12        98.33 
TCGA-KL-8344 TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 TCGA-3Z-A93Z TCGA-6D-AA2E 
       28.80         0.99       100.87        10.68        12.66        11.90 
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3349 
        0.53        24.16        49.08        49.02        52.93        45.53 
TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NN 
       51.25        53.29        55.76        20.28        33.47         0.10 
TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3461 
        0.10        29.10        73.68        78.64        94.29        72.89 
TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       12.13         3.32         1.41         4.57         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4819 
        1.38        65.10         5.98        46.59         0.59         6.02 
TCGA-B0-4827 TCGA-B0-4843 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       29.10        10.52        70.52        11.24        11.90        34.36 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5109 
        8.05         2.24        21.86        62.89        58.59        19.30 
TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B2-5636 
       38.43        56.98        71.41       130.65        79.89        30.21 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 
        5.46        23.31        17.19        27.02        50.14        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4167 
        0.53        34.39        17.06        16.27        14.17        89.36 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4332 TCGA-BP-4337 TCGA-BP-4341 
       23.05        62.24        54.90        37.25         0.07        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4354 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 
       62.86        49.84        33.99        71.80        61.68        10.82 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       15.78        48.95        36.53        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4982 
       58.68        58.98        14.24        48.89        49.38        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 
       46.45        31.30         3.88        30.64        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
        6.35        79.30         9.63        38.30        37.25        22.78 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4641 TCGA-CJ-4872 TCGA-CJ-4881 
       33.47        19.82       115.00        54.61        47.18        66.21 
TCGA-CJ-4882 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4902 TCGA-CJ-4905 
       61.91        63.98       115.69        39.45        49.97        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5677 
       49.28        50.33         3.06        18.81       131.08        25.71 
TCGA-CJ-5680 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6088 
       25.25        62.66         7.36        66.31         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 
       83.90        18.77        47.08        69.21         6.77        79.63 
TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-T7-A92I 
       22.78        12.00         3.91        35.87        19.43        11.70 
TCGA-2Z-A9JK TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-7828 
       38.99        31.20        11.57        19.36        19.63         7.82 
TCGA-A4-7915 TCGA-AL-7173 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 
        0.23        67.73         8.88        22.92        40.83        25.35 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-DZ-6132 TCGA-EV-5903 
       10.82         2.76        93.34        49.84        80.88        24.89 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LE TCGA-GL-7966 TCGA-GL-A4EM TCGA-KV-A6GD 
        4.01        11.05        80.65         3.68         1.05        18.41 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-UZ-A9PN TCGA-Y8-A8S1 
       16.01        14.07        37.35        13.28 

$subtype3
TCGA-A3-3307 TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       47.21        42.97        58.49        28.73        22.45        19.73 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       52.21        18.51       133.94        15.78        70.68       119.38 
TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4342 TCGA-BP-4344 
       24.82       111.02        32.61         3.58        74.17        54.77 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4799 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4993 
       60.59        11.64        37.25        61.51        53.65         5.82 
TCGA-BP-4995 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       45.07        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-BQ-5892 TCGA-KN-8436 TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3320 
       11.67        11.97        42.35        39.16        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3346 
       48.59        36.36        38.99        37.38        48.82         4.50 
TCGA-A3-3351 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3378 
       29.92        28.70        74.63        74.76        24.16        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        18.87        28.31        65.52        15.39        22.65 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       11.18        10.62       117.80       122.56       109.41        15.78 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4693 
       68.61       109.51        48.36        38.40        82.45         2.53 
TCGA-B0-4696 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       28.47         7.82         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       58.45        15.72         5.52        45.07        33.50        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
       40.44        36.53        14.93        54.48        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5092 
        2.27        36.85        20.94        43.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       10.95        15.95        90.87        90.48        52.54        30.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5121 
       66.05        38.63        52.73        41.88        51.02        48.82 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        58.85        80.91        73.84       149.16       105.37 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
      131.15        89.49        91.46        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         1.25         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        49.97        42.71        25.05        45.37        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5546 
       50.14        40.04        23.74         0.85        24.23        16.60 
TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54G TCGA-B8-A54J TCGA-BP-4159 TCGA-BP-4161 
        6.38        14.30         1.74        17.36        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
      101.06        93.34        99.85         0.43        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4338 
       97.45        53.42        27.78        62.07        15.62        93.99 
TCGA-BP-4340 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 
       18.48        49.08        44.94        31.89        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 
       72.59        77.98        41.75        48.07        13.15         5.33 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       13.51        56.91        68.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4973 
        6.71        87.45        60.30         6.74        57.40        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4987 TCGA-BP-4991 
        6.94        47.11        14.93        36.07        36.95        46.45 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5173 
       16.47        18.51        38.70        37.02        37.48         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 
       74.20        30.64        52.27        74.40        42.44        37.22 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 
       13.35        33.24        23.47        13.41        24.62        34.95 
TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4875 
       58.95        11.05        83.97        49.25        79.66       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       64.27        71.87        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       51.52        50.01        24.66       109.84        50.24        47.67 
TCGA-CJ-4903 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5675 
       51.29        54.48        45.14         4.57        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        18.87        22.32        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       73.35        67.00        53.42       119.64        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5590 
       81.83         5.39        85.78        73.18        78.18        35.34 
TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       74.66        25.45        58.75        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       14.63        62.63        53.46        18.12         6.77         4.18 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-WN-A9G9 
       10.29         2.01        19.96        16.37        26.01 

subtype1 subtype2 subtype3 
    0.10     0.07     0.23 
subtype1 subtype2 subtype3 
  194.79   131.08   149.16 
subtype1 subtype2 subtype3 
   29.41    33.47    41.75 
[1] "0.1 - 194.8 (29.4)" "0.1 - 131.1 (33.5)" "0.2 - 149.2 (41.8)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     191       50        59       18
  subtype2      93       15        52       34
  subtype3     163       36        78       52
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        191       93      163
  STAGE II        50       15       36
  STAGE III       59       52       78
  STAGE IV        18       34       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 212  62  66   4
  subtype2  96  16  76   9
  subtype3 166  47 115   2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      212       96      166
  T2       62       16       47
  T3       66       76      115
  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  94  24   2
  subtype2  79  14   4
  subtype3 145   6   0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       94       79      145
  N1       24       14        6
  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"
D9V6, binary
          cls
clus         0   1
  subtype1 135  13
  subtype2 134  26
  subtype3 266  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135   13
  subtype2  134   26
  subtype3  266   50
   clus
vv  subtype1 subtype2 subtype3
  0      135      134      266
  1       13       26       50
[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"
D9V7, binary
          cls
clus         0   1
  subtype1  98 248
  subtype2  73 124
  subtype3 114 216
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98  248
  subtype2   73  124
  subtype3  114  216
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       98       73      114
  MALE        248      124      216
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1 266   1
  subtype2  61   0
  subtype3  83   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  266    1
  subtype2   61    0
  subtype3   83    2
     clus
vv    subtype1 subtype2 subtype3
  NO       266       61       83
  YES        1        0        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"
D9V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 59                                29
  subtype2                  6                               160
  subtype3                  1                               327
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   258
  subtype2                                    31
  subtype3                                     2
D9V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3
  KIDNEY CHROMOPHOBE                          59        6        1
  KIDNEY CLEAR CELL RENAL CARCINOMA           29      160      327
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      258       31        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"
D9V11, continuous
D9V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     9                        66
  subtype2                                0     3                        35
  subtype3                                0     4                        20
          vv
clus       WHITE
  subtype1   254
  subtype2   156
  subtype3   300
D9V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   9        3        4
  BLACK OR AFRICAN AMERICAN              66       35       20
  WHITE                                 254      156      300
[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"
D9V14, binary
          cls
clus         0   1
  subtype1  14 271
  subtype2   7 132
  subtype3  19 217
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  271
  subtype2    7  132
  subtype3   19  217
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        7       19
  NOT HISPANIC OR LATINO      271      132      217
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  65  11
  subtype2 212 137
  subtype3 174  59
  subtype4 191  18
subtype1 subtype2 subtype3 subtype4 
      76      349      233      209 
subtype1 subtype2 subtype3 subtype4 
      11      137       59       18 
$subtype1
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BQ-7055 TCGA-KL-8323 
      102.81        28.11        47.24       130.13        26.27        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        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-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
      105.47       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       43.20       117.80       112.08        94.19        46.78        40.01 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4834 TCGA-B0-5083 TCGA-B0-5117 TCGA-B2-3923 
       12.13        40.70        68.71        34.36        52.87        32.61 
TCGA-B8-4619 TCGA-BP-4334 TCGA-BP-4994 TCGA-5P-A9KH 
       17.19        21.21        43.00        67.43 

$subtype2
TCGA-KM-8439 TCGA-KM-8441 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       23.28        28.80       109.91        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B8-5162 TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4342 
       18.51       112.80         1.18        15.42        94.72        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       54.77        12.33        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-5009 
       37.25         6.94        25.81        27.22         5.82        35.90 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       31.79        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4862 
      108.56        53.26       118.85        75.58        46.16       107.54 
TCGA-CZ-4865 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 
        5.46        65.88        12.16        37.15        66.28        23.90 
TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-5P-A9JV TCGA-A4-A5Y1 
       81.21        23.01        75.42        39.88        67.17        12.99 
TCGA-AL-A5DJ TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       49.25        11.97        44.84        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DZ-6134 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-KM-8639 
      129.86        61.02        29.26        19.73        41.33        31.33 
TCGA-KN-8427 TCGA-KN-8437 TCGA-KO-8404 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 
        0.99       100.87        10.68        11.90         0.53        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3331 TCGA-A3-3346 
       49.08        49.02        37.15        36.36        48.82         4.50 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3378 TCGA-A3-3382 
       52.93        88.37        28.70        24.16        20.71        18.87 
TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 
       20.28         0.10        29.10        73.68       109.51        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-B0-4688 
       94.29        83.21        37.58        38.40        72.89         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-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4811 
        3.62        65.10         5.98         6.64        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
        0.59        33.50         6.02        40.44        36.53        14.93 
TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 
       29.10        40.70        45.30        27.42        53.88        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 
       10.52        10.29        29.03        20.94        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
        7.30        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5120 
       52.08        62.89        30.48        58.59        19.30        38.43 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 
       56.98        42.41        85.78        86.47        80.91        71.41 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B2-5636 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 
      105.37       130.65        30.21        32.98        21.57         5.75 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4620 
        5.10         0.53         5.46         0.23        23.31        25.55 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
       40.04        27.02        50.14        16.60        48.53         0.53 
TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       34.39        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
       14.17        90.28        93.34        89.36        23.05        62.24 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4332 TCGA-BP-4337 TCGA-BP-4338 
       64.27        54.90        53.42        37.25         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4354 
       18.48        62.86        49.84        49.08        11.31        33.99 
TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       12.30         5.98        41.75        61.68        10.82         5.33 
TCGA-BP-4777 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       56.91        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4970 
        6.71        47.97        87.45        71.41        58.68        14.24 
TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4998 
       48.89         6.94        46.45        31.30         3.88        30.64 
TCGA-BP-5000 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 
       18.51        35.21        28.87         6.35        79.30        30.64 
TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
       38.30        13.35        24.62        33.47        19.82        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4871 
       73.22        14.17       114.41        54.61        83.97        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4887 
       47.18        74.27        66.21        61.91        57.83        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 
       51.52        63.98       115.69        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       131.08       133.71 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-6028 
       25.71        22.32        25.25        18.15       122.83        53.42 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5590 
       62.66         7.36        64.57        92.02        66.31        35.34 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
        1.35        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 
       14.66       107.41        58.82        23.74        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       91.69        69.96        22.52         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-A4VX TCGA-DV-A4VZ 
       67.96        65.65        14.63        22.78        53.46        12.00 
TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A5PC TCGA-MM-A563 TCGA-MM-A564 TCGA-T7-A92I 
        3.91         4.18         7.96        19.43        19.96        11.70 
TCGA-2Z-A9J2 TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9K3 
       59.01        38.99        24.33        31.20        11.57        15.48 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       43.04        19.36        19.63        35.18         7.82         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 
       29.46        23.28        19.73         9.63        62.66        67.73 
TCGA-B1-A656 TCGA-B3-4104 TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
       20.32        34.49        14.86        19.27         8.88        22.92 
TCGA-BQ-5880 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       43.20        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 
        7.66         0.95         7.92         2.76        93.34        61.28 
TCGA-BQ-7053 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-EV-5903 TCGA-F9-A4JJ 
       49.84         7.17        79.86        80.88        24.89        10.68 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LD 
        1.18         0.43         4.01        11.05        20.52        16.90 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-7130 TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-8537 
        3.68         1.05        58.19        96.69        22.26        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL 
       10.09        18.41        42.94         6.61        92.58        16.01 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-WN-AB4C 
       14.07        11.93        37.35        86.27        26.01        39.06 
TCGA-Y8-A8S1 
       13.28 

$subtype3
TCGA-A3-3307 TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5693 
       47.21        42.97        58.49        28.73        22.45       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-A54H 
       15.78        70.68       119.38       126.05        24.82         8.42 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4775 TCGA-BP-4965 
      111.02        32.61         3.58        80.68        60.59        61.51 
TCGA-BP-4976 TCGA-BP-4995 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       53.65        45.07        48.10        62.86        49.15        27.02 
TCGA-CJ-4894 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 
       27.65       103.43         0.59        43.69        45.96        11.67 
TCGA-DV-5575 TCGA-3Z-A93Z TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 
       56.84        12.66        39.16        49.58        48.59        38.99 
TCGA-A3-3326 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       37.38        45.53        29.92        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI 
       53.29        55.76        18.64        28.31        65.52        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 
       15.39        22.65         0.10        11.18        10.62       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3460 TCGA-B0-4693 
      109.41        15.78        68.61        48.36        82.45         2.53 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4814 
        7.82         2.14        57.70         3.25        15.72         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4841 
       45.07        16.77        54.48        10.09        78.44         6.71 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       43.30        25.32        15.95        90.87        90.48        52.54 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5121 
       66.05        38.63        52.73        41.88        51.02        48.82 
TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 
       46.39       111.52       129.67       126.28        58.85        73.84 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
      149.16        79.89       131.15        89.49        91.46        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-A4SR TCGA-B4-5377 
       31.96        21.30        31.30        31.66        16.67        12.00 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        1.25         4.64         0.36        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 
       25.05        45.37        50.14        23.74         0.85        24.23 
TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4162 
        6.38        14.30        17.36        16.27        85.51       101.06 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 
       99.85         0.43        61.78        97.45        27.78        62.07 
TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4758 
       15.62        52.24        44.94        31.89        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4781 
       77.98        71.80        48.07        13.15        13.51        68.38 
TCGA-BP-4801 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       36.95        63.62        60.30         6.74        57.40        58.98 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       36.95        46.45        16.47        38.70        37.02        37.48 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 
        2.04        74.20        52.27         9.63        74.40        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.25        37.22        22.78        33.24        23.47        13.41 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       34.95         0.95       115.00       106.16        58.95        11.05 
TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 
       49.25       116.84        64.27        71.87       113.46        64.18 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4905 
       50.01        24.66       109.84        50.24        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5675 
       49.28        50.33        45.14         4.57        72.00       129.40 
TCGA-CJ-5678 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 
       18.87        62.10        73.35        67.00       119.64        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        5.39        85.78        73.18        78.18        74.66       105.93 
TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 
       25.45        58.75        63.39        93.04        63.42        79.53 
TCGA-CZ-5455 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       18.44        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 
       84.30         2.40        80.19        12.26        62.63        18.12 
TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MW-A4EC 
        6.77        10.29        35.87         2.01        16.37 

$subtype4
TCGA-B8-4621 TCGA-G6-A8L7 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       25.91        70.13        34.85        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        12.26        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DW-7836 
       19.23        26.04        13.25        96.92        13.61        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A5Z9 
       17.95        84.89        67.17        16.34        12.13        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       12.49        35.38        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-A3-3363 TCGA-B0-5707 TCGA-B2-4098 TCGA-2K-A9WE 
       15.62         6.74        10.49       123.09         1.68         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        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.81        54.64        51.52        30.71        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        12.82       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       78.64        71.80        62.93        12.99        12.39        27.09 
TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 
       27.78        18.21         0.10        19.13        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       25.64        23.97        23.31         0.76        19.63        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 
       12.46        70.19        49.32        66.71         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 
       37.51        36.49        20.25        16.77        33.83        29.03 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       30.58        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5882 
       17.49        12.30        86.76        63.72        47.80        21.63 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
      123.62        48.26        50.40         7.63         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7Q0 
       40.77        51.19        74.60        34.19        19.00        13.08 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        2.40        51.78        90.90        39.25        71.44        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        23.08        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       12.92        27.65        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IZ-8196 
       16.80        19.99         2.04        85.78        88.24        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        12.76        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       99.78        87.09        99.12        52.27        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
       47.90        49.45        44.61        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        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS 
       26.20       117.40       103.63       125.29        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.64        18.05        25.28         6.02 

subtype1 subtype2 subtype3 subtype4 
    2.50     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  153.73   133.71   149.16   194.79 
subtype1 subtype2 subtype3 subtype4 
  66.985   30.640   45.500   25.910 
[1] "2.5 - 153.7 (67.0)" "0.1 - 133.7 (30.6)" "0.1 - 149.2 (45.5)"
[4] "0.1 - 194.8 (25.9)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      28       29        15        4
  subtype2     139       32       103       70
  subtype3     138       23        48       25
  subtype4     142       17        23        5
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         28      139      138      142
  STAGE II        29       32       23       17
  STAGE III       15      103       48       23
  STAGE IV         4       70       25        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  29  29  19   0
  subtype2 145  41 151  13
  subtype3 140  29  64   1
  subtype4 160  26  23   1
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       29      145      140      160
  T2       29       41       29       26
  T3       19      151       64       23
  T4        0       13        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  48   2   2
  subtype2 134  32   4
  subtype3 100   3   0
  subtype4  36   7   0
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       48      134      100       36
  N1        2       32        3        7
  N2        2        4        0        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"
D10V6, binary
          cls
clus         0   1
  subtype1  50   2
  subtype2 227  61
  subtype3 196  24
  subtype4  62   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    2
  subtype2  227   61
  subtype3  196   24
  subtype4   62    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       50      227      196       62
  1        2       61       24        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  28  49
  subtype2 112 238
  subtype3  99 135
  subtype4  46 166
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   49
  subtype2  112  238
  subtype3   99  135
  subtype4   46  166
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28      112       99       46
  MALE         49      238      135      166
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1  67   0
  subtype2 108   2
  subtype3  70   0
  subtype4 165   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    0
  subtype2  108    2
  subtype3   70    0
  subtype4  165    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        67      108       70      165
  YES        0        2        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"
D10V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                 60                                15
  subtype2                  6                               262
  subtype3                  0                               234
  subtype4                  0                                 5
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                     2
  subtype2                                    82
  subtype3                                     0
  subtype4                                   207
D10V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                          60        6        0        0
  KIDNEY CLEAR CELL RENAL CARCINOMA           15      262      234        5
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        2       82        0      207
[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"
D10V11, continuous
D10V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         6
  subtype2                                0     9                        47
  subtype3                                0     2                        22
  subtype4                                2     3                        46
          vv
clus       WHITE
  subtype1    67
  subtype2   288
  subtype3   206
  subtype4   149
D10V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        2
  ASIAN                                   2        9        2        3
  BLACK OR AFRICAN AMERICAN               6       47       22       46
  WHITE                                  67      288      206      149
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   4  41
  subtype2  17 245
  subtype3  12 152
  subtype4   7 182
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   41
  subtype2   17  245
  subtype3   12  152
  subtype4    7  182
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4       17       12        7
  NOT HISPANIC OR LATINO       41      245      152      182
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 142  14
  subtype2  58  10
  subtype3  37  27
  subtype4  85  38
subtype1 subtype2 subtype3 subtype4 
     156       68       64      123 
subtype1 subtype2 subtype3 subtype4 
      14       10       27       38 
$subtype1
TCGA-B8-4621 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-A4-7288 
       25.91        34.85        33.07        25.58        22.49        61.05 
TCGA-A4-7734 TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 
        0.89        27.68        21.07        21.86        11.87        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 
       13.25        96.92        11.28        48.85        13.61        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-GL-A59T 
       37.55        24.46        13.78         3.75         3.02        17.95 
TCGA-IA-A83W TCGA-MH-A855 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-UZ-A9PO 
       67.17        12.13        19.73        17.75        35.38        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-2K-A9WE TCGA-2Z-A9J1 
       86.37        21.60        15.62         6.74         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       59.01        58.22       100.27        56.91        54.64        51.52 
TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JW 
       30.71        29.36         5.29         0.13        12.82       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       49.58        90.21        22.26        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       27.09        27.78        18.21        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        66.71         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A5W9 
       20.25        33.83        26.40         0.46        43.99         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5890 
       17.49        12.30        63.72        47.80        26.04         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 
        0.95       123.62        48.26        61.28        50.40         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.04         7.17         3.81        80.88        51.19        74.60 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       19.00        10.68        13.08        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       71.44        25.84        25.25        17.98        23.08        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
      194.79        12.92        27.65        12.89        11.21        16.31 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       56.75        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GE 
       88.24        22.26        21.34        12.36        12.76        29.10 
TCGA-KV-A74V TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       11.41        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-AAVK TCGA-P4-AAVM TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       42.94        52.27        50.60        47.90        49.45        44.61 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       27.06        19.00        16.31        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV 
       26.20       117.40       103.63        98.96        30.67        47.47 
TCGA-UZ-A9PX TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       65.13        31.73        26.01        18.05        25.28         6.02 

$subtype2
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-B8-A54K 
      102.81        28.11        23.28        28.80        47.24        15.42 
TCGA-2Z-A9J9 TCGA-BQ-7055 TCGA-MH-A857 TCGA-SX-A7SO TCGA-KL-8323 TCGA-KL-8324 
       75.42        26.27        29.26        41.33        38.07       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      137.06        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       30.25        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       28.80        54.74       151.96        31.33       129.37        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.48        25.91        65.19         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 
       19.33         2.50        11.21        59.08        42.35       100.87 
TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
      100.47        16.67       104.55       103.10        99.88        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-T7-A92I 
       90.48        92.55        94.19        12.13        32.61        11.70 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-5P-A9K8 TCGA-A4-8312 TCGA-B9-A69E TCGA-BQ-5882 
       24.33        31.20        43.04        23.28        14.86        21.63 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5893 TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-7501 
       40.83        25.35         7.92        79.86         1.18        20.52 
TCGA-HE-7130 TCGA-WN-AB4C 
       58.19        39.06 

$subtype3
TCGA-B0-5691 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-5P-A9JV TCGA-A4-A5Y1 
      112.80        70.13        23.01        39.88        67.17        12.99 
TCGA-BQ-7049 TCGA-BQ-7056 TCGA-DW-7834 TCGA-DZ-6134 TCGA-KN-8427 TCGA-KO-8404 
       44.84        20.12       129.86        61.02         0.99        10.68 
TCGA-6D-AA2E TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-5702 TCGA-B8-A8YJ TCGA-BP-4173 
       11.90         1.38        65.10        71.41        14.17        62.24 
TCGA-BP-4770 TCGA-BP-4804 TCGA-BP-4985 TCGA-CJ-4881 TCGA-CW-6087 TCGA-CZ-4860 
       10.82        47.97        31.30        66.21         1.35         6.77 
TCGA-2Z-A9JK TCGA-4A-A93Y TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7828 
       38.99        11.57        19.36        19.63        35.18         7.82 
TCGA-A4-7915 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-4104 
        0.23        19.73         9.63        67.73        20.32        34.49 
TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5889 
       12.46        19.27         8.88        22.92        43.20        10.82 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A97G 
        2.76        93.34        49.84        34.19        24.89         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A83V 
        4.01        11.05        16.90         3.68         1.05        96.69 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ 
       10.55        10.09        18.41         6.61        16.01        14.07 
TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       11.93        37.35        86.27        13.28 

$subtype4
TCGA-A3-3358 TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.97        43.96        18.51       133.94        15.78        70.68 
TCGA-B2-5635 TCGA-B8-A54H TCGA-BP-4807 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4995 
       24.82         8.42         6.94        53.65        27.22        45.07 
TCGA-BP-5009 TCGA-CZ-4854 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 
       35.90        46.16        43.69        45.96        11.67        37.15 
TCGA-BQ-5892 TCGA-3Z-A93Z TCGA-A3-3317 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       11.97        12.66        49.02        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3458 TCGA-B0-4706 
       22.65         0.10        11.18        10.62        38.40         2.14 
TCGA-B0-4710 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4836 TCGA-B0-4837 
       57.70        15.72        46.59        40.44        40.70        45.30 
TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5696 
       36.85        11.24        25.32        46.39       129.67        85.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5709 TCGA-B2-3924 TCGA-B2-5633 
      126.28        58.85       149.16       130.65        35.90        31.66 
TCGA-B2-5636 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-5545 TCGA-B8-5550 
       30.21        32.98        12.00         4.64        50.14        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
        0.53        34.39        14.30         4.93        17.36        16.27 
TCGA-BP-4340 TCGA-BP-4761 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4959 
       18.48         5.98        15.78        48.95        36.53        87.45 
TCGA-BP-4961 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4974 
       63.62         6.74        57.40        58.98        14.24         6.94 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 
       36.07        33.34         3.88        16.47        30.64        38.70 
TCGA-BP-5008 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4887 
       35.21        49.25       116.84        64.27        71.87        30.64 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-5671 TCGA-CJ-5675 
       63.98       115.69        39.45        56.35       131.08       129.40 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
      133.71        18.15        62.10        67.00        62.66       119.64 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4864 
       85.78        78.18       105.93        47.08        69.21        93.04 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 
       79.53        23.74        18.44        90.54        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        69.96        22.52         2.40        31.10        12.69 
TCGA-CZ-5989 TCGA-EU-5904 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       62.63        18.12         7.96        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-AL-3473 
       19.43        19.96        62.66 

subtype1 subtype2 subtype3 subtype4 
    0.13     1.18     0.23     0.10 
subtype1 subtype2 subtype3 subtype4 
  194.79   153.73   129.86   149.16 
subtype1 subtype2 subtype3 subtype4 
  26.025   41.840   19.315   36.070 
[1] "0.1 - 194.8 (26.0)" "1.2 - 153.7 (41.8)" "0.2 - 129.9 (19.3)"
[4] "0.1 - 149.2 (36.1)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     107       10        20        4
  subtype2      27       17        18        6
  subtype3      25        4        19       15
  subtype4      62       16        24       21
D11V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I        107       27       25       62
  STAGE II        10       17        4       16
  STAGE III       20       18       19       24
  STAGE IV         4        6       15       21
[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 119  16  20   1
  subtype2  27  17  24   1
  subtype3  27   5  27   6
  subtype4  65  18  40   1
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1      119       27       27       65
  T2       16       17        5       18
  T3       20       24       27       40
  T4        1        1        6        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 27  7  0
  subtype2 33  5  2
  subtype3 15 15  4
  subtype4 51  4  0
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       27       33       15       51
  N1        7        5       15        4
  N2        0        2        4        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"
D11V6, binary
          cls
clus        0  1
  subtype1 48  1
  subtype2 34  4
  subtype3 28  8
  subtype4 88 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    1
  subtype2   34    4
  subtype3   28    8
  subtype4   88   20
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       48       34       28       88
  1        1        4        8       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus         0   1
  subtype1  35 123
  subtype2  31  38
  subtype3  26  39
  subtype4  41  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  123
  subtype2   31   38
  subtype3   26   39
  subtype4   41   83
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       31       26       41
  MALE        123       38       39       83
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus         0   1
  subtype1 119   0
  subtype2  61   0
  subtype3  31   0
  subtype4  43   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119    0
  subtype2   61    0
  subtype3   31    0
  subtype4   43    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       119       61       31       43
  YES        0        0        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"
D11V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                  0                                 1
  subtype2                 46                                 5
  subtype3                  2                                16
  subtype4                  0                               122
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                   157
  subtype2                                    18
  subtype3                                    47
  subtype4                                     2
D11V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                           0       46        2        0
  KIDNEY CLEAR CELL RENAL CARCINOMA            1        5       16      122
  KIDNEY PAPILLARY RENAL CELL CARCINOMA      157       18       47        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"
D11V11, continuous
D11V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     2                        25
  subtype2                                0     2                        11
  subtype3                                0     3                        14
  subtype4                                0     3                        21
          vv
clus       WHITE
  subtype1   122
  subtype2    52
  subtype3    47
  subtype4    97
D11V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0
  ASIAN                                   2        2        3        3
  BLACK OR AFRICAN AMERICAN              25       11       14       21
  WHITE                                 122       52       47       97
[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"
D11V14, binary
          cls
clus         0   1
  subtype1   7 134
  subtype2   4  36
  subtype3   3  49
  subtype4   6  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  134
  subtype2    4   36
  subtype3    3   49
  subtype4    6   89
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7        4        3        6
  NOT HISPANIC OR LATINO      134       36       49       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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 84  7
  subtype2 51 33
  subtype3 46  3
  subtype4 18  2
  subtype5 28 17
  subtype6 57 20
  subtype7 38  7
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      91       84       49       20       45       77       45 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       7       33        3        2       17       20        7 
$subtype1
TCGA-B8-4621 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JT TCGA-A4-7288 TCGA-B1-A47O 
       25.91        34.85        33.07        22.49        61.05        27.68 
TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       26.04        96.92        13.61        37.55        13.78         3.75 
TCGA-GL-A59T TCGA-IA-A83W TCGA-MH-A855 TCGA-UZ-A9PO TCGA-Y8-A8RZ TCGA-2K-A9WE 
       17.95        67.17        12.13        62.83         6.74         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       75.55        58.22       100.27        56.91        54.64        51.52 
TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        5.29        12.82       106.55        49.58        90.21        22.26 
TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KF TCGA-A4-7286 TCGA-A4-7996 TCGA-A4-7997 
       12.99        27.09        27.78        18.21        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-B9-4115 TCGA-B9-4117 TCGA-B9-5156 
       15.75         8.28        41.13        26.40         0.46        43.99 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7051 
       17.49        12.30        63.72         7.66       123.62        50.40 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 
        7.63         7.04         3.81        51.19        74.60        19.00 
TCGA-F9-A7Q0 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-A8LB TCGA-G7-A8LC 
       13.08        51.78        90.90        39.25        17.98        23.08 
TCGA-GL-8500 TCGA-GL-A9DC TCGA-GL-A9DE TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       27.65        12.89        16.31        16.80        19.99         2.04 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-AAVM TCGA-SX-A71R 
       12.36        29.10        11.41        99.78        50.60        47.90 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       44.61        27.06        19.00        16.31        26.47        53.10 
TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-V9-A7HT 
       26.20       103.63        98.96        30.67        47.47        31.73 
TCGA-Y8-A897 
       18.05 

$subtype2
TCGA-B8-A54K TCGA-CZ-4854 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ 
       15.42        46.16        70.13        23.01        75.42        39.88 
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-7049 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DZ-6134 
       12.99        11.87        44.84        20.12        11.28        61.02 
TCGA-PJ-A5Z8 TCGA-6D-AA2E TCGA-A3-3317 TCGA-B2-5636 TCGA-B8-A54I TCGA-BP-4173 
       19.73        11.90        49.02        30.21         4.93        62.24 
TCGA-BP-4340 TCGA-BP-4761 TCGA-BP-4804 TCGA-CJ-4881 TCGA-CJ-4900 TCGA-CW-6087 
       18.48         5.98        47.97        66.21        56.35         1.35 
TCGA-CZ-4857 TCGA-CZ-5469 TCGA-G6-A5PC TCGA-2Z-A9J2 TCGA-2Z-A9JK TCGA-4A-A93Y 
       47.08        31.10         7.96        59.01        38.99        11.57 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7828 
       62.93        19.36        12.39        19.63        35.18         7.82 
TCGA-A4-7915 TCGA-A4-8518 TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 
        0.23        19.73         8.48         9.63        62.66        67.73 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
       20.32        33.83        34.49        19.27         8.88        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 
       43.20        21.63        25.35        10.82         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7053 TCGA-BQ-7061 TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5903 
        2.76        49.84         7.17        80.88        34.19        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LD 
       10.68         1.18         0.43         4.01        11.05        16.90 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-7130 TCGA-IA-A83V TCGA-IZ-8195 TCGA-J7-8537 
        3.68         1.05        58.19        96.69        22.26        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVL 
       10.09        18.41        42.94         6.61        52.27        16.01 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8S1 
       14.07        11.93        37.35        86.27        26.01        13.28 

$subtype3
TCGA-2Z-A9JQ TCGA-A4-7734 TCGA-B1-A657 TCGA-B9-5155 TCGA-BQ-5888 TCGA-DW-5560 
       25.58         0.89        21.07        21.86        13.25        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 TCGA-PJ-A5Z9 TCGA-SX-A71W 
      129.86        35.93        24.46         3.02        17.75        35.38 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-4A-A93W 
       86.37        21.60        15.62        30.71        29.36         0.13 
TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-8121 TCGA-B9-A5W9 
       66.71         2.20        36.49        20.25        12.46         0.16 
TCGA-BQ-5881 TCGA-BQ-7045 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LE 
       47.80        48.26        71.44        25.84        25.25        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A9DD TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A83S 
      194.79        12.92        11.21        56.75        25.22        85.78 
TCGA-IA-A83T TCGA-IZ-8196 TCGA-J7-6720 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       88.24        21.34        12.76        17.62        31.13        15.48 
TCGA-P4-A5E7 TCGA-SX-A71S TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PX TCGA-Y8-A8RY 
       87.09        49.45        43.76       117.40        65.13        25.28 
TCGA-Y8-A8S0 
        6.02 

$subtype4
TCGA-KM-8439 TCGA-KM-8441 TCGA-MH-A857 TCGA-SX-A7SO TCGA-KM-8639 TCGA-KN-8437 
       23.28        28.80        29.26        41.33        31.33       100.87 
TCGA-CJ-5681 TCGA-T7-A92I TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-5P-A9K8 TCGA-A4-8312 
       18.15        11.70        24.33        31.20        43.04        23.28 
TCGA-B9-A69E TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-DZ-6131 
       14.86        40.83        26.04        93.34        61.28        79.86 
TCGA-G7-7501 TCGA-WN-AB4C 
       20.52        39.06 

$subtype5
TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-BP-4807 TCGA-BP-4988 TCGA-BP-4995 
       43.96        18.51       112.80         6.94        27.22        45.07 
TCGA-5P-A9JV TCGA-KN-8427 TCGA-KO-8404 TCGA-3Z-A93Z TCGA-A3-A6NI TCGA-B0-4698 
       67.17         0.99        10.68        12.66        33.47         1.38 
TCGA-B0-4700 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-5080 TCGA-B0-5702 TCGA-B0-5709 
       65.10        40.70        45.30        11.24        71.41       130.65 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A7U6 TCGA-B8-A8YJ 
       50.14        48.53         0.53        34.39        16.27        14.17 
TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4959 TCGA-BP-4967 
       10.82        15.78        48.95        36.53        87.45         6.74 
TCGA-BP-4968 TCGA-BP-4974 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 
       57.40         6.94        31.30         3.88        30.64        35.21 
TCGA-CJ-4876 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-5671 TCGA-CJ-6031 
       64.27        63.98       115.69        39.45       131.08        62.66 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-MM-A563 
       69.21         6.77        19.43 

$subtype6
TCGA-A3-3358 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B2-5635 TCGA-B8-A54H 
       42.97       133.94        15.78        70.68        24.82         8.42 
TCGA-BP-4976 TCGA-BP-5009 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 
       53.65        35.90        43.69        45.96        11.67        37.15 
TCGA-BQ-5892 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       11.97        20.28        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3458 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4810 TCGA-B0-4811 
       10.62        38.40         2.14        57.70        15.72        46.59 
TCGA-B0-4821 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5696 
       40.44        36.85        25.32        46.39       129.67        85.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5639 
      126.28        58.85       149.16        35.90        31.66        32.98 
TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4961 TCGA-BP-4969 
       12.00         4.64        14.30        17.36        63.62        58.98 
TCGA-BP-4970 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4992 TCGA-BP-5001 TCGA-CJ-4870 
       14.24        36.07        33.34        16.47        38.70        49.25 
TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4887 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5683 
      116.84        71.87        30.64       129.40       133.71        62.10 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4864 
       67.00       119.64        85.78        78.18       105.93        93.04 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 
       79.53        23.74        18.44        90.54        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5989 
       21.76        69.96        22.52         2.40        12.69        62.63 
TCGA-EU-5904 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 
       18.12        10.29        35.87         2.01        19.96 

$subtype7
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-BQ-7055 TCGA-KL-8323 TCGA-KL-8324 
      102.81        28.11        47.24        26.27        38.07       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      137.06        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       30.25        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 
       28.80        54.74       151.96       129.37        23.47        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19         3.55        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 
        2.50        11.21        59.08        42.35       100.47        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      104.55       103.10        99.88        96.62        90.48        92.55 
TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 
       94.19        12.13        32.61 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.46     0.23     0.13    11.70     0.53     0.10     2.50 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  123.62    96.69   194.79   100.87   131.08   149.16   153.73 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   26.40    19.73    25.58    30.23    35.21    36.07    66.54 
[1] "0.5 - 123.6 (26.4)"  "0.2 - 96.7 (19.7)"   "0.1 - 194.8 (25.6)" 
[4] "11.7 - 100.9 (30.2)" "0.5 - 131.1 (35.2)"  "0.1 - 149.2 (36.1)" 
[7] "2.5 - 153.7 (66.5)" 
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      59        9        11        2
  subtype2      30        8        28       15
  subtype3      43        0         2        1
  subtype4      14        0         4        1
  subtype5      24        2         5       13
  subtype6      38       11        19       10
  subtype7      13       17        12        4
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         59       30       43       14       24       38       13
  STAGE II         9        8        0        0        2       11       17
  STAGE III       11       28        2        4        5       19       12
  STAGE IV         2       15        1        1       13       10        4
[1] 4 7
[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 68 12 12  0
  subtype2 34 11 37  2
  subtype3 44  1  2  1
  subtype4 14  0  6  0
  subtype5 25  2 13  6
  subtype6 40 13 25  0
  subtype7 13 17 16  0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       68       34       44       14       25       40       13
  T2       12       11        1        0        2       13       17
  T3       12       37        2        6       13       25       16
  T4        0        2        1        0        6        0        0
[1] 4 7
[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 17  4  0
  subtype2 21 20  4
  subtype3  7  1  0
  subtype4  4  1  0
  subtype5 20  1  0
  subtype6 28  2  0
  subtype7 29  2  2
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       17       21        7        4       20       28       29
  N1        4       20        1        1        1        2        2
  N2        0        4        0        0        0        0        2
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
          cls
clus        0  1
  subtype1 26  0
  subtype2 38 12
  subtype3 14  0
  subtype4  6  1
  subtype5 29  9
  subtype6 57  9
  subtype7 28  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    0
  subtype2   38   12
  subtype3   14    0
  subtype4    6    1
  subtype5   29    9
  subtype6   57    9
  subtype7   28    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       26       38       14        6       29       57       28
  1        0       12        0        1        9        9        2
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1 18 74
  subtype2 32 52
  subtype3 10 40
  subtype4 12  8
  subtype5 10 36
  subtype6 31 47
  subtype7 20 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   74
  subtype2   32   52
  subtype3   10   40
  subtype4   12    8
  subtype5   10   36
  subtype6   31   47
  subtype7   20   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       18       32       10       12       10       31       20
  MALE         74       52       40        8       36       47       26
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus        0  1
  subtype1 70  0
  subtype2 44  0
  subtype3 38  0
  subtype4 14  0
  subtype5 15  0
  subtype6 29  1
  subtype7 44  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    0
  subtype2   44    0
  subtype3   38    0
  subtype4   14    0
  subtype5   15    0
  subtype6   29    1
  subtype7   44    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        70       44       38       14       15       29       44
  YES        0        0        0        0        0        1        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, continuous
          vv
clus       KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  subtype1                  0                                 1
  subtype2                  0                                18
  subtype3                  0                                 0
  subtype4                  4                                 2
  subtype5                  2                                43
  subtype6                  0                                77
  subtype7                 42                                 3
          vv
clus       KIDNEY PAPILLARY RENAL CELL CARCINOMA
  subtype1                                    91
  subtype2                                    66
  subtype3                                    50
  subtype4                                    14
  subtype5                                     1
  subtype6                                     1
  subtype7                                     1
D12V10, multiclass
                                       clus
vv                                      subtype1 subtype2 subtype3 subtype4
  KIDNEY CHROMOPHOBE                           0        0        0        4
  KIDNEY CLEAR CELL RENAL CARCINOMA            1       18        0        2
  KIDNEY PAPILLARY RENAL CELL CARCINOMA       91       66       50       14
                                       clus
vv                                      subtype5 subtype6 subtype7
  KIDNEY CHROMOPHOBE                           2        0       42
  KIDNEY CLEAR CELL RENAL CARCINOMA           43       77        3
  KIDNEY PAPILLARY RENAL CELL CARCINOMA        1        1        1
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
[1] "Remove cluster labels:" "subtype5"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      16       12       14        7        2        2        6 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype1" "subtype7" "subtype7" "subtype7"
[13] "subtype4" "subtype7" "subtype7" "subtype7" "subtype4" "subtype1"
[19] "subtype1" "subtype4" "subtype4" "subtype3" "subtype2" "subtype2"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype4"
[31] "subtype2" "subtype2" "subtype1" "subtype4" "subtype1" "subtype2"
[37] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[43] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[49] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype4"
[55] "subtype3"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        17
  subtype2                                0     4                        17
  subtype3                                0     1                         6
  subtype4                                0     0                         8
  subtype5                                0     1                         8
  subtype6                                0     2                        13
  subtype7                                0     1                         2
          vv
clus       WHITE
  subtype1    69
  subtype2    58
  subtype3    40
  subtype4    12
  subtype5    37
  subtype6    61
  subtype7    41
D12V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0        0
  ASIAN                                   1        4        1        0        1
  BLACK OR AFRICAN AMERICAN              17       17        6        8        8
  WHITE                                  69       58       40       12       37
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   2        1
  BLACK OR AFRICAN AMERICAN              13        2
  WHITE                                  61       41
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
          cls
clus        0  1
  subtype1  1 81
  subtype2  4 64
  subtype3  4 42
  subtype4  1 16
  subtype5  2 29
  subtype6  4 58
  subtype7  4 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   81
  subtype2    4   64
  subtype3    4   42
  subtype4    1   16
  subtype5    2   29
  subtype6    4   58
  subtype7    4   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        4        4        1        2        4
  NOT HISPANIC OR LATINO       81       64       42       16       29       58
                        clus
vv                       subtype7
  HISPANIC OR LATINO            4
  NOT HISPANIC OR LATINO       18
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
