[1] "ofn"        "-oTKIRC-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/KIRC-TP/15081616/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.mergedcluster.txt"

nPatients in clinical file=533, in cluster file=537, common to both=533
[1]  12 533
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
34 24 14 
 1  2  3 
34 24 14 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
12 12  4 11 13  9 11 
 1  2  3  4  5  6  7 
12 12  4 11 13  9 11 
[1] "CN_CNMF"
[1] 3
  1   2   3 
237 133 154 
  1   2   3 
237 133 154 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
128  77 110 
  1   2   3 
128  77 110 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5   6 
108  62  77  81  81  45 
  1   2   3   4   5   6 
108  62  77  81  81  45 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
122 200 132 
  1   2   3 
122 200 132 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
114 222 193 
  1   2   3 
114 222 193 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
118  34 183 132  35  27 
  1   2   3   4   5   6 
118  34 183 132  35  27 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
125 204 183 
  1   2   3 
125 204 183 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
144 136 195  37 
  1   2   3   4 
144 136 195  37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
36 22 49 35 
 1  2  3  4 
36 22 49 35 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
38 56 48 
 1  2  3 
38 56 48 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 533 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=160,	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=355,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              19-3-2015 5-3-2015
freq.values   "532"     "1"     
freq.contrast "1"       "532"   
both >= 3     "FALSE"   "FALSE" 
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "532"  
freq.contrast "532"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 533 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
272  69 181  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
272  69 181  11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
272  69 181  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
272  69 181  11 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=10, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=7, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 30  4
  subtype2 15  9
  subtype3 13  1
subtype1 subtype2 subtype3 
      34       24       14 
subtype1 subtype2 subtype3 
       4        9        1 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       36.82        47.21        49.58        48.59        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       37.38        23.21        48.82        31.07        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 
       18.44        82.32        51.25        28.70        24.16        18.64 
TCGA-A3-3383 TCGA-AK-3444 TCGA-AK-3455 TCGA-AS-3778 TCGA-B2-3924 TCGA-B2-4099 
       28.31        48.36        22.45         1.41        35.90        12.30 
TCGA-B2-4102 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 
       31.30        27.55        24.66        17.19       101.06        32.61 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       59.84        75.88        58.95        11.05 

$subtype2
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 
        0.53        39.16        49.08        49.02        37.15        36.36 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 
       21.86         4.50        52.93        43.20        20.71        18.87 
TCGA-AK-3426 TCGA-B2-4098 TCGA-B8-4143 TCGA-B8-4620 TCGA-BP-4161 TCGA-BP-4163 
       29.10         1.68        23.31        25.55        90.28        93.34 
TCGA-BP-4167 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       89.36        63.25        73.22        14.17        65.69        54.61 

$subtype3
TCGA-A3-3313 TCGA-A3-3328 TCGA-A3-3336 TCGA-A3-3363 TCGA-AK-3427 TCGA-AK-3440 
       24.16        45.53        34.29        10.49        84.36        57.37 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        45.93        37.58        12.13        40.70 
TCGA-B2-3923 TCGA-B8-4148 
       32.61        27.16 

subtype1 subtype2 subtype3 
    1.41     0.53    10.49 
subtype1 subtype2 subtype3 
  101.06    93.34    84.36 
subtype1 subtype2 subtype3 
  31.955   38.155   38.795 
[1] "1.4 - 101.1 (32.0)" "0.5 - 93.3 (38.2)"  "10.5 - 84.4 (38.8)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      23        4         6        1
  subtype2       9        3         8        4
  subtype3       8        6         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         23        9        8
  STAGE II         4        3        6
  STAGE III        6        8        0
  STAGE IV         1        4        0
[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
  subtype1 23  4  7
  subtype2 10  4 10
  subtype3  8  6  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       23       10        8
  T2        4        4        6
  T3        7       10        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"
D1V5, binary
          cls
clus        0  1
  subtype1 18  0
  subtype2 10  3
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    0
  subtype2   10    3
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0       18       10        7
  1        0        3        0
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 33  1
  subtype2 20  4
  subtype3 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    1
  subtype2   20    4
  subtype3   14    0
   clus
vv  subtype1 subtype2 subtype3
  0       33       20       14
  1        1        4        0
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 15 19
  subtype2 10 14
  subtype3  4 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   19
  subtype2   10   14
  subtype3    4   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       10        4
  MALE         19       14       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    32
  subtype2     0                         2    20
  subtype3     1                         3    10
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN        0        2        3
  WHITE                           32       20       10
[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"
D1V12, binary
          cls
clus        0  1
  subtype1  5 19
  subtype2  2 11
  subtype3  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   19
  subtype2    2   11
  subtype3    0   12
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        0
  NOT HISPANIC OR LATINO       19       11       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  1
  subtype2 10  2
  subtype3  2  2
  subtype4  5  6
  subtype5 10  3
  subtype6  9  0
  subtype7 11  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      12       12        4       11       13        9       11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       1        2        2        6        3        0        0 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3343 
       36.82        47.21        38.99        37.38        23.21        31.07 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3383 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 
       29.92        18.44        28.31        35.90        12.30        31.30 

$subtype2
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 
        0.53        39.16        49.08        37.15        36.36        21.86 
TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 TCGA-B8-4620 TCGA-BP-4161 
        4.50        43.20        20.71        18.87        25.55        90.28 

$subtype3
TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 
       24.16        10.49        37.58         1.68 

$subtype4
TCGA-A3-3317 TCGA-A3-3347 TCGA-AK-3426 TCGA-B8-4143 TCGA-BP-4163 TCGA-BP-4167 
       49.02        52.93        29.10        23.31        93.34        89.36 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        65.69        54.61 

$subtype5
TCGA-A3-3320 TCGA-A3-3331 TCGA-A3-3359 TCGA-AK-3444 TCGA-AK-3455 TCGA-B8-4151 
       49.58        48.82        82.32        48.36        22.45        27.55 
TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 TCGA-CJ-4639 TCGA-CJ-4643 
       24.66        17.19       101.06        32.61        75.88        58.95 
TCGA-CJ-4644 
       11.05 

$subtype6
TCGA-A3-3322 TCGA-A3-3325 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 
       48.59        24.69        45.53        51.25        28.70        24.16 
TCGA-A3-3380 TCGA-AS-3778 TCGA-CJ-4634 
       18.64         1.41        59.84 

$subtype7
TCGA-A3-3328 TCGA-A3-3336 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       45.53        34.29        84.36        57.37        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 
       45.93        12.13        40.70        32.61        27.16 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   12.30     0.53     1.68    14.17    11.05     1.41    12.13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   47.21    90.28    37.58    93.34   101.06    59.84    84.36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  31.185   30.955   17.325   54.610   48.360   28.700   40.700 
[1] "12.3 - 47.2 (31.2)"  "0.5 - 90.3 (31.0)"   "1.7 - 37.6 (17.3)"  
[4] "14.2 - 93.3 (54.6)"  "11.1 - 101.1 (48.4)" "1.4 - 59.8 (28.7)"  
[7] "12.1 - 84.4 (40.7)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       8        2         2        0
  subtype2       8        2         2        0
  subtype3       2        2         0        0
  subtype4       0        1         6        4
  subtype5       7        2         3        1
  subtype6       8        0         1        0
  subtype7       7        4         0        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          8        8        2        0        7        8        7
  STAGE II         2        2        2        1        2        0        4
  STAGE III        2        2        0        6        3        1        0
  STAGE IV         0        0        0        4        1        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       T1 T2 T3
  subtype1  8  2  2
  subtype2  8  2  2
  subtype3  2  2  0
  subtype4  1  2  8
  subtype5  7  2  4
  subtype6  8  0  1
  subtype7  7  4  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        8        8        2        1        7        8        7
  T2        2        2        2        2        2        0        4
  T3        2        2        0        8        4        1        0
[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"
D2V5, binary
          cls
clus       0 1
  subtype1 6 0
  subtype2 5 0
  subtype3 3 0
  subtype4 5 3
  subtype5 9 0
  subtype6 3 0
  subtype7 4 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    0
  subtype2    5    0
  subtype3    3    0
  subtype4    5    3
  subtype5    9    0
  subtype6    3    0
  subtype7    4    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        6        5        3        5        9        3        4
  1        0        0        0        3        0        0        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"
D2V6, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2 12  0
  subtype3  4  0
  subtype4  7  4
  subtype5 12  1
  subtype6  9  0
  subtype7 11  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2   12    0
  subtype3    4    0
  subtype4    7    4
  subtype5   12    1
  subtype6    9    0
  subtype7   11    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       12       12        4        7       12        9       11
  1        0        0        0        4        1        0        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"
D2V7, binary
          cls
clus        0  1
  subtype1  0 12
  subtype2  3  9
  subtype3  1  3
  subtype4  6  5
  subtype5 12  1
  subtype6  3  6
  subtype7  4  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   12
  subtype2    3    9
  subtype3    1    3
  subtype4    6    5
  subtype5   12    1
  subtype6    3    6
  subtype7    4    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        0        3        1        6       12        3        4
  MALE         12        9        3        5        1        6        7
[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"
D2V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype4 
       1 
character(0)
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    11
  subtype2     0                         1    10
  subtype3     1                         3     0
  subtype4     0                         0    10
  subtype5     0                         0    13
  subtype6     0                         0     8
  subtype7     0                         1    10
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        1        3        0        0
  WHITE                           11       10        0       10       13
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            8       10
[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"
D2V12, binary
          cls
clus        0  1
  subtype1  1  7
  subtype2  0  4
  subtype3  0  2
  subtype4  2  6
  subtype5  3  7
  subtype6  1  5
  subtype7  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2    0    4
  subtype3    0    2
  subtype4    2    6
  subtype5    3    7
  subtype6    1    5
  subtype7    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        0        2        3        1
  NOT HISPANIC OR LATINO        7        4        2        6        7        5
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       11
[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(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 180  57
  subtype2  85  46
  subtype3  89  65
subtype1 subtype2 subtype3 
     237      131      154 
subtype1 subtype2 subtype3 
      57       46       65 
$subtype1
TCGA-3Z-A93Z TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       12.66        47.21        39.16        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3351 
       38.99        37.38        48.82        21.86        31.07        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        82.32        51.25        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 
       74.76        53.29        20.71        18.64        28.31        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3429 
       15.39        22.65         0.10        11.18        10.62        66.31 
TCGA-AK-3431 TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       60.92        48.36        48.69        22.45        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 
       28.04         1.41         2.53         5.98         2.14         3.25 
TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 
       15.72         5.52        45.07        16.77        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4846 
       29.10        78.44        45.30         6.71        11.64        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5085 
       26.07         2.27        70.52        20.94        43.30        25.32 
TCGA-B0-5088 TCGA-B0-5099 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
       18.51        15.95        90.48        29.95        35.90        26.20 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 
        1.94        16.21        18.21        21.44        79.17        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
      101.13        15.78        56.78        60.33        84.92        90.12 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       39.55       120.59        79.36        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       97.41        35.90        12.30        21.30        31.30        11.77 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 
       32.98        16.67         9.57         1.25         4.64         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5163 
       16.80        27.16        25.05        24.66        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        0.85        34.39        14.30        27.29        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        8.42        17.36        16.27       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
       97.45         3.58        27.78        62.07        37.25        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        54.77        49.08        44.94        12.23 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4774 TCGA-BP-4776 
       31.33        72.59        41.75        71.80        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4969 
       56.91        48.95        36.95         6.94        61.51        58.98 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38         7.23        47.11        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5001 
       36.95        46.45         5.82        45.07        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5174 
       37.02        27.62        37.48        35.21        48.10        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        49.15        38.30        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 
       44.55        34.95         0.95        59.84        63.25        75.88 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
       53.52        58.95        21.24        83.97        49.25        75.06 
TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4892 
       71.87        57.83        69.86        64.18        30.64        50.01 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 
       27.65        50.24        49.97        58.92        50.33        45.14 
TCGA-CJ-5672 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CW-5581 TCGA-CW-5583 
       72.00        62.10        73.35        53.26        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4856 
       85.78        73.18        78.18       105.93        25.45         0.59 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 
       58.75        14.66        93.04         5.46        63.42         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 
       23.74        18.44        56.94        55.33        21.76        57.21 
TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 
        2.40        80.19        12.26        22.78        62.63        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       12.16        11.67        37.15        66.02        18.12         6.77 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
       10.29         2.01        10.85 

$subtype2
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3374 
       12.16         0.53        24.16        45.53        10.49        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3433 TCGA-AK-3440 
       55.76        65.52        84.36        73.08        72.07        57.37 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        45.93        37.58        12.13        40.70 
TCGA-B0-4688 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.32        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4834 
       20.25        46.59        33.50         6.02        36.53        68.71 
TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5081 
       53.88        56.68        10.29        36.85        11.24        11.90 
TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5117 TCGA-B0-5400 
       21.86        62.89        52.54        30.48        17.59        37.22 
TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5712 TCGA-B2-3923 
      112.80        46.68        52.77       102.48        89.49        32.61 
TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4619 
        1.68        10.36         5.75         5.46        27.55        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       25.91        23.01         1.18        24.23        17.16        16.60 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4167 TCGA-BP-4173 
       14.27        29.88        15.42        14.17        89.36        62.24 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4337 TCGA-BP-4354 TCGA-BP-4759 
       54.90        53.42        21.21         0.07        33.99        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4782 
       77.62        44.15        61.68        10.82        60.59        11.64 
TCGA-BP-4784 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4961 
       60.95        36.53        20.38        37.25        47.97        63.62 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4983 
       61.22         6.74        57.40        14.24        53.65        46.45 
TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5170 
       27.22        43.00        30.64        36.23        28.87        79.30 
TCGA-CJ-4637 TCGA-CJ-4641 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4888 
       73.22        54.61        47.18        77.36        61.91        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 
       63.98        68.55        26.93        59.44        49.18        49.28 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       54.48        38.56         3.06         4.57        18.81        63.88 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-6087 TCGA-CW-6093 
       84.66        18.15        67.00        62.66         1.35       103.43 
TCGA-CW-6097 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5470 
       18.77        60.59        63.39        61.41        55.33        12.69 
TCGA-DV-5567 TCGA-DV-5574 TCGA-DV-5576 TCGA-EU-5905 TCGA-MM-A84U 
       65.88        66.28        23.90         3.91        15.25 

$subtype3
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
       36.82        49.08        49.02        37.15        24.69        34.29 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ 
        4.50        52.93        18.44        24.16        18.87         0.10 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 
      109.91        29.10        15.78        68.61        67.20        42.08 
TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
       58.49        28.73         1.41         4.57         3.48        28.47 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4813 TCGA-B0-4815 
       19.73         3.16        43.96         6.64         0.59        52.21 
TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4845 TCGA-B0-4848 
       40.44        10.09        40.70        27.42        65.29        29.03 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
        7.30        15.09        10.95         8.05         2.24        52.08 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5701 
       90.87        19.30        11.80        21.60        14.76        56.94 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4620 
       21.57         0.23         0.53         0.36        23.31        25.55 
TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4164 
       20.91         6.38         0.53         4.93        90.28        32.61 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 
       61.78        64.27        80.68        93.99        74.17        62.86 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4766 
       31.89        11.31        12.33        12.30         5.98        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 
       13.15         5.33        68.38        15.78        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4971 
        6.71        87.45        71.41        58.68        60.30        48.89 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 
       45.50        31.30        25.81         3.88        16.47        18.51 
TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 
        6.35         1.78        30.64        62.86        74.40        42.44 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 
       37.22        31.79        33.47        19.82        31.27        46.55 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 
       14.17        65.69        11.05        79.66        74.27        64.27 
TCGA-CJ-4881 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       66.21        24.66        39.45        56.35        47.67        51.29 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
       79.89        25.71        18.87        22.32        25.25        61.91 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        53.42        75.58        83.77         7.36        64.57 
TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4857 
        5.39        66.31        74.66        83.90        46.16        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 
       69.21         6.77        58.82        56.28        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.22        47.54        22.52         1.94        31.10        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A5PC 
       65.65        14.63        43.69        56.84         4.18         7.96 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A564 
       70.13        35.87        19.43        19.96 

subtype1 subtype2 subtype3 
    0.10     0.07     0.10 
subtype1 subtype2 subtype3 
  120.59   112.80   109.91 
subtype1 subtype2 subtype3 
  36.950   38.560   31.285 
[1] "0.1 - 120.6 (37.0)" "0.1 - 112.8 (38.6)" "0.1 - 109.9 (31.3)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     140       29        49       19
  subtype2      66       13        31       23
  subtype3      54       15        47       38
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        140       66       54
  STAGE II        29       13       15
  STAGE III       49       31       47
  STAGE IV        19       23       38
[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 140  34  62   1
  subtype2  67  16  44   6
  subtype3  58  19  73   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      140       67       58
  T2       34       16       19
  T3       62       44       73
  T4        1        6        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus         0   1
  subtype1 108   3
  subtype2  58   4
  subtype3  66  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108    3
  subtype2   58    4
  subtype3   66   11
   clus
vv  subtype1 subtype2 subtype3
  0      108       58       66
  1        3        4       11
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 203  19
  subtype2 105  21
  subtype3 110  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  203   19
  subtype2  105   21
  subtype3  110   38
   clus
vv  subtype1 subtype2 subtype3
  0      203      105      110
  1       19       21       38
[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  92 145
  subtype2  56  77
  subtype3  40 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  145
  subtype2   56   77
  subtype3   40  114
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       92       56       40
  MALE        145       77      114
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        1        3 
[1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        20   212
  subtype2     4                        22   106
  subtype3     2                        10   139
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        4        2
  BLACK OR AFRICAN AMERICAN       20       22       10
  WHITE                          212      106      139
[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"
D3V12, binary
          cls
clus         0   1
  subtype1  13 149
  subtype2   7  95
  subtype3   6 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  149
  subtype2    7   95
  subtype3    6  101
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        7        6
  NOT HISPANIC OR LATINO      149       95      101
[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 106  21
  subtype2  51  25
  subtype3  56  54
subtype1 subtype2 subtype3 
     127       76      110 
subtype1 subtype2 subtype3 
      21       25       54 
$subtype1
TCGA-3Z-A93Z TCGA-A3-3358 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3385 TCGA-A3-A6NJ 
       12.66        42.97        74.76        53.29        65.52        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 
       22.65         0.10         0.10        11.18        10.62        73.08 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 
       60.92        72.07        57.37        58.49        45.93        28.73 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4706 TCGA-B0-4818 TCGA-B0-4823 
       38.40        31.27        28.04         2.14        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       54.48         6.71        39.45        26.07         2.27        36.85 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 
       90.87        90.48        35.90        11.80        26.20        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
        1.94        16.21        21.44        79.17       112.80       101.13 
TCGA-B0-5695 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5707 TCGA-B0-5710 
       46.68        35.57        39.55       120.59        92.98        47.97 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-5639 TCGA-B2-A4SR 
       96.36        61.32        97.41        35.90        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        9.57         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 
       23.74        24.23        17.16        16.60         6.38        34.39 
TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4801 
       14.30        17.06         8.42        17.36        16.27        36.95 
TCGA-BP-4993 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
        5.82        48.10         1.78        74.20        52.27         9.63 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 
       49.15        42.44        37.25        37.22        22.78        23.47 
TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4897 TCGA-CJ-4903 
       13.41        44.55        34.95         0.95        59.44        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       58.92        49.18        50.33        18.15        62.10        73.35 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 
       83.77        92.02        81.83        85.78        78.18       105.93 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 
      103.43         0.59        58.75        93.04        63.42         0.82 
TCGA-CZ-5454 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 
       23.74        55.33        21.76         2.40        80.19        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 
       22.78        62.63        43.69        45.96        11.67        37.15 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       56.84        18.12         6.77        10.29        35.87         2.01 
TCGA-MW-A4EC 
       10.85 

$subtype2
TCGA-6D-AA2E TCGA-A3-3376 TCGA-AK-3425 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
       12.16        55.76       109.91         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4842 
        3.62        65.10        52.21        33.50         6.02        56.68 
TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5092 TCGA-B0-5098 TCGA-B0-5108 
       70.52        11.24        34.36        15.09        52.08        29.95 
TCGA-B0-5109 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5709 
       19.30        37.22        48.89        60.33        52.77       102.48 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4621 
       11.77        10.36        30.21         5.75         0.53        25.91 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54E 
        1.18        27.02         0.85        14.27         0.53        29.88 
TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4177 TCGA-BP-4760 
        1.74         4.93        15.42        14.17        54.90        77.62 
TCGA-BP-4770 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5182 
       10.82        11.64        20.38        79.30        30.64        38.30 
TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-CJ-4869 TCGA-CJ-4882 
       13.35        31.79        24.62        33.47        83.97        61.91 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5686 TCGA-CJ-6031 
       45.14         3.06        18.81        72.00        67.00        62.66 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4863 TCGA-CZ-4865 
       73.18        66.31         1.35        18.77        63.39         5.46 
TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5462 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5574 
       58.82        56.94        10.22        65.88        12.16        66.28 
TCGA-DV-5576 TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A84U 
       23.90         3.91        70.13        15.25 

$subtype3
TCGA-A3-3357 TCGA-A3-3367 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-4688 
       88.37        74.63        20.28        68.61        42.08         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4701 TCGA-B0-4703 
        1.41         4.57         2.53        28.47         7.82         5.98 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4821 
       15.72        46.59         0.59         5.52        45.07        40.44 
TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       36.53        29.10        10.09        11.64        10.29        65.29 
TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       29.03        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 
       62.89        52.54        30.48        21.60        18.21        14.76 
TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5706 
       15.78        56.78        84.92        90.12        56.94        79.36 
TCGA-B0-5712 TCGA-B2-4101 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4153 
       89.49        21.30        21.57         0.23         5.46        25.05 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-A54D TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5178 
       23.01        20.91        27.29        28.87         6.35        62.86 
TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4901 
       74.40        27.02        33.24        19.82        31.27        47.67 
TCGA-CJ-4902 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5671 
       49.97        49.28        54.48        38.56         4.57        63.88 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6033 
       61.91        53.26        60.99        53.42        75.58         7.36 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4853 
       64.57         5.39        35.34        74.66        83.90        25.45 
TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       61.41        18.44        56.28        55.33        47.01        10.85 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       57.21        47.54        22.52         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4W0 TCGA-EU-5907 TCGA-G6-A5PC 
       67.96        65.65        14.63        66.02         4.18         7.96 
TCGA-MM-A563 TCGA-MM-A564 
       19.43        19.96 

subtype1 subtype2 subtype3 
    0.10     0.53     0.23 
subtype1 subtype2 subtype3 
  120.59   109.91    90.12 
subtype1 subtype2 subtype3 
  35.570   28.450   27.155 
[1] "0.1 - 120.6 (35.6)" "0.5 - 109.9 (28.4)" "0.2 - 90.1 (27.2)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      87       17        14       10
  subtype2      43        2        20       12
  subtype3      23       12        41       34
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         87       43       23
  STAGE II        17        2       12
  STAGE III       14       20       41
  STAGE IV        10       12       34
[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 87 21 20  0
  subtype2 45  3 25  4
  subtype3 24 17 65  4
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       87       45       24
  T2       21        3       17
  T3       20       25       65
  T4        0        4        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 52  1
  subtype2 31  3
  subtype3 48  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    1
  subtype2   31    3
  subtype3   48    5
   clus
vv  subtype1 subtype2 subtype3
  0       52       31       48
  1        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1 103  10
  subtype2  58  10
  subtype3  73  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  103   10
  subtype2   58   10
  subtype3   73   33
   clus
vv  subtype1 subtype2 subtype3
  0      103       58       73
  1       10       10       33
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 61 67
  subtype2 31 46
  subtype3 21 89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   67
  subtype2   31   46
  subtype3   21   89
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       61       31       21
  MALE         67       46       89
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       3        2        3 
[1] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        19   109
  subtype2     0                        17    60
  subtype3     1                         9    97
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN       19       17        9
  WHITE                          109       60       97
[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"
D4V12, binary
          cls
clus        0  1
  subtype1  4 98
  subtype2  2 63
  subtype3  4 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   98
  subtype2    2   63
  subtype3    4   94
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        4
  NOT HISPANIC OR LATINO       98       63       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 80 28
  subtype2 19 43
  subtype3 53 24
  subtype4 54 27
  subtype5 50 31
  subtype6 40  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     108       62       77       81       81       45 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      28       43       24       27       31        5 
$subtype1
TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3380 TCGA-A3-3383 
       36.82        49.58        18.44        74.63        18.64        28.31 
TCGA-A3-3385 TCGA-AK-3434 TCGA-B0-4693 TCGA-B0-4706 TCGA-B0-4811 TCGA-B0-4816 
       65.52        68.61         2.53         2.14        46.59        45.07 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4849 
       16.77        54.48         6.71        65.29        39.45         2.27 
TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5102 TCGA-B0-5115 TCGA-B0-5119 
       36.85        25.32        18.51        90.87        26.20         1.94 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 
       18.21        21.44        14.76        79.17        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5705 TCGA-B0-5711 
       15.78        46.68        84.92        90.12       120.59        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       89.49        61.32        97.41        12.30        21.30        31.30 
TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-5159 
        9.57         4.64         0.36         0.23        25.05        23.74 
TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 
      111.02        90.28        32.61        97.45         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4759 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4776 
       62.07        15.16        77.98        13.15        61.97        13.51 
TCGA-BP-4961 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4991 TCGA-BP-4995 
       63.62        47.11        14.93        36.07        46.45        45.07 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5176 
       41.62        38.70        37.48        48.10        79.30        52.27 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5192 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4870 
       74.40        49.15        23.47        31.27        59.84        49.25 
TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4903 
       79.66        75.06        71.87        24.66        59.44        51.29 
TCGA-CJ-4904 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
       58.92        45.14        79.89        84.66        18.87        25.25 
TCGA-CJ-5683 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CZ-4853 
       62.10        92.02        81.83        85.78        73.18        25.45 
TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5455 TCGA-CZ-5465 TCGA-CZ-5467 
       58.75        93.04        63.42        18.44        47.54         2.40 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-EU-5906 
       80.19        65.65        12.26        62.63        43.69         6.77 

$subtype2
TCGA-A3-3308 TCGA-AK-3436 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
        0.53        67.20         1.41         4.57         3.48        28.47 
TCGA-B0-4698 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 
        1.38        19.73        43.96         6.64        20.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4828 
        0.59         5.52        40.44        36.53        29.10        10.09 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5094 
       56.68        11.64        10.29        29.03        15.09        10.95 
TCGA-B0-5107 TCGA-B0-5696 TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-4622 TCGA-B8-5158 
       30.48        56.78       102.48         5.46        23.01        20.91 
TCGA-BP-4173 TCGA-BP-4326 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 
       62.24        53.42        74.17        11.31        33.99         5.98 
TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4992 
        5.33        15.78        10.98        46.45        31.30        16.47 
TCGA-BP-5000 TCGA-BP-5175 TCGA-CJ-4638 TCGA-CJ-4869 TCGA-CJ-4875 TCGA-CJ-4881 
       18.51        30.64        14.17        83.97        77.36        66.21 
TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5679 TCGA-CJ-5689 
       26.93        39.45        38.56         4.57        22.32        53.26 
TCGA-CJ-6027 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-5460 
       60.99         1.35        46.16        47.08        69.21        47.01 
TCGA-CZ-5468 TCGA-CZ-5987 
        1.94        14.63 

$subtype3
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3336 
       39.16        49.02        37.15        36.36        21.86        34.29 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3372 TCGA-A3-3387 TCGA-B0-4838 TCGA-B0-4839 
       52.93        29.92        24.16        20.28        27.42        53.88 
TCGA-B0-4847 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5691 TCGA-B0-5697 
       26.07        70.52        20.94        11.90       112.80        60.33 
TCGA-B0-5701 TCGA-B0-5707 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       56.94        92.98        11.77        10.36        32.98        21.57 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4143 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 
        0.23         0.53        23.31         0.85        16.60        14.27 
TCGA-B8-5553 TCGA-BP-4331 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4351 TCGA-BP-4756 
       14.30        80.68        62.86        49.08        31.89        12.30 
TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-5189 TCGA-BP-5190 
        6.71        60.30        57.40        45.50        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5195 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 
       31.79        24.62        46.55        65.69        74.27        64.27 
TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5672 
       57.83        30.64        51.52        49.28        54.48        72.00 
TCGA-CJ-5677 TCGA-CJ-6030 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5589 TCGA-CW-5590 
       25.71        75.58        64.57         5.39        78.18        35.34 
TCGA-CW-5591 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 
       74.66        60.59        63.39        61.41        58.82        56.28 
TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5469 
       56.94        10.85        21.76        57.21        22.52        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-DV-5573 TCGA-EU-5905 TCGA-EU-5907 
       12.69        67.96        37.15         3.91         4.18 

$subtype4
TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3357 
       24.16        48.59        38.99        37.38         4.50        88.37 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 
       51.25        10.49        53.29        43.20        20.71        18.87 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3444 TCGA-AK-3456 TCGA-B0-4699 TCGA-B0-4714 
       84.36        73.08        48.36        37.58         3.62         3.25 
TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-5077 TCGA-B0-5084 
       52.21        33.50        78.44        68.71        43.30         7.30 
TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5700 
        2.24        52.08        19.30        17.59        37.22        35.57 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B8-4146 
       52.77        39.55        32.61        35.90         1.68        16.80 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4165 TCGA-BP-4170 
       25.55        25.91         6.38         0.53        99.85        77.03 
TCGA-BP-4174 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4353 
       61.78        37.25        21.21        93.99        52.24        12.33 
TCGA-BP-4766 TCGA-BP-4777 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4964 
       48.07        56.91        37.25        36.95        87.45        61.22 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4993 
        6.74        58.98        49.38        27.22         3.88         5.82 
TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5187 
       43.00        37.02         6.35        62.86        37.22        13.35 
TCGA-BP-5194 TCGA-BP-5198 TCGA-CJ-4885 TCGA-CJ-4901 TCGA-CJ-5681 TCGA-CJ-6028 
       13.41        19.82        69.86        47.67        18.15        53.42 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CZ-4861 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5457 
       62.66         7.36        14.66         5.46         0.82        55.33 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-DV-5575 
       55.33        10.22        56.84 

$subtype5
TCGA-A3-3316 TCGA-A3-3349 TCGA-A3-3365 TCGA-A3-3376 TCGA-AK-3451 TCGA-B0-4688 
       49.08        45.53        28.70        55.76        48.69         3.32 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4819 TCGA-B0-4823 
       19.00        65.10         7.82         5.98         6.02        14.93 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-5080 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5100 
       40.70        45.30        11.24         8.05        21.86        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5706 TCGA-B0-5710 TCGA-B2-5636 
       90.48        52.54        29.95        79.36        47.97        30.21 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-BP-4169 
        5.75         1.25         1.18        27.02        17.16        23.05 
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-4784 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4960 
       61.68        10.82        60.95        36.53        47.97        71.41 
TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4998 TCGA-BP-5010 
       58.68        14.24        48.89         7.23        30.64        28.87 
TCGA-BP-5177 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 
        9.63        33.47        44.55        34.95        21.24        47.18 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 
       61.91        64.18        63.98        68.55        50.01        27.65 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4918 
       50.24        56.35        49.97        49.18        50.33         3.06 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CW-6088 
       18.81        63.88        61.91        73.35        67.00       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-4860 TCGA-CZ-5454 TCGA-CZ-5988 
       83.90        18.77         0.59         6.77        23.74        22.78 
TCGA-DV-5567 TCGA-DV-5574 TCGA-EU-5904 
       65.88        66.28        18.12 

$subtype6
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3370 TCGA-B0-4710 TCGA-B0-5099 TCGA-B0-5110 
       23.21        48.82        74.76         3.16        15.95        35.90 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5120 TCGA-B8-5165 TCGA-B8-5552 TCGA-BP-4344 
       11.80        21.60        16.21        24.23        34.39        54.77 
TCGA-BP-4347 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4781 
       44.94        72.59        77.62        44.15        60.59        68.38 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4982 
       48.95        36.39         6.94        61.51        53.65        33.34 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5173 
       25.81        36.95        27.62        35.21        36.23         1.78 
TCGA-BP-5174 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5202 
       74.20        38.30        42.44        37.25        22.78         0.95 
TCGA-CJ-4642 TCGA-CJ-6032 TCGA-CW-5588 TCGA-CW-6093 TCGA-CW-6096 TCGA-DV-5566 
       53.52        83.77        66.31       103.43        88.80        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5576 
       12.16        11.67        23.90 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.23     0.53     0.23     0.53     0.07     0.95 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  120.59   102.48   112.80    99.85   105.93   103.43 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  46.520   22.665   36.360   37.220   40.700   36.950 
[1] "0.2 - 120.6 (46.5)" "0.5 - 102.5 (22.7)" "0.2 - 112.8 (36.4)"
[4] "0.5 - 99.8 (37.2)"  "0.1 - 105.9 (40.7)" "0.9 - 103.4 (37.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      58       12        24       14
  subtype2       8        4        26       24
  subtype3      33       10        23       11
  subtype4      47        7        18        9
  subtype5      38        9        16       18
  subtype6      35        2         8        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         58        8       33       47       38       35
  STAGE II        12        4       10        7        9        2
  STAGE III       24       26       23       18       16        8
  STAGE IV        14       24       11        9       18        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 58 16 33  1
  subtype2  9  9 40  4
  subtype3 35 10 32  0
  subtype4 48  7 25  1
  subtype5 39 10 27  5
  subtype6 35  2  8  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       58        9       35       48       39       35
  T2       16        9       10        7       10        2
  T3       33       40       32       25       27        8
  T4        1        4        0        1        5        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 51  1
  subtype2 26  8
  subtype3 40  2
  subtype4 38  3
  subtype5 39  2
  subtype6 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    1
  subtype2   26    8
  subtype3   40    2
  subtype4   38    3
  subtype5   39    2
  subtype6   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       51       26       40       38       39       14
  1        1        8        2        3        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 94 14
  subtype2 38 24
  subtype3 66 11
  subtype4 72  9
  subtype5 64 17
  subtype6 45  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94   14
  subtype2   38   24
  subtype3   66   11
  subtype4   72    9
  subtype5   64   17
  subtype6   45    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       94       38       66       72       64       45
  1       14       24       11        9       17        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 46 62
  subtype2 16 46
  subtype3 23 54
  subtype4 22 59
  subtype5 25 56
  subtype6 19 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   62
  subtype2   16   46
  subtype3   23   54
  subtype4   22   59
  subtype5   25   56
  subtype6   19   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       46       16       23       22       25       19
  MALE         62       46       54       59       56       26
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype2 subtype3 subtype4 
       1        1        1 
character(0)
D5V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         5   101
  subtype2     2                         0    60
  subtype3     1                         1    71
  subtype4     1                         7    73
  subtype5     3                         5    73
  subtype6     1                         2    42
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        1        1        3
  BLACK OR AFRICAN AMERICAN        5        0        1        7        5
  WHITE                          101       60       71       73       73
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           42
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
          cls
clus        0  1
  subtype1  6 72
  subtype2  3 45
  subtype3  5 53
  subtype4  1 45
  subtype5  1 55
  subtype6  3 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   72
  subtype2    3   45
  subtype3    5   53
  subtype4    1   45
  subtype5    1   55
  subtype6    3   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        3        5        1        1        3
  NOT HISPANIC OR LATINO       72       45       53       45       55       25
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  90  32
  subtype2 153  47
  subtype3  53  79
subtype1 subtype2 subtype3 
     122      200      132 
subtype1 subtype2 subtype3 
      32       47       79 
$subtype1
TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3336 
       36.82        49.02        37.15        36.36        37.38        34.29 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3383 TCGA-A3-3385 
       29.92        18.44        74.63        24.16        28.31        65.52 
TCGA-B0-4693 TCGA-B0-4811 TCGA-B0-4816 TCGA-B0-4824 TCGA-B0-4845 TCGA-B0-4846 
        2.53        46.59        45.07        54.48        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 
       26.07         2.27        36.85        20.94        43.30        11.90 
TCGA-B0-5092 TCGA-B0-5116 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       15.09        21.60        21.44        14.76        79.17        48.89 
TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5705 
       15.78        60.33        84.92        90.12        56.94       120.59 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
       61.32        97.41        21.30        31.30        10.36        32.98 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5835 TCGA-B4-5843 TCGA-B8-4153 TCGA-B8-5159 
       21.57         9.57         0.53         0.36        25.05        23.74 
TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4164 
        0.85        16.60        14.27       111.02        90.28        32.61 
TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4343 TCGA-BP-4346 
       62.24        97.45        62.07        80.68        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4959 TCGA-BP-4963 
       44.94        31.89        12.30        13.15        87.45        60.30 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4991 TCGA-BP-4992 
       61.51        57.40        45.50        14.93        46.45        16.47 
TCGA-BP-5000 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 
       18.51         1.78        74.20        42.44        37.22        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4873 
       33.24        31.79        46.55        65.69        83.97        74.27 
TCGA-CJ-4876 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4912 
       64.27        57.83        30.64        59.44        49.28        54.48 
TCGA-CJ-4916 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CW-5580 
       45.14        72.00        79.89        25.71        18.87        64.57 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5591 TCGA-CW-6096 
       92.02         5.39        85.78        73.18        74.66        88.80 
TCGA-CZ-4853 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       25.45        60.59        63.39        93.04        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5466 TCGA-CZ-5467 
       58.82        18.44        56.94        55.33        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 
       31.10        67.96        65.65        12.26        62.63        43.69 
TCGA-EU-5906 TCGA-EU-5907 
        6.77         4.18 

$subtype2
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 
        0.53        39.16        49.08        49.58        48.59        38.99 
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 
       23.21        48.82        45.53        88.37        51.25        28.70 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 
       74.76        53.29        55.76        18.64        18.87        20.28 
TCGA-AK-3444 TCGA-AK-3451 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4823 
       48.36        48.69        19.00         7.82         3.16        14.93 
TCGA-B0-4839 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 
       53.88        70.52        11.24        25.32        18.51         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5106 
        2.24        21.86        15.95        62.89        90.87        52.54 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5121 
       29.95        35.90        11.80        26.20        16.21        18.21 
TCGA-B0-5693 TCGA-B0-5700 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 
      101.13        35.57        52.77        79.36        47.97        96.36 
TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5636 
       89.49        35.90         1.68        12.30        11.77        30.21 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B8-4146 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5165 
        5.75         1.25        16.80         1.18        27.02        24.23 
TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4165 TCGA-BP-4169 
       17.16         6.38        34.39        14.30        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4326 TCGA-BP-4332 TCGA-BP-4341 TCGA-BP-4342 
       77.03        61.78        53.42        37.25        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 
       54.77        12.23        12.33        31.33        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 
       77.62        44.15        41.75        71.80        61.68        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 
       60.59        13.51        56.91        68.38        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 
        6.94        63.62        58.68        61.22         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38         7.23        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 
       36.07        33.34        25.81        36.95         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       30.64        41.62        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 
       36.23        28.87        48.10        52.27         9.63        49.15 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 
       38.30        37.25        22.78        13.35        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
        0.95        59.84        53.52        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
       47.18        75.06        71.87        64.18        63.98        68.55 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        27.65        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-4920 
       51.29        58.92        49.18        50.33         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.81        63.88        84.66        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-5589 
       67.00        75.58        83.77        81.83        66.31        78.18 
TCGA-CW-5590 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4856 
       35.34       105.93        83.90       103.43        18.77         0.59 
TCGA-CZ-4859 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5461 
       58.75         5.46         0.82        23.74        55.33        10.85 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 
       21.76        47.54        80.19        22.78        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 
       18.12         3.91 

$subtype3
TCGA-A3-3313 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3363 TCGA-A3-3374 
       24.16        21.86         4.50        52.93        10.49        43.20 
TCGA-A3-3378 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3456 
       20.71        84.36        73.08        68.61        67.20        37.58 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 
        3.32         1.41         4.57         3.48        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 
        3.62        65.10         5.98         2.14        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        20.25        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       52.21        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 
       27.42         6.71        56.68        11.64        10.29        29.03 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5109 
        7.30        10.95        52.08        90.48        30.48        19.30 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 
       17.59         1.94        37.22       112.80        46.68        56.78 
TCGA-B0-5703 TCGA-B0-5707 TCGA-B0-5709 TCGA-B2-3923 TCGA-B4-5832 TCGA-B4-5836 
       39.55        92.98       102.48        32.61         0.23         4.64 
TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
        5.46         0.23        23.31        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5551 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4335 
       20.91         0.53         3.58        27.78        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 
        0.07        93.99        49.84        11.31        33.99         5.98 
TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4960 
       48.07        10.82         5.33        15.78        10.98        71.41 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 
       46.45        31.30        27.22         3.88        43.00        37.02 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-CJ-4638 
        6.35        79.30        30.64        62.86        74.40        14.17 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4891 
       77.36        66.21        61.91        69.86        51.52        26.93 
TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4913 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       50.01        39.45        38.56        22.32        25.25        18.15 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-6087 
       53.26        60.99        53.42        62.66         7.36         1.35 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5456 
       46.16        47.08        69.21         6.77        14.66        56.28 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5987 
       47.01        10.22        57.21         1.94        12.69        14.63 

subtype1 subtype2 subtype3 
    0.36     0.53     0.07 
subtype1 subtype2 subtype3 
  120.59   105.93   112.80 
subtype1 subtype2 subtype3 
  44.315   38.845   27.075 
[1] "0.4 - 120.6 (44.3)" "0.5 - 105.9 (38.8)" "0.1 - 112.8 (27.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      54       15        39       14
  subtype2     130       16        37       17
  subtype3      35       13        39       45
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         54      130       35
  STAGE II        15       16       13
  STAGE III       39       37       39
  STAGE IV        14       17       45
[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  55  17  49   1
  subtype2 132  19  48   1
  subtype3  37  18  68   9
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55      132       37
  T2       17       19       18
  T3       49       48       68
  T4        1        1        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 63  2
  subtype2 78  4
  subtype3 67 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2   78    4
  subtype3   67   10
   clus
vv  subtype1 subtype2 subtype3
  0       63       78       67
  1        2        4       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1 109  13
  subtype2 182  18
  subtype3  88  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109   13
  subtype2  182   18
  subtype3   88   44
   clus
vv  subtype1 subtype2 subtype3
  0      109      182       88
  1       13       18       44
[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"
D6V7, binary
          cls
clus         0   1
  subtype1  34  88
  subtype2  77 123
  subtype3  40  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   88
  subtype2   77  123
  subtype3   40   92
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       77       40
  MALE         88      123       92
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        2 
character(0)
D6V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype3 
       1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4   115
  subtype2     4                         9   184
  subtype3     3                         7   121
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        4        3
  BLACK OR AFRICAN AMERICAN        4        9        7
  WHITE                          115      184      121
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
          cls
clus         0   1
  subtype1   9  82
  subtype2   8 117
  subtype3   2  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   82
  subtype2    8  117
  subtype3    2   96
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            9        8        2
  NOT HISPANIC OR LATINO       82      117       96
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  81  32
  subtype2 173  48
  subtype3 105  88
subtype1 subtype2 subtype3 
     113      221      193 
subtype1 subtype2 subtype3 
      32       48       88 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3328 TCGA-A3-3349 
       12.66        12.16        24.16        49.02        45.53        45.53 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3374 TCGA-A3-3376 TCGA-AK-3427 
       51.25        10.49        28.70        43.20        55.76        84.36 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       73.08        60.92        72.07        57.37        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       45.93        37.58        28.04        12.13        40.70         3.32 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4811 TCGA-B0-4823 
       28.47         3.62         5.98         2.14        46.59        14.93 
TCGA-B0-4834 TCGA-B0-4841 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5100 TCGA-B0-5109 
       68.71         6.71        11.24        34.36        62.89        19.30 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5691 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5707 
       17.59        16.21       112.80        60.33        52.77        92.98 
TCGA-B0-5709 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5838 
      102.48        97.41        32.61        30.21         5.75         5.46 
TCGA-B8-4619 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-A54E 
       17.19        24.23        17.16        16.60        34.39        29.88 
TCGA-B8-A54F TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4163 TCGA-BP-4166 
       17.06        15.42        14.17        85.51        93.34         0.43 
TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4337 
       23.05        54.90        27.78        37.25        21.21         0.07 
TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4355 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       54.77        49.84        31.33        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       41.75        61.68        10.82        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4994 TCGA-BP-4995 
       20.38        36.95        14.24        49.38        43.00        45.07 
TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5199 
       30.64        35.21         9.63        38.30        13.35        44.55 
TCGA-CJ-4642 TCGA-CJ-4889 TCGA-CJ-4899 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4918 
       53.52        63.98        50.24        49.18        49.28         3.06 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5689 TCGA-CW-5580 
       25.25        18.15        61.91        62.10        53.26        64.57 
TCGA-CW-5583 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-5467 TCGA-DV-5565 TCGA-DV-5567 
       81.83        78.18        74.66         2.40        43.69        65.88 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 TCGA-MM-A563 
       11.67        37.15        66.28        23.90        19.43 

$subtype2
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 
       36.82        47.21        39.16        49.58        48.59        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3351 
       24.69        37.38        23.21        48.82        31.07        29.92 
TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       18.44        42.97        82.32        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       53.29        18.64        28.31        65.52        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3434 
        0.10         0.10        11.18        10.62        66.31        68.61 
TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       48.36        58.49        28.73        22.45        38.40        31.27 
TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4814 
        1.41         2.53         7.82         3.16         3.25         5.52 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 
       16.77        54.48        10.09        78.44        27.42        53.88 
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-B0-5088 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       43.30        25.32        18.51        15.95        90.87        90.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
       35.90        11.80        26.20         1.94        18.21        21.44 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       14.76        79.17        48.89       101.13        46.68        56.78 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 
       84.92        90.12        35.57        39.55       120.59        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       96.36        89.49        61.32        35.90        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 
       31.30        10.36        32.98        16.67         9.57         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5549 
       25.05        24.66        23.01        23.74         0.85         6.38 
TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
       14.30         8.42        17.36        16.27       111.02        94.72 
TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4327 
      101.06        32.61        99.85        77.03        97.45         3.58 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 
       62.07        80.68        15.16        18.48        52.24        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 
       44.94        12.23        12.30        72.59        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       13.15        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 
        6.94        63.62        61.22        61.51        57.40        58.98 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 
       45.50         7.23        47.11        53.65        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       36.95        46.45         5.82        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       27.62        37.48        48.10         1.78        74.20        52.27 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5190 
       49.15        42.44        37.25        37.22        22.78        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       23.47        13.41        34.95        31.27         0.95        59.84 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4875 
       75.88        58.95        11.05        49.25        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4892 
       64.27        71.87        69.86        64.18        30.64        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 
       24.66        27.65        59.44        51.29        58.92        50.33 
TCGA-CJ-4916 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5684 TCGA-CJ-6032 TCGA-CW-5581 
       45.14        72.00        79.89        73.35        83.77        92.02 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
        5.39        85.78        73.18       105.93       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 
        0.59        58.75        63.39        93.04        63.42         0.82 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 
       18.44        55.33        56.94        47.01        21.76        47.54 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5575 TCGA-EU-5904 
       80.19        12.26        62.63        45.96        56.84        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        10.85 

$subtype3
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3346 
        0.53        49.08        37.15        36.36        21.86         4.50 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 
       52.93        88.37        20.71        18.87        20.28       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3451 TCGA-B0-4690 TCGA-B0-4691 
       29.10        67.20        42.08        48.69         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4707 TCGA-B0-4712 
        3.48        19.00         1.38        65.10        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        6.64        20.25        15.72         0.59        52.21        45.07 
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-B0-5075 
       45.30        56.68        11.64        10.29        29.03        20.94 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.90         7.30        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5116 
       21.86        52.08        52.54        30.48        29.95        21.60 
TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-4098 TCGA-B2-5633 
       37.22        15.78        56.94        79.36         1.68        11.77 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 
       21.57         0.23         0.53        23.31        25.55        25.91 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D 
       20.91         1.18        27.02        14.27         0.53        27.29 
TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 
        1.74         4.93        90.28        89.36        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 
       64.27        53.42        93.99        74.17        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4771 TCGA-BP-4781 
       11.31        12.33        33.99         5.98         5.33        68.38 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 
       15.78        36.39        10.98        37.25         6.71        47.97 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4971 
       87.45        71.41        58.68        60.30         6.74        48.89 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 
       14.93        46.45        31.30        25.81        27.22         3.88 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       16.47        18.51        36.23        28.87         6.35        79.30 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5195 
       30.64        62.86        74.40        27.02        31.79        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       33.47        19.82        46.55        63.25        73.22        14.17 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
       65.69        54.61        21.24        83.97        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4888 TCGA-CJ-4890 
       74.27        66.21        61.91        57.83        51.52        68.55 
TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4912 
       26.93        39.45        56.35        47.67        49.97        54.48 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81        63.88        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       22.32        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5590 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
        7.36        66.31        35.34         1.35        83.90        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16        47.08        69.21         6.77        14.66        60.59 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5459 
        5.46        61.41        58.82        23.74        56.28        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       10.85        10.22        57.21        22.52         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5568 
       12.69        67.96        65.65        14.63        22.78        12.16 
TCGA-DV-A4W0 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A564 
       66.02         3.91         4.18         7.96        70.13        19.96 
TCGA-MM-A84U 
       15.25 

subtype1 subtype2 subtype3 
    0.07     0.10     0.23 
subtype1 subtype2 subtype3 
  112.80   120.59   109.91 
subtype1 subtype2 subtype3 
   37.58    37.38    30.48 
[1] "0.1 - 112.8 (37.6)" "0.1 - 120.6 (37.4)" "0.2 - 109.9 (30.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      70       12        20       12
  subtype2     134       23        41       24
  subtype3      61       22        65       45
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         70      134       61
  STAGE II        12       23       22
  STAGE III       20       41       65
  STAGE IV        12       24       45
[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  70  13  28   3
  subtype2 134  27  59   2
  subtype3  66  29  92   6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       70      134       66
  T2       13       27       29
  T3       28       59       92
  T4        3        2        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus         0   1
  subtype1  50   3
  subtype2 100   2
  subtype3  88  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    3
  subtype2  100    2
  subtype3   88   12
   clus
vv  subtype1 subtype2 subtype3
  0       50      100       88
  1        3        2       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1  96  11
  subtype2 185  23
  subtype3 141  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96   11
  subtype2  185   23
  subtype3  141   45
   clus
vv  subtype1 subtype2 subtype3
  0       96      185      141
  1       11       23       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  39  75
  subtype2 101 121
  subtype3  47 146
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   75
  subtype2  101  121
  subtype3   47  146
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       39      101       47
  MALE         75      121      146
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        3        4 
[1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        19    90
  subtype2     2                        19   197
  subtype3     2                        14   175
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        2        2
  BLACK OR AFRICAN AMERICAN       19       19       14
  WHITE                           90      197      175
[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"
D7V12, binary
          cls
clus         0   1
  subtype1   3  80
  subtype2  16 140
  subtype3   7 130
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   80
  subtype2   16  140
  subtype3    7  130
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3       16        7
  NOT HISPANIC OR LATINO       80      140      130
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  86  32
  subtype2  27   6
  subtype3 144  38
  subtype4  61  71
  subtype5  20  15
  subtype6  21   6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     118       33      182      132       35       27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      32        6       38       71       15        6 
$subtype1
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3351 
       12.66        36.82        39.16        36.36        21.86        29.92 
TCGA-A3-3365 TCGA-A3-3380 TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3428 TCGA-AK-3431 
       28.70        18.64        20.28         0.10        73.08        60.92 
TCGA-AK-3434 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
       68.61        38.40        31.27        28.04         1.41         2.14 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4828 
       20.25        46.59         5.52        45.07        14.93        10.09 
TCGA-B0-4841 TCGA-B0-4848 TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5106 TCGA-B0-5116 
        6.71        29.03        43.30        18.51        52.54        21.60 
TCGA-B0-5120 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5702 TCGA-B0-5812 
       16.21        14.76        56.78        84.92        52.77        97.41 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-A4SR TCGA-B8-4622 TCGA-B8-5545 
       21.30        11.77        10.36        16.67        23.01        17.16 
TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54F TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
        6.38        34.39        17.06        85.51        94.72        90.28 
TCGA-BP-4166 TCGA-BP-4173 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4344 
        0.43        62.24        27.78        37.25        15.16        54.77 
TCGA-BP-4351 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4782 
       31.89        77.98        44.15        41.75        13.15        11.64 
TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4963 
       36.53        36.95         6.71         6.94        63.62        60.30 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 
        6.74        57.40        14.24        14.93        36.07         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5180 
       46.45        16.47        30.64        37.48        35.21        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5195 
       38.30        42.44        13.35        27.02        33.24        24.62 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4887 TCGA-CJ-4889 
       31.27        53.52        79.66        77.36        30.64        63.98 
TCGA-CJ-4899 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CW-5580 
       50.24        49.28        50.33        18.87        61.91        64.57 
TCGA-CW-5590 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5454 TCGA-CZ-5455 
       35.34        14.66        60.59         5.46        23.74        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5466 TCGA-CZ-5467 
       56.94        55.33        47.01        10.85        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-A4W0 
       12.69        14.63        22.78        43.69        12.16        66.02 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-MM-A563 TCGA-MM-A564 
        4.18        10.29        19.43        19.96 

$subtype2
TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3362 TCGA-A3-3363 TCGA-AK-3453 TCGA-AK-3456 
       12.16        24.16        51.25        10.49        45.93        37.58 
TCGA-AK-3465 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5700 TCGA-B0-5707 
       12.13       112.80        46.68        60.33        35.57        92.98 
TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5835 TCGA-B8-4621 TCGA-B8-5165 TCGA-B8-5546 
        1.68        32.98         0.53        25.91        24.23        16.60 
TCGA-B8-A54E TCGA-BP-4756 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       29.88        12.30        79.89        18.15        62.10        73.35 
TCGA-CJ-5689 TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5589 TCGA-CW-5591 TCGA-DV-5566 
       53.26        92.02         5.39        78.18        74.66        45.96 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       11.67        37.15        66.28 

$subtype3
TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       47.21        49.58        48.59        38.99        24.69        37.38 
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3352 TCGA-A3-3358 
       23.21        48.82        31.07        45.53        18.44        42.97 
TCGA-A3-3359 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       82.32        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       28.31        65.52        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       10.62        66.31        48.36        58.49        28.73        22.45 
TCGA-AS-3777 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4818 
       40.70         2.53         7.82         3.16         3.25        16.77 
TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4845 TCGA-B0-4846 
       54.48        78.44        27.42        53.88        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5085 TCGA-B0-5099 
       26.07         2.27        36.85        70.52        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        35.90        11.80        26.20         1.94 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5699 
       18.21        21.44        79.17        48.89       101.13        90.12 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       39.55       120.59        47.97        96.36        89.49        61.32 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 
       35.90        12.30        31.30         9.57         1.25         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J 
       24.66        23.74         0.85        14.30         8.42        17.36 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4170 
       16.27       111.02       101.06        32.61        99.85        77.03 
TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4340 
       61.78        97.45         3.58        62.07        80.68        18.48 
TCGA-BP-4341 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4765 
       52.24        44.94        12.23        31.33        72.59        71.80 
TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 
       48.07        61.97        60.59        13.51        56.91        48.95 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       61.22        61.51        58.98        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4999 
       47.11        53.65        33.34        36.95         5.82        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5176 
       38.70        37.02        27.62        48.10         1.78        52.27 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 
        9.63        49.15        37.25        37.22        22.78        23.47 
TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 
       13.41        34.95         0.95        59.84        75.88        65.69 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       58.95        11.05        49.25        75.06        64.27        71.87 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
       69.86        64.18        50.01        24.66        27.65        59.44 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 
       51.29        58.92        49.18        45.14         4.57        72.00 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 
       67.00        83.77        81.83        85.78        73.18       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 
      103.43        25.45         0.59        58.75        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 
       63.42         0.82        55.33        21.76        47.54        80.19 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L8 
       12.26        62.63        56.84        18.12         6.77        35.87 
TCGA-GK-A6C7 TCGA-MW-A4EC 
        2.01        10.85 

$subtype4
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-3425 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4688 
       18.87       109.91        29.10        67.20        42.08         3.32 
TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        1.41         3.48        28.47        19.00         1.38        65.10 
TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 
        5.98        19.73        43.96        15.72         0.59        52.21 
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-B0-5080 TCGA-B0-5081 
       45.30        56.68        11.64        10.29        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
        7.30        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5701 TCGA-B0-5706 
       29.95        19.30        37.22        15.78        56.94        79.36 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5162 
       21.57         0.23        23.31        25.55        20.91         1.18 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4167 TCGA-BP-4169 
       27.02         0.53         4.93        14.17        89.36        23.05 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       64.27        53.42        93.99        74.17        62.86        49.84 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4781 
       11.31        12.33        33.99         5.98        10.82        68.38 
TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4983 
       15.78        10.98        37.25        47.97        71.41        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 
       31.30        25.81        27.22        18.51        36.23        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5196 
        6.35        79.30        30.64        62.86        31.79        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4868 TCGA-CJ-4872 
       19.82        44.55        46.55        73.22        21.24        47.18 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 
       74.27        66.21        61.91        51.52        68.55        26.93 
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-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       63.88        84.66        22.32        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CZ-4854 
       62.66         7.36        66.31         1.35        83.90        46.16 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5462 TCGA-CZ-5464 
       47.08        69.21         6.77        56.28        10.22        57.21 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-EU-5905 TCGA-G6-A8L7 
        1.94        31.10        67.96        65.65         3.91        70.13 

$subtype5
TCGA-A3-3317 TCGA-A3-3357 TCGA-AK-3451 TCGA-B0-4691 TCGA-B0-4713 TCGA-B0-5075 
       49.02        88.37        48.69         4.57         6.64        20.94 
TCGA-B0-5092 TCGA-B0-5107 TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-5550 TCGA-B8-A54D 
       15.09        30.48       102.48         5.46        14.27        27.29 
TCGA-B8-A54G TCGA-BP-4163 TCGA-BP-4337 TCGA-BP-4346 TCGA-BP-4771 TCGA-BP-4797 
        1.74        93.34         0.07        49.08         5.33        36.39 
TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-5174 TCGA-CJ-4636 TCGA-CJ-4638 
       87.45        58.68        48.89        74.20        63.25        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-MM-A84U 
       18.77        61.41        58.82         7.96        15.25 

$subtype6
TCGA-A3-3328 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
       45.53        43.20        84.36        72.07        57.37        46.78 
TCGA-AK-3447 TCGA-B0-4699 TCGA-B0-4834 TCGA-B0-5083 TCGA-B0-5100 TCGA-B0-5117 
       40.01         3.62        68.71        34.36        62.89        17.59 
TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-A54K TCGA-BP-4177 
       32.61        30.21         5.75        17.19        15.42        54.90 
TCGA-BP-4334 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4994 
       21.21        77.62        61.68        60.95        20.38        43.00 
TCGA-BP-4995 TCGA-DV-5567 TCGA-DV-5576 
       45.07        65.88        23.90 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.53     0.10     0.23     0.07     3.62 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   97.41   112.80   120.59   109.91   102.48    84.36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  30.280   37.150   42.295   31.545   36.390   43.200 
[1] "0.1 - 97.4 (30.3)"  "0.5 - 112.8 (37.1)" "0.1 - 120.6 (42.3)"
[4] "0.2 - 109.9 (31.5)" "0.1 - 102.5 (36.4)" "3.6 - 84.4 (43.2)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      62       12        24       20
  subtype2      25        4         2        3
  subtype3     116       19        36       12
  subtype4      37       13        47       35
  subtype5       5        5        15       10
  subtype6      20        4         2        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         62       25      116       37        5       20
  STAGE II        12        4       19       13        5        4
  STAGE III       24        2       36       47       15        2
  STAGE IV        20        3       12       35       10        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  63  17  36   2
  subtype2  25   4   5   0
  subtype3 116  21  46   0
  subtype4  39  15  71   7
  subtype5   7   8  19   1
  subtype6  20   4   2   1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       63       25      116       39        7       20
  T2       17        4       21       15        8        4
  T3       36        5       46       71       19        2
  T4        2        0        0        7        1        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 43  1
  subtype2 15  1
  subtype3 84  1
  subtype4 66 10
  subtype5 17  4
  subtype6 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    1
  subtype2   15    1
  subtype3   84    1
  subtype4   66   10
  subtype5   17    4
  subtype6   13    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       43       15       84       66       17       13
  1        1        1        1       10        4        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1  94  18
  subtype2  28   3
  subtype3 158  13
  subtype4  95  34
  subtype5  22  10
  subtype6  25   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94   18
  subtype2   28    3
  subtype3  158   13
  subtype4   95   34
  subtype5   22   10
  subtype6   25    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       94       28      158       95       22       25
  1       18        3       13       34       10        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  16 102
  subtype2  16  18
  subtype3 101  82
  subtype4  31 101
  subtype5  17  18
  subtype6   6  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16  102
  subtype2   16   18
  subtype3  101   82
  subtype4   31  101
  subtype5   17   18
  subtype6    6   21
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       16       16      101       31       17        6
  MALE        102       18       82      101       18       21
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8        6       16        9        1        3 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
 [7] "subtype2" "subtype3" "subtype6" "subtype4" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype4"
[19] "subtype4" "subtype1" "subtype1" "subtype4" "subtype3" "subtype3"
[25] "subtype4" "subtype3" "subtype1" "subtype2" "subtype6" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype3" "subtype6" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
D8V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        2        4        3        2 
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
 [7] "subtype1" "subtype4" "subtype1" "subtype4" "subtype1"
D8V10, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
[4] "subtype5"              
clus
subtype1 subtype3 subtype4 subtype5 
       3        2        2        1 
[1] "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        11   100
  subtype2     2                         9    23
  subtype3     1                        16   164
  subtype4     2                         6   124
  subtype5     0                         4    30
  subtype6     0                         6    21
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        1        2        0
  BLACK OR AFRICAN AMERICAN       11        9       16        6        4
  WHITE                          100       23      164      124       30
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        6
  WHITE                           21
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus         0   1
  subtype1   6  74
  subtype2   2  29
  subtype3  12 110
  subtype4   5  88
  subtype5   1  26
  subtype6   0  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   74
  subtype2    2   29
  subtype3   12  110
  subtype4    5   88
  subtype5    1   26
  subtype6    0   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        2       12        5        1        0
  NOT HISPANIC OR LATINO       74       29      110       88       26       23
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1  92  32
  subtype2 154  49
  subtype3  98  85
subtype1 subtype2 subtype3 
     124      203      183 
subtype1 subtype2 subtype3 
      32       49       85 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       12.66        12.16         0.53        24.16        49.08        49.02 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3373 TCGA-A3-3376 
       52.93        45.53        51.25        28.70        53.29        55.76 
TCGA-A3-3387 TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3431 TCGA-AK-3461 
       20.28         0.10         0.10       109.91        60.92        28.04 
TCGA-B0-4688 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4811 TCGA-B0-4816 
        3.32        19.00        65.10         5.98        46.59        45.07 
TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4839 TCGA-B0-4843 TCGA-B0-4945 TCGA-B0-5080 
       14.93        29.10        53.88        11.64        70.52        11.24 
TCGA-B0-5095 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5691 
        8.05        62.89        29.95         1.94        16.21       112.80 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 TCGA-B2-5636 TCGA-B4-5836 
       52.77       102.48        47.97        97.41        30.21         4.64 
TCGA-B4-5838 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 
        5.46         1.18        27.02        17.16        14.27        34.39 
TCGA-B8-A54H TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4166 TCGA-BP-4167 
        8.42        16.27        14.17        94.72         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4337 
       23.05        62.24        54.90        80.68        37.25         0.07 
TCGA-BP-4341 TCGA-BP-4345 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 
       52.24        49.84        12.33        77.62        44.15        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4801 
       61.68        10.82        48.95        36.53        20.38        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4970 
       47.97         6.94        63.62        61.51        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4982 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5177 
       48.89        49.38        33.34        28.87        79.30         9.63 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       38.30        37.25        22.78        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4872 TCGA-CJ-4882 
       34.95        59.84        63.25        53.52        47.18        61.91 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 
       64.18        63.98        68.55        49.97        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5680 TCGA-CJ-6031 TCGA-CW-5583 
       50.33         3.06        63.88        25.25        62.66        81.83 
TCGA-CW-5588 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4865 TCGA-CZ-5988 
       66.31       105.93        83.90         6.77         5.46        22.78 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       12.16        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5905 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 
        3.91        70.13        35.87        19.43 

$subtype2
TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       47.21        39.16        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3367 TCGA-A3-3370 
       37.38        48.82        29.92        42.97        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       24.16        18.64        28.31        65.52        15.39        22.65 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 
       11.18        10.62        73.08        66.31        68.61        48.36 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3460 TCGA-B0-4693 TCGA-B0-4701 
       58.49        28.73        22.45        31.27         2.53         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4824 
        2.14         3.16         3.25         5.52        16.77        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 
       10.09        78.44        27.42         6.71        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 
       26.07         2.27        36.85        43.30        25.32        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       90.87        90.48        35.90        11.80        26.20        21.60 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 
       18.21        21.44        14.76        79.17        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 
       15.78        46.68        56.78        84.92        90.12        35.57 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
       39.55       120.59        96.36        89.49        61.32        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       12.30        21.30        31.30        32.98        16.67         9.57 
TCGA-B4-5834 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        1.25         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 
       25.05        24.66        23.01        23.74         0.85        24.23 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4159 
       16.60         6.38        14.30        17.36       111.02        85.51 
TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4327 
      101.06        32.61        99.85        61.78        97.45         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4344 TCGA-BP-4347 
       27.78        62.07        15.16        18.48        54.77        44.94 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 
       31.33        12.30        72.59        77.98        48.07        13.15 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       60.59        13.51        45.50         7.23        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       36.07        36.95        46.45        16.47         5.82        45.07 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 
       38.70        37.02        37.48        48.10         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 
       52.27        49.15        42.44        37.22        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4639 
       23.47        13.41        24.62        31.27         0.95        75.88 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4885 
       58.95        11.05        49.25        77.36        71.87        69.86 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 
       50.01        24.66        27.65        59.44        50.24        51.29 
TCGA-CJ-4904 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5681 
       58.92        45.14         4.57        72.00        79.89        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
       61.91        62.10        73.35        67.00        83.77        92.02 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 TCGA-CZ-4853 
        5.39        85.78        73.18        78.18       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
        0.59        58.75        60.59        63.39        93.04        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       47.01        10.22        21.76        47.54         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5904 
       12.26        62.63        43.69        45.96        11.67        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
        6.77         4.18        10.29         2.01        10.85 

$subtype3
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3357 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3378 
       37.15         4.50        88.37        10.49        43.20        20.71 
TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 
       18.87        29.10        84.36        15.78        72.07        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        40.01        48.69        45.93 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       37.58        38.40        12.13        40.70         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 
        3.48        28.47         1.38         3.62        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4817 
        6.64        20.25        15.72         0.59        52.21        33.50 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
        6.02        40.44        36.53        68.71        40.70        45.30 
TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5083 
       56.68        10.29        29.03        20.94        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
        7.30        18.51        15.09        10.95         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 
       52.08        52.54        30.48        19.30        17.59        37.22 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 
       60.33        56.94        79.36        92.98        32.61         1.68 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5835 
       11.77        10.36        21.57         5.75         0.23         0.53 
TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 TCGA-B8-5551 
       23.31        17.19        25.55        25.91        20.91         0.53 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54K 
       27.29        29.88        17.06         1.74         4.93        15.42 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4338 
       90.28        93.34        64.27        53.42        21.21        93.99 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       74.17        62.86        49.08        31.89        11.31        33.99 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.98        41.75         5.33        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4959 
       15.78        36.39        10.98        37.25         6.71        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4977 
       71.41        58.68        60.30         6.74        57.40        14.93 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4994 
       46.45        31.30        25.81        27.22         3.88        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5175 
       30.64        18.51        35.21        36.23         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4637 
       62.86        74.40        27.02        31.79        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
       14.17        65.69        54.61        83.97        79.66        74.27 
TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 
       64.27        66.21        57.83        30.64        51.52        26.93 
TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5676 
       39.45        56.35        47.67        54.48        18.81        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       25.71        18.87        22.32        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 
       75.58         7.36        64.57        35.34        74.66         1.35 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4866 
       18.77        46.16        47.08        69.21        14.66        61.41 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
       58.82        56.28        10.85        57.21        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5567 
       31.10        12.69        67.96        65.65        14.63        65.88 
TCGA-G6-A5PC TCGA-MM-A564 TCGA-MM-A84U 
        7.96        19.96        15.25 

subtype1 subtype2 subtype3 
    0.07     0.23     0.23 
subtype1 subtype2 subtype3 
  112.80   120.59    93.99 
subtype1 subtype2 subtype3 
  41.225   36.850   31.890 
[1] "0.1 - 112.8 (41.2)" "0.2 - 120.6 (36.9)" "0.2 - 94.0 (31.9)" 
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      76       11        28       10
  subtype2     110       20        46       28
  subtype3      65       24        52       42
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         76      110       65
  STAGE II        11       20       24
  STAGE III       28       46       52
  STAGE IV        10       28       42
[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  77  11  33   4
  subtype2 111  26  65   2
  subtype3  68  30  80   5
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       77      111       68
  T2       11       26       30
  T3       33       65       80
  T4        4        2        5
[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"
D9V5, binary
          cls
clus        0  1
  subtype1 56  3
  subtype2 87  2
  subtype3 83 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    3
  subtype2   87    2
  subtype3   83   13
   clus
vv  subtype1 subtype2 subtype3
  0       56       87       83
  1        3        2       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 105   9
  subtype2 168  27
  subtype3 133  42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105    9
  subtype2  168   27
  subtype3  133   42
   clus
vv  subtype1 subtype2 subtype3
  0      105      168      133
  1        9       27       42
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  44  81
  subtype2  88 116
  subtype3  48 135
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   81
  subtype2   88  116
  subtype3   48  135
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       88       48
  MALE         81      116      135
[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, continuous
D9V9, continuous
D9V10, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        3        2 
[1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        19   104
  subtype2     3                        15   182
  subtype3     4                        18   159
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        4
  BLACK OR AFRICAN AMERICAN       19       15       18
  WHITE                          104      182      159
[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"
D9V12, binary
          cls
clus         0   1
  subtype1   2  82
  subtype2  12 132
  subtype3  10 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   82
  subtype2   12  132
  subtype3   10  126
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2       12       10
  NOT HISPANIC OR LATINO       82      132      126
[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  94  49
  subtype2  87  49
  subtype3 150  44
  subtype4  13  24
subtype1 subtype2 subtype3 subtype4 
     143      136      194       37 
subtype1 subtype2 subtype3 subtype4 
      49       49       44       24 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3349 
       12.66        12.16         0.53        49.08        52.93        45.53 
TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3382 TCGA-AK-3425 
       51.25        74.76        53.29        55.76        18.87       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3454 TCGA-AK-3461 TCGA-B0-4688 
       29.10        67.20        42.08        28.73        28.04         3.32 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4813 
       19.00         1.38        65.10         5.98        15.72         0.59 
TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4827 TCGA-B0-4945 TCGA-B0-5080 
       45.07         6.02        40.44        29.10        70.52        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       11.90         7.30        18.51         8.05         2.24        52.08 
TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 
       62.89        29.95        19.30         1.94        16.21        37.22 
TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 TCGA-B2-5636 
      112.80        52.77       102.48        47.97        97.41        30.21 
TCGA-B2-5641 TCGA-B4-5378 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5162 TCGA-B8-5545 
       21.57         5.75        23.31        25.55         1.18        17.16 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I 
       14.27         0.53        34.39        17.06         8.42         4.93 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4169 TCGA-BP-4173 
       15.42        16.27        14.17        94.72        23.05        62.24 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4345 TCGA-BP-4352 
       54.90        53.42        80.68         0.07        49.84        11.31 
TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       12.33        31.33        77.62        44.15        41.75        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4790 
       61.68        10.82        68.38        11.64        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       20.38        37.25        36.95        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 
       71.41        61.51         6.74        57.40        14.24        49.38 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 
       46.45        31.30        27.22         3.88        30.64        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5187 TCGA-BP-5196 
       28.87         6.35        79.30         9.63        13.35        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4882 TCGA-CJ-4889 TCGA-CJ-4901 
       19.82        34.95        59.84        61.91        63.98        47.67 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-5671 
       49.97        49.18        49.28        50.33         3.06        63.88 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-6087 
       75.58        62.66         7.36        81.83        66.31         1.35 
TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4865 TCGA-CZ-5456 TCGA-CZ-5464 
       18.77        69.21         6.77         5.46        56.28        57.21 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       22.78        43.69        65.88        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A563 
       23.90        18.12         3.91        70.13        19.43 

$subtype2
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3357 TCGA-A3-3363 
       49.02        37.15        48.82         4.50        88.37        10.49 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3427 
       24.16        43.20        20.71        20.28         0.10        84.36 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3451 
       15.78        72.07        57.37        46.78        40.01        48.69 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4691 TCGA-B0-4696 
       37.58        38.40        12.13        40.70         4.57        28.47 
TCGA-B0-4699 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4817 TCGA-B0-4828 TCGA-B0-4834 
        3.62         6.64        20.25        33.50        10.09        68.71 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-5075 TCGA-B0-5083 
       27.42        53.88        56.68        26.07        20.94        34.36 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5402 
       15.09        10.95        30.48        21.60        17.59        14.76 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5707 
       56.78        60.33        56.94        39.55        79.36        92.98 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61         1.68        32.98         0.23         0.53         5.46 
TCGA-B4-5844 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5546 
        0.23        17.19        25.91        23.01        20.91        16.60 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
       27.29        29.88         1.74        90.28        93.34        32.61 
TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
       64.27        27.78        37.25        21.21        15.16        93.99 
TCGA-BP-4346 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4797 
       49.08        12.30         5.98         5.33        56.91        36.39 
TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
        6.71        58.68        60.30        48.89        45.50        14.93 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5175 TCGA-BP-5178 
        5.82        43.00        18.51        36.23        30.64        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 
       74.40        38.30        27.02        33.24        31.79        24.62 
TCGA-BP-5201 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4873 
       31.27        14.17        65.69        54.61        83.97        74.27 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 
       77.36        66.21        57.83        30.64        51.52        26.93 
TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       56.35        58.92        72.00        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5590 TCGA-CW-5591 
       18.15        53.42        64.57        92.02        35.34        74.66 
TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5458 TCGA-CZ-5466 
       14.66        61.41        58.82        23.74        56.94        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        1.94        31.10        12.69        67.96        65.65        14.63 
TCGA-DV-5568 TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-MM-A84U 
       12.16        66.02         7.96        15.25 

$subtype3
TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       47.21        39.16        24.16        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3365 TCGA-A3-3367 
       38.99        37.38        29.92        42.97        28.70        74.63 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       18.64        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 
       11.18        10.62        73.08        66.31        68.61        48.36 
TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3460 TCGA-B0-4693 TCGA-B0-4701 
       58.49        45.93        22.45        31.27         2.53         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4818 
        2.14         3.16         3.25        46.59         5.52        16.77 
TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4849 
       54.48        78.44         6.71        65.29        39.45         2.27 
TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       36.85        43.30        25.32        15.95        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 TCGA-B0-5399 
       52.54        35.90        11.80        26.20        18.21        21.44 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       79.17        48.89       101.13        15.78        46.68        84.92 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       90.12        35.57       120.59        96.36        89.49        61.32 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
       35.90        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4146 
       16.67         9.57         1.25         4.64         0.36        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 
       27.16        27.55        25.05        24.66        23.74         0.85 
TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4159 
       24.23         6.38        14.30        17.36       111.02        85.51 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4327 
      101.06        99.85         0.43        61.78        97.45         3.58 
TCGA-BP-4330 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 
       62.07        18.48        52.24        54.77        44.94        31.89 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 
       72.59        77.98        48.07        13.15        60.59        13.51 
TCGA-BP-4961 TCGA-BP-4969 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 
       63.62        58.98         7.23        47.11        53.65        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-5001 
       33.34        36.95        46.45        16.47        45.07        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       37.02        37.48        48.10         1.78        74.20        52.27 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 
       49.15        42.44        37.25        37.22        22.78        23.47 
TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       13.41        44.55         0.95        75.88        58.95        11.05 
TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 
       49.25        64.27        71.87        69.86        64.18        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4912 
       24.66        27.65        59.44        50.24        51.29        54.48 
TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 
       45.14         4.57        79.89        84.66        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       73.35        67.00        83.77         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
       78.18       105.93       103.43        25.45         0.59        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5455 
       60.59        63.39        93.04        63.42         0.82        18.44 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       55.33        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
       47.54         2.40        80.19        12.26        62.63        45.96 
TCGA-DV-5569 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       11.67         6.77         4.18        10.29        35.87         2.01 
TCGA-MM-A564 TCGA-MW-A4EC 
       19.96        10.85 

$subtype4
TCGA-AK-3431 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       60.92         1.41         3.48        19.73        43.96        52.21 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4844 
       36.53        14.93        40.70        45.30        11.64        10.29 
TCGA-B0-4848 TCGA-B0-5097 TCGA-B8-5163 TCGA-BP-4167 TCGA-BP-4342 TCGA-BP-4343 
       29.03        21.86        27.02        89.36        74.17        62.86 
TCGA-BP-4354 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4986 TCGA-CJ-4635 TCGA-CJ-4636 
       33.99        15.78        10.98        25.81        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4642 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4890 TCGA-CJ-4895 
       73.22        53.52        79.66        47.18        68.55        39.45 
TCGA-CJ-4923 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4854 
       18.81        22.32        53.26        60.99        83.90        46.16 
TCGA-CZ-4857 
       47.08 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.10     1.41 
subtype1 subtype2 subtype3 subtype4 
  112.80    93.99   120.59    89.36 
subtype1 subtype2 subtype3 subtype4 
   33.47    32.20    38.09    43.96 
[1] "0.1 - 112.8 (33.5)" "0.1 - 94.0 (32.2)"  "0.1 - 120.6 (38.1)"
[4] "1.4 - 89.4 (44.0)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      81       10        36       17
  subtype2      51       17        35       33
  subtype3     110       24        43       18
  subtype4       9        4        12       12
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         81       51      110        9
  STAGE II        10       17       24        4
  STAGE III       36       35       43       12
  STAGE IV        17       33       18       12
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  82  11  46   5
  subtype2  53  23  57   3
  subtype3 112  28  54   1
  subtype4   9   5  21   2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       82       53      112        9
  T2       11       23       28        5
  T3       46       57       54       21
  T4        5        3        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 61  8
  subtype2 65  8
  subtype3 84  1
  subtype4 16  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61    8
  subtype2   65    8
  subtype3   84    1
  subtype4   16    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       61       65       84       16
  1        8        8        1        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"
D10V6, binary
          cls
clus         0   1
  subtype1 119  15
  subtype2  98  32
  subtype3 165  18
  subtype4  24  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119   15
  subtype2   98   32
  subtype3  165   18
  subtype4   24   13
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      119       98      165       24
  1       15       32       18       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  54  90
  subtype2  36 100
  subtype3  84 111
  subtype4   6  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   90
  subtype2   36  100
  subtype3   84  111
  subtype4    6   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       54       36       84        6
  MALE         90      100      111       31
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      15       11       17        1 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
[25] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype1"
[31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[43] "subtype3"
D10V9, continuous
D10V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        3        3 
[1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        20   120
  subtype2     2                        14   117
  subtype3     2                        18   171
  subtype4     0                         0    37
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        2        0
  BLACK OR AFRICAN AMERICAN       20       14       18        0
  WHITE                          120      117      171       37
[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"
D10V12, binary
          cls
clus         0   1
  subtype1   2  93
  subtype2   4  98
  subtype3  14 123
  subtype4   4  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   93
  subtype2    4   98
  subtype3   14  123
  subtype4    4   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4       14        4
  NOT HISPANIC OR LATINO       93       98      123       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 26  8
  subtype2 18  4
  subtype3 37 12
  subtype4 17 18
subtype1 subtype2 subtype3 subtype4 
      34       22       49       35 
subtype1 subtype2 subtype3 subtype4 
       8        4       12       18 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       12.66        12.16        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5635 
       10.62        57.37        12.13        32.61        35.90        10.36 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4340 
        8.42        17.36        15.42        16.27        62.24        18.48 
TCGA-BP-4961 TCGA-BP-4981 TCGA-BP-4982 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4881 
       63.62        36.07        33.34        49.25        77.36        66.21 
TCGA-CJ-4900 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
       56.35        46.16        47.08         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
        2.01        19.43        19.96        15.25 

$subtype2
TCGA-A3-3317 TCGA-A3-3387 TCGA-B0-4811 TCGA-B0-5080 TCGA-B0-5691 TCGA-B0-5702 
       49.02        20.28        46.59        11.24       112.80        52.77 
TCGA-B0-5709 TCGA-B2-5636 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-A8YJ 
      102.48        30.21        17.16        14.27        34.39        14.17 
TCGA-BP-4770 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4970 
       10.82        48.95        36.53        47.97         6.94        14.24 
TCGA-BP-5008 TCGA-CJ-4889 TCGA-CJ-5671 TCGA-CJ-6031 
       35.21        63.98        63.88        62.66 

$subtype3
TCGA-A3-3358 TCGA-AK-3458 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4852 TCGA-B0-5085 
       42.97        38.40         2.14         3.16        36.85        25.32 
TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
       21.44        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 
       90.12        35.57       120.59        32.98         9.57         4.64 
TCGA-B8-5553 TCGA-BP-4969 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4995 TCGA-BP-5001 
       14.30        58.98         7.23        53.65        45.07        38.70 
TCGA-CJ-4878 TCGA-CJ-4887 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5683 
       71.87        30.64        79.89        84.66        18.15        62.10 
TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4864 TCGA-CZ-5453 
       83.77        85.78        78.18       105.93        93.04         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5466 
       23.74        18.44        55.33        55.33        21.76        22.52 
TCGA-CZ-5467 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 
        2.40        62.63        43.69        45.96        11.67        37.15 
TCGA-EU-5904 
       18.12 

$subtype4
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4821 TCGA-B0-4836 
        1.38        65.10        43.96        15.72        40.44        40.70 
TCGA-B0-4837 TCGA-B0-5088 TCGA-B2-5633 TCGA-B8-4621 TCGA-B8-5551 TCGA-B8-A54I 
       45.30        18.51        11.77        25.91         0.53         4.93 
TCGA-BP-4761 TCGA-BP-4787 TCGA-BP-4959 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4985 
        5.98        15.78        87.45         6.74        57.40        31.30 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5009 TCGA-CJ-4876 
       27.22         3.88        16.47        30.64        36.23        64.27 
TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-5686 TCGA-CW-6087 TCGA-CZ-4858 TCGA-CZ-4860 
       68.55        39.45        67.00         1.35        69.21         6.77 
TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-G6-A8L7 
       10.22        57.21        31.10        12.69        70.13 

subtype1 subtype2 subtype3 subtype4 
    0.10     6.94     0.82     0.53 
subtype1 subtype2 subtype3 subtype4 
   77.36   112.80   120.59    87.45 
subtype1 subtype2 subtype3 subtype4 
  18.955   35.870   38.700   30.640 
[1] "0.1 - 77.4 (19.0)"  "6.9 - 112.8 (35.9)" "0.8 - 120.6 (38.7)"
[4] "0.5 - 87.5 (30.6)" 
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      22        5         4        5
  subtype2      15        1         4        2
  subtype3      22        7        12        8
  subtype4      14        4         6       11
D11V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         22       15       22       14
  STAGE II         5        1        7        4
  STAGE III        4        4       12        6
  STAGE IV         5        2        8       11
[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 22  6  7  1
  subtype2 16  1  4  1
  subtype3 22  8 19  0
  subtype4 15  4 13  3
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       22       16       22       15
  T2        6        1        8        4
  T3        7        4       19       13
  T4        1        1        0        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
          cls
clus        0  1
  subtype1  7  1
  subtype2  9  1
  subtype3 23  0
  subtype4 17  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    9    1
  subtype3   23    0
  subtype4   17    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        7        9       23       17
  1        1        1        0        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 14  4
  subtype2 20  1
  subtype3 41  8
  subtype4 23 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    4
  subtype2   20    1
  subtype3   41    8
  subtype4   23   10
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       14       20       41       23
  1        4        1        8       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"
D11V7, binary
          cls
clus        0  1
  subtype1 17 19
  subtype2  6 16
  subtype3 20 29
  subtype4  6 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   19
  subtype2    6   16
  subtype3   20   29
  subtype4    6   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17        6       20        6
  MALE         19       16       29       29
[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, continuous
D11V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype4 
       5        1        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
D11V10, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype4 
       4        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        22    14
  subtype2     1                         2    18
  subtype3     0                         0    48
  subtype4     2                         4    28
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        2
  BLACK OR AFRICAN AMERICAN       22        2        0        4
  WHITE                           14       18       48       28
[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"
D11V12, binary
          cls
clus        0  1
  subtype1  0 29
  subtype2  1 13
  subtype3  4 37
  subtype4  1 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   29
  subtype2    1   13
  subtype3    4   37
  subtype4    1   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        4        1
  NOT HISPANIC OR LATINO       29       13       37       22
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 28  8
  subtype2 35 21
  subtype3 35 13
subtype1 subtype2 subtype3 
      36       56       48 
subtype1 subtype2 subtype3 
       8       21       13 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       12.66        12.16        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
       10.62        57.37        12.13        32.61        35.90        11.77 
TCGA-B2-5635 TCGA-B2-5636 TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       10.36        30.21         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4340 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4981 
       16.27        62.24        18.48        47.97        63.62        36.07 
TCGA-BP-4982 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4900 TCGA-CZ-4854 
       33.34        49.25        77.36        66.21        56.35        46.16 
TCGA-CZ-4857 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A84U 
       47.08         7.96        10.29        35.87         2.01        15.25 

$subtype2
TCGA-A3-3317 TCGA-A3-3387 TCGA-AK-3458 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4712 
       49.02        20.28        38.40         1.38        65.10        43.96 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-5080 
       15.72        46.59        40.44        40.70        45.30        11.24 
TCGA-B0-5088 TCGA-B0-5399 TCGA-B0-5691 TCGA-B0-5696 TCGA-B0-5702 TCGA-B0-5709 
       18.51        21.44       112.80        56.78        52.77       102.48 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A8YJ TCGA-BP-4761 
       17.16        14.27         0.53        34.39        14.17         5.98 
TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4807 TCGA-BP-4959 
       10.82        15.78        48.95        36.53         6.94        87.45 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4985 TCGA-BP-4988 
        6.74        57.40        14.24         7.23        31.30        27.22 
TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 
        3.88        30.64        35.21        63.98        68.55        39.45 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6031 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       63.88        84.66        62.66        78.18         1.35       105.93 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-DV-5573 TCGA-G6-A8L7 
       69.21         6.77        57.21        31.10        37.15        70.13 
TCGA-MM-A563 TCGA-MM-A564 
       19.43        19.96 

$subtype3
TCGA-A3-3358 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5692 
       42.97         2.14         3.16        36.85        25.32        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 
      101.13        15.78        46.68        90.12        35.57       120.59 
TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-4621 TCGA-B8-5553 TCGA-BP-4969 
       32.98         9.57         4.64        25.91        14.30        58.98 
TCGA-BP-4976 TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5009 TCGA-CJ-4876 
       53.65        16.47        45.07        38.70        36.23        64.27 
TCGA-CJ-4878 TCGA-CJ-4887 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
       71.87        30.64        79.89        18.15        62.10        67.00 
TCGA-CJ-6032 TCGA-CW-5585 TCGA-CZ-4864 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       83.77        85.78        93.04         0.82        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        55.33        10.22        21.76        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5904 
       12.69        62.63        43.69        45.96        11.67        18.12 

subtype1 subtype2 subtype3 
    0.10     0.53     0.82 
subtype1 subtype2 subtype3 
   77.36   112.80   120.59 
subtype1 subtype2 subtype3 
   17.92    35.87    36.54 
[1] "0.1 - 77.4 (17.9)"  "0.5 - 112.8 (35.9)" "0.8 - 120.6 (36.5)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      25        4         4        5
  subtype2      27        4        12       13
  subtype3      21        9        10        8
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         25       27       21
  STAGE II         4        4        9
  STAGE III        4       12       10
  STAGE IV         5       13        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 26  5  6  1
  subtype2 27  4 21  4
  subtype3 22 10 16  0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       26       27       22
  T2        5        4       10
  T3        6       21       16
  T4        1        4        0
[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"
D12V5, binary
          cls
clus        0  1
  subtype1  8  1
  subtype2 26  4
  subtype3 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2   26    4
  subtype3   22    0
   clus
vv  subtype1 subtype2 subtype3
  0        8       26       22
  1        1        4        0
[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"
D12V6, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 41 11
  subtype3 40  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   41   11
  subtype3   40    8
   clus
vv  subtype1 subtype2 subtype3
  0       17       41       40
  1        4       11        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1 17 21
  subtype2 10 46
  subtype3 22 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   21
  subtype2   10   46
  subtype3   22   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       10       22
  MALE         21       46       26
[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"
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        3        1 
[1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
D12V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 
       3        2 
[1] "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        21    17
  subtype2     3                         6    46
  subtype3     0                         1    45
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        3        0
  BLACK OR AFRICAN AMERICAN       21        6        1
  WHITE                           17       46       45
[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"
D12V12, binary
          cls
clus        0  1
  subtype1  0 31
  subtype2  3 35
  subtype3  3 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   31
  subtype2    3   35
  subtype3    3   35
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        3        3
  NOT HISPANIC OR LATINO       31       35       35
[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"
