[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/19775258/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/20125734/KIRC-TP.mergedcluster.txt"

nPatients in clinical file=537, in cluster file=537, common to both=537
[1]  12 537
[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 
238 135 155 
  1   2   3 
238 135 155 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
130  78 111 
  1   2   3 
130  78 111 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6 
89 87 91 84 94 33 
 1  2  3  4  5  6 
89 87 91 84 94 33 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
137 114  85 142 
  1   2   3   4 
137 114  85 142 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
116 223 194 
  1   2   3 
116 223 194 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
118  35 184 133  35  28 
  1   2   3   4   5   6 
118  35 184 133  35  28 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
126 205 185 
  1   2   3 
126 205 185 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
146 137 196  37 
  1   2   3   4 
146 137 196  37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
38 22 49 35 
 1  2  3  4 
38 22 49 35 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
40 56 48 
 1  2  3 
40 56 48 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 537 columns.

[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=167,	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=363,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "139"   "2"    
freq.contrast "2"     "139"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 537 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"                "PATHOLOGIC_STAGE"             
 [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
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
275  69 182  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
275  69 182  11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
275  69 182  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
275  69 182  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=13, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=10, 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 29  5
  subtype2 15  9
  subtype3 13  1
subtype1 subtype2 subtype3 
      34       24       14 
subtype1 subtype2 subtype3 
       5        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        38.47 
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        31.96 
TCGA-B2-4102 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 
       31.30        42.71        45.37        17.19       101.06        32.61 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
      115.00       106.16        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 
       62.01         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       114.41        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       117.80        94.19 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        83.21        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 
  115.00   114.41   117.80 
subtype1 subtype2 subtype3 
  37.100   41.180   38.795 
[1] "1.4 - 115.0 (37.1)"  "0.5 - 114.4 (41.2)"  "10.5 - 117.8 (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 
       2 
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  8  1
  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        1        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        31.96        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        62.01 
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       114.41        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        42.71 
TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-BP-4164 TCGA-CJ-4639 TCGA-CJ-4643 
       45.37        17.19       101.06        32.61       106.16        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        38.47        45.53        51.25        28.70        24.16 
TCGA-A3-3380 TCGA-AS-3778 TCGA-CJ-4634 
       18.64         1.41       115.00 

$subtype7
TCGA-A3-3328 TCGA-A3-3336 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       45.53        34.29       117.80        94.19        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 
       83.21        12.13        40.70        32.61        27.16 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   18.44     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   114.41   106.16   115.00   117.80 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  31.630   36.755   17.325   54.610   48.360   38.470   40.700 
[1] "18.4 - 47.2 (31.6)"  "0.5 - 90.3 (36.8)"   "1.7 - 37.6 (17.3)"  
[4] "14.2 - 114.4 (54.6)" "11.1 - 106.2 (48.4)" "1.4 - 115.0 (38.5)" 
[7] "12.1 - 117.8 (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 
       2 
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 179  59
  subtype2  86  47
  subtype3  86  69
subtype1 subtype2 subtype3 
     238      133      155 
subtype1 subtype2 subtype3 
      59       47       69 
$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        62.01        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3455 TCGA-AK-3458 
      109.41        73.68        48.36        94.29        22.45        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4703 TCGA-B0-4706 
       82.45        72.89         1.41         2.53         5.98         2.14 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
        3.25        15.72         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4843 
       54.48        29.10        78.44        45.30         6.71        10.52 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       39.45        26.07         2.27        70.52        20.94        43.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5099 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5110 
       25.32        18.51        15.95        90.48        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 
       52.73        51.02        38.43        48.82        46.39       111.52 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      129.67       133.94        15.78        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 
      126.28        73.84       149.16       105.37        79.89       131.15 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       91.46       126.05        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 
       31.66        32.98        16.67        12.00         0.85         4.64 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 
        0.23        16.80        27.16        25.05        45.37        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
       27.02         0.85        34.39        14.30        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 
        1.74         8.42        17.36        16.27       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       94.72       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       77.03        97.45         3.58        27.78        62.07        37.25 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       15.16        18.48        52.24        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4774 
       12.23        31.33        72.59        41.75        71.80        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4965 
       13.51        56.91        48.95        36.95         6.94        61.51 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       58.98        49.38         6.90        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       33.34        36.95        46.45         5.82        45.07        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 
       38.70        37.02        27.62        37.48        35.21        48.10 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
       74.20        52.27         9.63        49.15        38.30        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       22.78        13.35        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       24.62        44.55        34.95         0.95       115.00        63.25 
TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      106.16       105.37        58.95        21.24        83.97        49.25 
TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       75.06        71.87        57.83       113.46        64.18        30.64 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4908 
       50.01        27.65        50.24        49.97       108.56        50.33 
TCGA-CJ-4916 TCGA-CJ-5672 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CW-5581 
       45.14        72.00        62.10        73.35        53.26        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 
       81.83        85.78        73.18        78.18       105.93        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
        0.59        58.75        14.66        93.04         5.46        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 
       79.53        23.74        18.44        91.69        55.33        21.76 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
       69.96         2.40        80.19        12.26        22.78        62.63 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-EU-5904 
       45.96        12.16        11.67        37.15        81.21        18.12 
TCGA-EU-5906 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
        6.77        10.29         2.01        16.37 

$subtype2
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3374 
       11.90         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       117.80        73.08       112.08        94.19 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        83.21        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 
       58.45        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        52.87        56.98 
TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5712 TCGA-B2-3923 
      112.80        70.68        71.41       130.65        89.49        32.61 
TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4619 
        1.68        24.82         5.75         5.46        42.71        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       25.91        50.14         1.18        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4167 TCGA-BP-4173 
       48.53        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        10.72       116.84        61.91        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 
       63.98       115.69        26.93       109.84        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       131.08 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-6087 TCGA-CW-6093 
      133.71        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       107.54        63.39        61.41        90.54        12.69 
TCGA-DV-5567 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-MM-A84U 
       65.88        66.28        23.90        12.00         3.91        23.01 
TCGA-T7-A92I 
       11.70 

$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        38.47        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       109.51        78.64 
TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
       49.28        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        57.70        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        38.63        41.88        42.41        80.91 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4620 
       21.57         5.10         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         1.74        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       114.41        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        51.25 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      129.40        25.71        18.87        22.32        25.25       122.83 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
      118.85        53.42        75.58       119.64         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        79.63        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.22        84.30        22.52         1.94        31.10        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5575 TCGA-DV-A4VX TCGA-EU-5907 
       65.65        14.63        13.28        56.84        53.46         4.18 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A564 
        7.96        70.13        35.87        19.43        19.96 

subtype1 subtype2 subtype3 
    0.10     0.07     0.10 
subtype1 subtype2 subtype3 
  149.16   133.71   129.40 
subtype1 subtype2 subtype3 
  38.845   43.200   33.470 
[1] "0.1 - 149.2 (38.8)" "0.1 - 133.7 (43.2)" "0.1 - 129.4 (33.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     141       29        48       20
  subtype2      68       13        30       24
  subtype3      54       15        47       39
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        141       68       54
  STAGE II        29       13       15
  STAGE III       48       30       47
  STAGE IV        20       24       39
[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 141  34  62   1
  subtype2  69  16  44   6
  subtype3  58  19  74   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      141       69       58
  T2       34       16       19
  T3       62       44       74
  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 109   2
  subtype2  58   4
  subtype3  67  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109    2
  subtype2   58    4
  subtype3   67   11
   clus
vv  subtype1 subtype2 subtype3
  0      109       58       67
  1        2        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  92 146
  subtype2  57  78
  subtype3  40 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  146
  subtype2   57   78
  subtype3   40  115
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       92       57       40
  MALE        146       78      115
[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
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        21   212
  subtype2     4                        24   106
  subtype3     2                        11   139
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        4        2
  BLACK OR AFRICAN AMERICAN       21       24       11
  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  13 151
  subtype2   7  97
  subtype3   6 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  151
  subtype2    7   97
  subtype3    6  102
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        7        6
  NOT HISPANIC OR LATINO      151       97      102
[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  23
  subtype2  52  25
  subtype3  54  57
subtype1 subtype2 subtype3 
     129       77      111 
subtype1 subtype2 subtype3 
      23       25       57 
$subtype1
TCGA-3Z-A93Z TCGA-A3-3358 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3385 TCGA-A3-A6NI 
       12.66        42.97        74.76        53.29        65.52        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3450 TCGA-AK-3453 
       73.08        73.68       112.08        94.19        49.28        83.21 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4706 TCGA-B0-4818 
       28.73        38.40        82.45        72.89         2.14        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       14.93        54.48         6.71        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       36.85        90.87        90.48        66.05        38.63        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5691 
       52.87        51.02        38.43        46.39       111.52       112.80 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5707 
      133.94        70.68        58.85        73.84       149.16       123.09 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-5639 
       79.89       131.15        91.46       126.05        35.90        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       16.67        12.00         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       16.80        23.74        24.23        50.14        16.60         6.38 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
       34.39        14.30        17.06         8.42        17.36        16.27 
TCGA-BP-4801 TCGA-BP-4993 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       36.95         5.82        48.10         1.74        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        9.63        49.15        42.44        37.25        37.22        22.78 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4897 
       23.47        13.41        44.55        34.95         0.95       109.84 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5681 TCGA-CJ-5683 
       51.25       108.56        49.18        50.33        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 
       73.35       119.64        92.02        81.83        85.78        78.18 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 
      105.93       103.43         0.59        58.75        93.04        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5982 
       79.53        23.74        55.33        21.76         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 
       12.26        22.78        62.63        13.28        45.96        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L8 
       37.15        56.84        18.12         6.77        10.29        35.87 
TCGA-GK-A6C7 TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        16.37        11.70 

$subtype2
TCGA-6D-AA2E TCGA-A3-3376 TCGA-AK-3425 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
       11.90        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        58.59 
TCGA-B0-5109 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5709 
       19.30        56.98       129.67        86.47        71.41       130.65 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4621 
       31.66        24.82        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        48.53         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        91.69        10.22        65.88        12.16        66.28 
TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A84U 
       23.90        12.00         3.91        70.13        23.01 

$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        78.64         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        57.70        43.96         6.64         3.25        58.45 
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        10.52        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        41.88        48.82        42.41 
TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5706 
       15.78        85.78       119.38       126.28        80.91       105.37 
TCGA-B0-5712 TCGA-B2-4101 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4153 
       89.49        21.30        21.57         5.10         5.46        25.05 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-A54D TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5178 
       50.14        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       131.08 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        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 
      122.83        53.26       118.85        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        79.63        90.54        94.45        10.85 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        84.30        22.52         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5907 
       67.96        65.65        14.63        53.46        81.21         4.18 
TCGA-G6-A5PC TCGA-MM-A563 TCGA-MM-A564 
        7.96        19.43        19.96 

subtype1 subtype2 subtype3 
    0.10     0.53     0.59 
subtype1 subtype2 subtype3 
  149.16   130.65   133.71 
subtype1 subtype2 subtype3 
   38.43    30.21    31.10 
[1] "0.1 - 149.2 (38.4)" "0.5 - 130.7 (30.2)" "0.6 - 133.7 (31.1)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      89       17        13       11
  subtype2      44        2        20       12
  subtype3      23       12        40       36
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         89       44       23
  STAGE II        17        2       12
  STAGE III       13       20       40
  STAGE IV        11       12       36
[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 89 21 20  0
  subtype2 46  3 25  4
  subtype3 24 17 66  4
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       89       46       24
  T2       21        3       17
  T3       20       25       66
  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 53  0
  subtype2 31  3
  subtype3 49  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53    0
  subtype2   31    3
  subtype3   49    5
   clus
vv  subtype1 subtype2 subtype3
  0       53       31       49
  1        0        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 62 68
  subtype2 31 47
  subtype3 21 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   68
  subtype2   31   47
  subtype3   21   90
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       62       31       21
  MALE         68       47       90
[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
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        21   109
  subtype2     0                        18    60
  subtype3     1                        10    97
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN       21       18       10
  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   4 101
  subtype2   2  64
  subtype3   4  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  101
  subtype2    2   64
  subtype3    4   95
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        4
  NOT HISPANIC OR LATINO      101       64       95
[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 63 26
  subtype2 65 22
  subtype3 33 58
  subtype4 61 23
  subtype5 60 34
  subtype6 30  3
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      89       87       91       84       94       33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      26       22       58       23       34        3 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 
       12.66        11.90        24.16        48.59        38.99        37.38 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3373 
       62.01         4.50        88.37        51.25        10.49        53.29 
TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3444 
       43.20        20.71        18.87       117.80        73.08        48.36 
TCGA-AK-3456 TCGA-B0-4699 TCGA-B0-4714 TCGA-B0-4817 TCGA-B0-4833 TCGA-B0-4834 
       37.58         3.62         3.25        33.50        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4945 TCGA-B0-5084 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 
       45.30        70.52         7.30         2.24        90.87        19.30 
TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5696 TCGA-B0-5700 TCGA-B0-5702 
       52.87        56.98       112.80        85.78        58.85        71.41 
TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4102 
       73.84        32.61        35.90         1.68        31.96        31.30 
TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54E 
       16.80        25.55        25.91         6.38         0.53        29.88 
TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4332 
        4.93        14.17        99.85        77.03        61.78        37.25 
TCGA-BP-4334 TCGA-BP-4341 TCGA-BP-4353 TCGA-BP-4756 TCGA-BP-4777 TCGA-BP-4799 
       21.21        52.24        12.33        12.30        56.91        37.25 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4988 TCGA-BP-4989 
       61.22         6.74        58.98        49.38        27.22         3.88 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5178 TCGA-BP-5185 
        5.82        43.00        37.02         6.35        62.86        37.22 
TCGA-BP-5187 TCGA-BP-5194 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4874 TCGA-CJ-4885 
       13.35        13.41        19.82       115.00        75.06       113.46 
TCGA-CJ-4886 TCGA-CJ-4902 TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CZ-4865 
       64.18        49.97        18.15        62.66         7.36         5.46 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-EU-5904 
       79.53        90.54        55.33        10.22        18.12 

$subtype2
TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3329 TCGA-A3-3385 TCGA-AK-3434 TCGA-B0-4706 
       36.82        49.58        23.21        65.52        68.61         2.14 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 
       45.07        16.77        54.48         6.71        65.29        39.45 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5116 
        2.27        36.85        43.30        25.32        15.95        41.88 
TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5693 
       51.02        48.82        46.39        42.41       111.52       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5711 TCGA-B0-5812 
       15.78        70.68       119.38       126.28       131.15       126.05 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-5553 TCGA-B8-A54J 
        4.64         0.36         0.23        25.05        14.30        17.36 
TCGA-BP-4161 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 
       90.28        97.45         3.58        27.78        62.07        15.16 
TCGA-BP-4759 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4975 TCGA-BP-4977 
       77.98        13.15        61.97        13.51        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4999 
       36.07        33.34        36.95        46.45        45.07        41.62 
TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 
       38.70        37.48        79.30        74.20        52.27        74.40 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5192 TCGA-CJ-4635 TCGA-CJ-4870 TCGA-CJ-4878 
       49.15        42.44        23.47        46.55        49.25        71.87 
TCGA-CJ-4897 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5680 TCGA-CJ-5683 TCGA-CJ-6032 
      109.84        45.14       129.40        25.25        62.10       119.64 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-6093 TCGA-CZ-4859 TCGA-CZ-5451 TCGA-CZ-5465 
       81.83        85.78       103.43        58.75        63.42        84.30 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-DV-5565 TCGA-DV-5566 TCGA-G6-A8L6 
       80.19        65.65        12.26        13.28        45.96        10.29 
TCGA-G6-A8L8 TCGA-MM-A564 TCGA-MW-A4EC 
       35.87        19.96        16.37 

$subtype3
TCGA-A3-3308 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3387 TCGA-AK-3436 TCGA-B0-4688 
        0.53        34.29        52.93        20.28       109.51         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4707 
        1.41         4.57         3.48        28.47         1.38        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
       57.70        43.96         6.64        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4842 
        5.52        40.44        36.53        29.10        10.09        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 
       10.52        10.29        29.03        15.09        10.95        52.08 
TCGA-B0-5107 TCGA-B0-5707 TCGA-B0-5709 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 
       30.48       123.09       130.65         5.10         5.46        23.31 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-A54F TCGA-BP-4173 TCGA-BP-4326 TCGA-BP-4338 
       50.14        20.91        17.06        62.24        53.42        93.99 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4770 
       74.17        62.86        11.31        33.99         5.98        10.82 
TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4985 
        5.33        15.78        10.98        71.41        46.45        31.30 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5175 TCGA-BP-5199 TCGA-CJ-4638 
       16.47        18.51        36.23        30.64        44.55        14.17 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4891 
       83.97        79.66        74.27       116.84        66.21        26.93 
TCGA-CJ-4895 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5677 
       39.45        47.67        54.48        38.56         4.57        25.71 
TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6087 
       22.32        53.26       118.85        53.42        66.31         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        79.63 
TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-G6-A5PC 
       94.45        69.96         1.94        14.63        53.46         7.96 
TCGA-G6-A8L7 
       70.13 

$subtype4
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3351 TCGA-A3-3352 
       39.16        49.02        37.15        36.36        29.92        18.44 
TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3383 TCGA-B0-4811 TCGA-B0-4838 TCGA-B0-4839 
       74.63        24.16        28.31        46.59        27.42        53.88 
TCGA-B0-4847 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5701 
       26.07        20.94        11.90       129.67        86.47        80.91 
TCGA-B0-5705 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4101 TCGA-B2-5635 TCGA-B2-5639 
      149.16        89.49        91.46        21.30        24.82        32.98 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5835 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 
       21.57        12.00         0.53        23.74         0.85        16.60 
TCGA-B8-5550 TCGA-B8-A54G TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4346 
       48.53         1.74       111.02        32.61        80.68        49.08 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4963 TCGA-BP-4968 
       44.94        31.89         6.71        87.45        60.30        57.40 
TCGA-BP-4973 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5201 
       45.50        27.02        33.24        31.79        24.62        31.27 
TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4893 
      114.41        64.27        57.83        30.64        51.52        24.66 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5672 TCGA-CJ-5678 TCGA-CW-5580 
       51.25       108.56        49.28        72.00        18.87        64.57 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-5591 
       92.02         5.39        73.18        78.18        35.34        74.66 
TCGA-CW-6096 TCGA-CZ-4853 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       88.80        25.45       107.54        63.39        93.04        61.41 
TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5470 
       58.82        18.44        91.69        21.76         2.40        12.69 
TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5573 TCGA-EU-5905 TCGA-EU-5907 TCGA-MM-A563 
       67.96        62.63        37.15         3.91         4.18        19.43 

$subtype5
TCGA-A3-3316 TCGA-A3-3349 TCGA-A3-3365 TCGA-A3-3376 TCGA-A3-3380 TCGA-AK-3451 
       49.08        45.53        28.70        55.76        18.64        94.29 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4815 TCGA-B0-4819 
       19.00        65.10         7.82         5.98        52.21         6.02 
TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-5080 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5097 
       14.93        40.70        11.24        18.51         8.05        21.86 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 
       62.89        90.48        52.54        58.59        38.63        52.73 
TCGA-B0-5120 TCGA-B0-5706 TCGA-B0-5710 TCGA-B2-5633 TCGA-B2-5636 TCGA-B2-A4SR 
       38.43       105.37        79.89        31.66        30.21        16.67 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-A54D 
        5.75         0.85         1.18        27.02        50.14        27.29 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4169 TCGA-BP-4337 TCGA-BP-4345 TCGA-BP-4349 
        8.42        15.42        23.05         0.07        49.84        12.23 
TCGA-BP-4355 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4784 
       31.33        44.15        41.75        71.80        61.68        60.95 
TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 
       36.53        47.97        63.62        58.68        14.24        48.89 
TCGA-BP-4974 TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5177 
        6.90        30.64        35.21        28.87        48.10         9.63 
TCGA-BP-5182 TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4882 
       38.30        33.47        34.95        21.24        10.72        61.91 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98       115.69        50.01        27.65        50.24        56.35 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 
       49.18        50.33         3.06        18.81       131.08       133.71 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6030 TCGA-CW-6088 TCGA-CW-6090 
      122.83        73.35        67.00        75.58       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-5454 TCGA-CZ-5461 TCGA-CZ-5466 TCGA-CZ-5469 
       18.77         0.59        23.74        10.85        22.52        31.10 
TCGA-DV-5567 TCGA-DV-5574 TCGA-DV-A4VZ TCGA-GK-A6C7 
       65.88        66.28        12.00         2.01 

$subtype6
TCGA-A3-3331 TCGA-A3-3370 TCGA-B0-4693 TCGA-B0-5110 TCGA-B8-5165 TCGA-B8-5552 
       48.82        74.76         2.53        66.05        24.23        34.39 
TCGA-B8-A7U6 TCGA-BP-4344 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4766 TCGA-BP-4775 
       16.27        54.77        72.59        77.62        48.07        60.59 
TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4965 
       68.38        48.95        36.39        36.95         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-5006 TCGA-BP-5173 TCGA-BP-5184 TCGA-BP-5186 
       53.65        25.81        27.62         1.74        37.25        22.78 
TCGA-BP-5202 TCGA-CJ-4642 TCGA-CZ-5988 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 
        0.95       105.37        22.78        12.16        11.67        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5906 
       23.90        81.21         6.77 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.53     0.23     0.53     0.53     0.07     0.95 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  117.80   133.94   130.65   149.16   133.71   105.37 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  37.250   45.140   30.640   38.155   37.415   36.950 
[1] "0.5 - 117.8 (37.2)" "0.2 - 133.9 (45.1)" "0.5 - 130.7 (30.6)"
[4] "0.5 - 149.2 (38.2)" "0.1 - 133.7 (37.4)" "0.9 - 105.4 (37.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      56        7        18        8
  subtype2      50       12        17        8
  subtype3      17        9        30       35
  subtype4      36        9        26       13
  subtype5      47       10        20       17
  subtype6      29        1         3        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         56       50       17       36       47       29
  STAGE II         7       12        9        9       10        1
  STAGE III       18       17       30       26       20        3
  STAGE IV         8        8       35       13       17        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 57  7 24  1
  subtype2 50 14 22  1
  subtype3 20 14 50  7
  subtype4 35 11 38  0
  subtype5 49 12 31  2
  subtype6 29  1  3  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       57       50       20       35       49       29
  T2        7       14       14       11       12        1
  T3       24       22       50       38       31        3
  T4        1        1        7        0        2        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 44  3
  subtype2 34  0
  subtype3 41  9
  subtype4 42  1
  subtype5 43  2
  subtype6 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    3
  subtype2   34    0
  subtype3   41    9
  subtype4   42    1
  subtype5   43    2
  subtype6   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       44       34       41       42       43       10
  1        3        0        9        1        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 77  8
  subtype2 76  6
  subtype3 56 32
  subtype4 69 13
  subtype5 72 17
  subtype6 31  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77    8
  subtype2   76    6
  subtype3   56   32
  subtype4   69   13
  subtype5   72   17
  subtype6   31    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       77       76       56       69       72       31
  1        8        6       32       13       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 30 59
  subtype2 39 48
  subtype3 29 62
  subtype4 25 59
  subtype5 26 68
  subtype6 13 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   59
  subtype2   39   48
  subtype3   29   62
  subtype4   25   59
  subtype5   26   68
  subtype6   13   20
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       30       39       29       25       26       13
  MALE         59       48       62       59       68       20
[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:" "subtype5"               "subtype6"              
clus
subtype1 subtype3 subtype4 subtype5 subtype6 
       4        5        4        2        1 
 [1] "subtype1" "subtype1" "subtype3" "subtype4" "subtype4" "subtype1"
 [7] "subtype3" "subtype4" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype4"
D5V10, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
[4] "subtype5"               "subtype6"              
clus
subtype3 subtype4 subtype5 subtype6 
       2        2        2        1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        11    76
  subtype2     1                         8    77
  subtype3     2                         5    84
  subtype4     0                         5    76
  subtype5     3                        11    78
  subtype6     0                         4    29
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        2        0        3
  BLACK OR AFRICAN AMERICAN       11        8        5        5       11
  WHITE                           76       77       84       76       78
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        4
  WHITE                           29
[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  4 51
  subtype2  7 54
  subtype3  3 66
  subtype4  3 63
  subtype5  3 65
  subtype6  1 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   51
  subtype2    7   54
  subtype3    3   66
  subtype4    3   63
  subtype5    3   65
  subtype6    1   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            4        7        3        3        3        1
  NOT HISPANIC OR LATINO       51       54       66       63       65       16
[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  97  40
  subtype2  70  44
  subtype3  34  51
  subtype4 111  31
subtype1 subtype2 subtype3 subtype4 
     137      114       85      142 
subtype1 subtype2 subtype3 subtype4 
      40       44       51       31 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3322 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 
       12.66        11.90        48.59        45.53        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 TCGA-AK-3451 
       28.70        74.76        53.29        55.76        18.64        94.29 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4823 
       19.00         7.82         5.98        52.21         6.02        14.93 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5088 
       40.70        27.42        53.88        70.52        11.24        18.51 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 
        2.24        21.86        62.89        90.48        52.54        58.59 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5693 TCGA-B0-5697 TCGA-B0-5702 
       38.63        52.73        38.43       133.94        86.47        71.41 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3924 
      105.37       123.09        79.89       131.15        89.49        35.90 
TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5636 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 
       31.96        31.66        30.21        16.67         5.75         0.85 
TCGA-B4-5835 TCGA-B8-4143 TCGA-B8-5162 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5550 
        0.53        23.31         1.18        50.14         6.38        48.53 
TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       34.39        27.29         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4331 TCGA-BP-4332 
       16.27        14.17        23.05        77.03        80.68        37.25 
TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       54.77        12.23        31.33        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4790 
       71.80        61.68        60.59        56.91        60.95        36.53 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4964 
       37.25        36.95        47.97         6.94        87.45        61.22 
TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4993 
       61.51        14.24        48.89        49.38         6.90         5.82 
TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5177 
       30.64        35.21        28.87        48.10        79.30         9.63 
TCGA-BP-5182 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4642 TCGA-CJ-4868 
       38.30        13.41        33.47        34.95       105.37        21.24 
TCGA-CJ-4872 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4894 TCGA-CJ-4899 
       10.72        64.18        63.98       115.69        27.65        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        49.97        51.25       108.56        49.18        50.33 
TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        3.06       131.08        72.00       133.71        18.15       122.83 
TCGA-CJ-5684 TCGA-CJ-6030 TCGA-CW-6088 TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-5454 
       73.35        75.58       105.93        18.77         0.59        23.74 
TCGA-CZ-5461 TCGA-CZ-5466 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       10.85        22.52        65.88        11.67        37.15        66.28 
TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-GK-A6C7 TCGA-MM-A563 
       23.90        12.00        18.12         2.01        19.43 

$subtype2
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 
       36.82         0.53        39.16        49.08        37.15        36.36 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3382 
       62.01        34.29        52.93        18.44        74.63        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3434 TCGA-B0-4691 TCGA-B0-4706 TCGA-B0-4718 
       28.31        65.52        68.61         4.57         2.14        58.45 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4841 TCGA-B0-4843 
       40.44        36.53        54.48        29.10         6.71        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 
       10.29        65.29        39.45        36.85        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5092 TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5694 
       11.90        15.09        51.02        46.39       111.52        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5812 TCGA-B2-5641 
       70.68       119.38       126.28        80.91       126.05        21.57 
TCGA-B4-5832 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-4622 TCGA-B8-5158 
        5.10         0.36         0.23        25.05        50.14        20.91 
TCGA-B8-5163 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 
       27.02       111.02        90.28        62.24        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4335 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
        3.58        27.78        15.16        74.17        62.86        49.84 
TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4967 
       12.33        13.15         6.71        71.41        60.30         6.74 
TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5178 
       14.93        31.30        25.81        16.47        18.51        62.86 
TCGA-BP-5180 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5199 TCGA-CJ-4635 TCGA-CJ-4869 
       74.40        31.79        24.62        44.55        46.55        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4901 
       79.66        74.27        66.21        57.83        30.64        47.67 
TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5683 
       54.48         4.57        18.81        25.71        22.32        62.10 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-5590 TCGA-CW-5591 
      118.85        53.42        64.57        66.31        35.34        74.66 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-5451 TCGA-CZ-5456 TCGA-CZ-5459 
       83.90        25.45        47.08        63.42        79.63        55.33 
TCGA-CZ-5460 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
       94.45         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-A4VX TCGA-G6-A8L7 TCGA-G6-A8L8 
       14.63        13.28        12.16        53.46        70.13        35.87 

$subtype3
TCGA-A3-3313 TCGA-A3-3324 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3378 TCGA-AK-3427 
       24.16        38.99         4.50        43.20        20.71       117.80 
TCGA-AK-3428 TCGA-AK-3436 TCGA-AK-3456 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 
       73.08       109.51        37.58         3.32         1.41         3.48 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4707 TCGA-B0-4712 
       28.47         1.38         3.62        65.10        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 
        6.64         3.25        15.72         0.59         5.52        33.50 
TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4848 TCGA-B0-5084 
       10.09        68.71        45.30        56.68        29.03         7.30 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 
       10.95         8.05        52.08        30.48        19.30        52.87 
TCGA-B0-5400 TCGA-B0-5703 TCGA-B0-5709 TCGA-B2-3923 TCGA-B4-5836 TCGA-B4-5838 
       56.98        73.84       130.65        32.61         4.64         5.46 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-A54E TCGA-BP-4334 
       25.55        25.91        16.60         0.53        29.88        21.21 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 
        0.07        93.99        11.31        33.99        12.30         5.98 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4962 TCGA-BP-4983 
       10.82         5.33        15.78        10.98        58.68        46.45 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-4638 
       27.22         3.88        43.00         6.35        19.82        14.17 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 
      116.84        61.91       113.46        51.52        26.93        50.01 
TCGA-CJ-4895 TCGA-CJ-4913 TCGA-CJ-5675 TCGA-CJ-5680 TCGA-CJ-5689 TCGA-CJ-6031 
       39.45        38.56       129.40        25.25        53.26        62.66 
TCGA-CJ-6033 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 
        7.36         1.35        46.16        69.21         6.77        14.66 
TCGA-CZ-5464 
       69.96 

$subtype4
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3351 
       49.02        49.58        37.38        23.21        48.82        29.92 
TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 TCGA-AK-3444 TCGA-B0-4693 TCGA-B0-4710 
       88.37        24.16        20.28        48.36         2.53        57.70 
TCGA-B0-4811 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4833 TCGA-B0-4847 TCGA-B0-4849 
       46.59        45.07        16.77        78.44        26.07         2.27 
TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5121 
       25.32        15.95        90.87        66.05        41.88        48.82 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5700 TCGA-B0-5705 
       42.41       112.80       129.67        85.78        58.85       149.16 
TCGA-B0-5713 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
       91.46         1.68        21.30        31.30        24.82        32.98 
TCGA-B4-5377 TCGA-B8-4146 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5553 
       12.00        16.80        23.74         0.85        24.23        14.30 
TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4174 TCGA-BP-4330 
       17.06         1.74        32.61        99.85        61.78        62.07 
TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 
       52.24        49.08        44.94        31.89        72.59        77.98 
TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4797 
       48.07        61.97        13.51        68.38        48.95        36.39 
TCGA-BP-4961 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
       63.62        57.40        58.98        45.50        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4999 
       36.07        33.34        36.95        46.45        45.07        41.62 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5173 
       38.70        37.02        27.62        37.48        36.23         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 
       74.20        30.64        52.27        49.15        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
       37.22        22.78        13.35        27.02        33.24        23.47 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4870 TCGA-CJ-4874 
       31.27         0.95       115.00       114.41        49.25        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4916 
       64.27        71.87        24.66       109.84        49.28        45.14 
TCGA-CJ-5678 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       18.87        67.00       119.64        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 TCGA-CW-6096 TCGA-CZ-4859 
       85.78        73.18        78.18       103.43        88.80        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        61.41        58.82 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5462 TCGA-CZ-5463 
       79.53        18.44        90.54        91.69        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
       84.30         2.40        80.19        12.26        22.78        62.63 
TCGA-DV-5566 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       45.96        56.84        81.21         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-MM-A564 TCGA-MW-A4EC 
        7.96        10.29        19.96        16.37 

subtype1 subtype2 subtype3 subtype4 
    0.53     0.23     0.07     0.85 
subtype1 subtype2 subtype3 subtype4 
  133.94   126.28   130.65   149.16 
subtype1 subtype2 subtype3 subtype4 
  37.250   39.945   25.910   45.105 
[1] "0.5 - 133.9 (37.2)" "0.2 - 126.3 (39.9)" "0.1 - 130.7 (25.9)"
[4] "0.8 - 149.2 (45.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      86       10        22       19
  subtype2      46       16        30       22
  subtype3      25        6        25       29
  subtype4      78       16        37       11
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         86       46       25       78
  STAGE II        10       16        6       16
  STAGE III       22       30       25       37
  STAGE IV        19       22       29       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 87 13 36  1
  subtype2 48 19 47  0
  subtype3 25  9 42  9
  subtype4 80 18 43  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       87       48       25       80
  T2       13       19        9       18
  T3       36       47       42       43
  T4        1        0        9        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 59  3
  subtype2 59  3
  subtype3 43  8
  subtype4 53  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59    3
  subtype2   59    3
  subtype3   43    8
  subtype4   53    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       59       59       43       53
  1        3        3        8        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"
D6V6, binary
          cls
clus         0   1
  subtype1 107  19
  subtype2  90  21
  subtype3  57  27
  subtype4 127   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107   19
  subtype2   90   21
  subtype3   57   27
  subtype4  127    9
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      107       90       57      127
  1       19       21       27        9
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 48 89
  subtype2 31 83
  subtype3 24 61
  subtype4 59 83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   89
  subtype2   31   83
  subtype3   24   61
  subtype4   59   83
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       48       31       24       59
  MALE         89       83       61       83
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        3        2        6 
 [1] "subtype1" "subtype1" "subtype4" "subtype2" "subtype4" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2" "subtype4" "subtype4"
[13] "subtype2" "subtype1"
D6V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype4 
       4        2        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        20   111
  subtype2     1                         4   107
  subtype3     2                         9    74
  subtype4     1                        11   128
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        1        2        1
  BLACK OR AFRICAN AMERICAN       20        4        9       11
  WHITE                          111      107       74      128
[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"
D6V12, binary
          cls
clus        0  1
  subtype1  4 96
  subtype2  4 75
  subtype3  2 60
  subtype4 11 84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   96
  subtype2    4   75
  subtype3    2   60
  subtype4   11   84
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        4        2       11
  NOT HISPANIC OR LATINO       96       75       60       84
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  82  33
  subtype2 170  52
  subtype3 104  90
subtype1 subtype2 subtype3 
     115      222      194 
subtype1 subtype2 subtype3 
      33       52       90 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3328 TCGA-A3-3349 
       12.66        11.90        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       117.80 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
       73.08        73.68       112.08        94.19        46.78        40.01 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       83.21        37.58        72.89        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 
       52.87        38.43       112.80        86.47        71.41       123.09 
TCGA-B0-5709 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5838 
      130.65       126.05        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        50.14        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 
      105.37        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       122.83        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        13.28        65.88 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-MM-A563 
       11.67        37.15        66.28        23.90        12.00        19.43 
TCGA-T7-A92I 
       11.70 

$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 
       38.47        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-A6NI TCGA-A3-A6NJ 
       53.29        18.64        28.31        65.52        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3429 
       22.65         0.10         0.10        11.18        10.62       109.41 
TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 
       68.61        48.36        49.28        28.73        22.45        38.40 
TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 
       82.45         1.41         2.53         7.82        57.70         3.25 
TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4838 
        5.52        16.77        54.48        10.09        78.44        27.42 
TCGA-B0-4839 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       53.88        65.29        39.45        26.07         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5099 TCGA-B0-5102 
       70.52        43.30        25.32        18.51        15.95        90.87 
TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 
       90.48        66.05        38.63        52.73        51.02        48.82 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       46.39        42.41       111.52       129.67       133.94        70.68 
TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 
       85.78       119.38       126.28        58.85        73.84       149.16 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
       79.89       131.15        89.49        91.46        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       21.30        31.30        24.82        32.98        16.67        12.00 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.85         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 
       42.71        25.05        45.37        50.14        23.74         0.85 
TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
        6.38        14.30         8.42        17.36        16.27       111.02 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4325 
       94.72       101.06        32.61        99.85        77.03        97.45 
TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
        3.58        62.07        80.68        15.16        18.48        52.24 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4765 
       49.08        44.94        12.23        12.30        72.59        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       48.07        13.15        61.97        60.59        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
       11.64         6.94        63.62        61.22        61.51        57.40 
TCGA-BP-4969 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 
       58.98        45.50         6.90        47.11        53.65        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5001 
       33.34        36.95        46.45         5.82        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 
       37.02        27.62        37.48        48.10         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       52.27        49.15        42.44        37.25        37.22        22.78 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.24        23.47        13.41        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 
      115.00       106.16        58.95        11.05        49.25        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
      116.84        64.27        71.87       113.46        64.18        30.64 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
       50.01        24.66        27.65       109.84        51.25       108.56 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5684 TCGA-CJ-6032 
       50.33        45.14        72.00       129.40        73.35       119.64 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CW-6093 
       92.02         5.39        85.78        73.18       105.93       103.43 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       25.45         0.59        58.75        63.39        93.04        63.42 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5463 
       79.53        18.44        90.54        91.69        94.45        21.76 
TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5575 
       84.30        80.19        12.26        62.63        45.96        56.84 
TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MW-A4EC 
       18.12         6.77        10.29        35.87         2.01        16.37 

$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        62.01         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       109.51        78.64        94.29         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        58.45        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        10.52        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        58.59        41.88 
TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-4098 TCGA-B2-5633 
       56.98        15.78        80.91       105.37         1.68        31.66 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 
       21.57         5.10         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        48.53         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 
      114.41        54.61        21.24        83.97        79.66        10.72 
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       115.69 
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       131.08       133.71        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       118.85        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       107.54 
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        79.63        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       10.85        10.22        69.96        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-A4VX TCGA-DV-A4W0 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L7 
       53.46        81.21         3.91         4.18         7.96        70.13 
TCGA-MM-A564 TCGA-MM-A84U 
       19.96        23.01 

subtype1 subtype2 subtype3 
    0.07     0.10     0.53 
subtype1 subtype2 subtype3 
  130.65   149.16   133.71 
subtype1 subtype2 subtype3 
   38.43    44.12    31.84 
[1] "0.1 - 130.7 (38.4)" "0.1 - 149.2 (44.1)" "0.5 - 133.7 (31.8)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      72       12        19       13
  subtype2     135       23        40       25
  subtype3      61       22        65       46
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         72      135       61
  STAGE II        12       23       22
  STAGE III       19       40       65
  STAGE IV        13       25       46
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  72  13  28   3
  subtype2 135  27  59   2
  subtype3  66  29  93   6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       72      135       66
  T2       13       27       29
  T3       28       59       93
  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 101   1
  subtype3  89  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    3
  subtype2  101    1
  subtype3   89   12
   clus
vv  subtype1 subtype2 subtype3
  0       50      101       89
  1        3        1       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  40  76
  subtype2 101 122
  subtype3  47 147
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   76
  subtype2  101  122
  subtype3   47  147
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40      101       47
  MALE         76      122      147
[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 
       2        3        7 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        21    90
  subtype2     2                        20   197
  subtype3     2                        15   175
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        2        2
  BLACK OR AFRICAN AMERICAN       21       20       15
  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  82
  subtype2  16 142
  subtype3   7 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   82
  subtype2   16  142
  subtype3    7  131
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3       16        7
  NOT HISPANIC OR LATINO       82      142      131
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  84  34
  subtype2  28   6
  subtype3 142  41
  subtype4  60  73
  subtype5  20  15
  subtype6  22   6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     118       34      183      133       35       28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      34        6       41       73       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        62.01        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        73.68 
TCGA-AK-3434 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
       68.61        38.40        82.45        72.89         1.41         2.14 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4828 
       58.45        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        41.88 
TCGA-B0-5120 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5702 TCGA-B0-5812 
       38.43        42.41        85.78       119.38        71.41       126.05 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-A4SR TCGA-B8-4622 TCGA-B8-5545 
       21.30        31.66        24.82        16.67        50.14        50.14 
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       105.37        79.66       116.84        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       122.83        64.57 
TCGA-CW-5590 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5454 TCGA-CZ-5455 
       35.34        14.66       107.54         5.46        23.74        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5466 TCGA-CZ-5467 
       91.69        55.33        94.45        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        13.28        12.16        81.21 
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 
       11.90        24.16        51.25        10.49        83.21        37.58 
TCGA-AK-3465 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5700 TCGA-B0-5707 
       12.13       112.80        70.68        86.47        58.85       123.09 
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       129.40        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 TCGA-T7-A92I 
       11.67        37.15        66.28        11.70 

$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        38.47        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       28.31        65.52        33.47        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 
       11.18        10.62       109.41        48.36        49.28        28.73 
TCGA-AK-3455 TCGA-AS-3777 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 
       22.45        40.70         2.53         7.82        57.70         3.25 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4845 
       16.77        54.48        78.44        27.42        53.88        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5085 
       39.45        26.07         2.27        36.85        70.52        25.32 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       15.95        90.87        90.48        66.05        38.63        52.73 
TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 
       51.02        48.82        46.39       111.52       129.67       133.94 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      126.28        73.84       149.16        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 TCGA-B4-5377 TCGA-B4-5834 
       91.46        35.90        31.96        31.30        12.00         0.85 
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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5553 TCGA-B8-A54H 
       25.05        45.37        23.74         0.85        14.30         8.42 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 
       17.36        16.27       111.02       101.06        32.61        99.85 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 
       77.03        61.78        97.45         3.58        62.07        80.68 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4758 
       18.48        52.24        44.94        12.23        31.33        72.59 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       71.80        48.07        61.97        60.59        13.51        56.91 
TCGA-BP-4789 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 
       48.95        61.22        61.51        58.98        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 
        6.90        47.11        53.65        33.34        36.95         5.82 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5173 
       41.62        38.70        37.02        27.62        48.10         1.74 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       52.27         9.63        49.15        37.25        37.22        22.78 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 
       23.47        13.41        34.95         0.95       115.00       106.16 
TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
      114.41        58.95        11.05        49.25        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       71.87       113.46        64.18        50.01        24.66        27.65 
TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4920 
      109.84        51.25       108.56        49.18        45.14         4.57 
TCGA-CJ-5672 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
       72.00        67.00       119.64        81.83        85.78        73.18 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 
      105.93       103.43        25.45         0.59        58.75        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 TCGA-CZ-5465 
       93.04        63.42        79.53        90.54        21.76        84.30 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
       80.19        12.26        62.63        56.84        18.12         6.77 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MW-A4EC 
       35.87         2.01        16.37 

$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       109.51        78.64         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        10.52        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 
       58.59        19.30        56.98        15.78        80.91       105.37 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5162 
       21.57         5.10        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        10.72 
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       115.69        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 
      131.08       133.71        22.32       118.85        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        79.63        10.22        69.96 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-A4VX TCGA-EU-5905 
        1.94        31.10        67.96        65.65        53.46         3.91 
TCGA-G6-A8L7 
       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        94.29         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       130.65         5.46        48.53        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        23.01 

$subtype6
TCGA-A3-3328 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
       45.53        43.20       117.80       112.08        94.19        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        52.87 
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 TCGA-DV-A4VZ 
       45.07        65.88        23.90        12.00 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.53     0.10     0.53     0.07     3.62 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  126.05   129.40   149.16   133.71   130.65   117.80 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  35.275   37.365   47.210   31.790   48.530   44.135 
[1] "0.1 - 126.0 (35.3)" "0.5 - 129.4 (37.4)" "0.1 - 149.2 (47.2)"
[4] "0.5 - 133.7 (31.8)" "0.1 - 130.7 (48.5)" "3.6 - 117.8 (44.1)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      62       12        24       20
  subtype2      26        4         2        3
  subtype3     117       19        35       13
  subtype4      37       13        47       36
  subtype5       5        5        14       11
  subtype6      21        4         2        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         62       26      117       37        5       21
  STAGE II        12        4       19       13        5        4
  STAGE III       24        2       35       47       14        2
  STAGE IV        20        3       13       36       11        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  26   4   5   0
  subtype3 117  21  46   0
  subtype4  39  15  72   7
  subtype5   7   8  19   1
  subtype6  21   4   2   1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       63       26      117       39        7       21
  T2       17        4       21       15        8        4
  T3       36        5       46       72       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 85  0
  subtype4 67 10
  subtype5 17  4
  subtype6 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    1
  subtype2   15    1
  subtype3   85    0
  subtype4   67   10
  subtype5   17    4
  subtype6   13    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       43       15       85       67       17       13
  1        1        1        0       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  17  18
  subtype3 101  83
  subtype4  31 102
  subtype5  17  18
  subtype6   6  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16  102
  subtype2   17   18
  subtype3  101   83
  subtype4   31  102
  subtype5   17   18
  subtype6    6   22
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       16       17      101       31       17        6
  MALE        102       18       83      102       18       22
[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 
      10        7       17       13        1        4 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
 [7] "subtype2" "subtype3" "subtype6" "subtype4" "subtype3" "subtype2"
[13] "subtype3" "subtype3" "subtype3" "subtype4" "subtype1" "subtype4"
[19] "subtype4" "subtype4" "subtype3" "subtype4" "subtype4" "subtype1"
[25] "subtype1" "subtype4" "subtype3" "subtype1" "subtype3" "subtype4"
[31] "subtype3" "subtype1" "subtype2" "subtype6" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype6" "subtype4" "subtype6"
[43] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype1"
[49] "subtype4" "subtype3" "subtype2"
D8V9, continuous
D8V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        1        2        3        3 
[1] "subtype4" "subtype5" "subtype1" "subtype4" "subtype5" "subtype1" "subtype4"
[8] "subtype1" "subtype5"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        11   100
  subtype2     2                        10    23
  subtype3     1                        17   164
  subtype4     2                         7   124
  subtype5     0                         4    30
  subtype6     0                         7    21
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        1        2        0
  BLACK OR AFRICAN AMERICAN       11       10       17        7        4
  WHITE                          100       23      164      124       30
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        7
  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  30
  subtype3  12 112
  subtype4   5  89
  subtype5   1  26
  subtype6   0  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   74
  subtype2    2   30
  subtype3   12  112
  subtype4    5   89
  subtype5    1   26
  subtype6    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        2       12        5        1        0
  NOT HISPANIC OR LATINO       74       30      112       89       26       24
[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  33
  subtype2 152  52
  subtype3  98  87
subtype1 subtype2 subtype3 
     125      204      185 
subtype1 subtype2 subtype3 
      33       52       87 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       12.66        11.90         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-A6NI TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3431 
       20.28        33.47         0.10         0.10       109.91        73.68 
TCGA-AK-3461 TCGA-B0-4688 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4811 
       72.89         3.32        19.00        65.10         5.98        46.59 
TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4839 TCGA-B0-4843 TCGA-B0-4945 
       45.07        14.93        29.10        53.88        10.52        70.52 
TCGA-B0-5080 TCGA-B0-5095 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5119 TCGA-B0-5120 
       11.24         8.05        62.89        58.59        51.02        38.43 
TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 TCGA-B2-5636 
      112.80        71.41       130.65        79.89       126.05        30.21 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 
        4.64         5.46         1.18        27.02        50.14        48.53 
TCGA-B8-5552 TCGA-B8-A54H TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4166 
       34.39         8.42        16.27        14.17        94.72         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4331 TCGA-BP-4332 
       89.36        23.05        62.24        54.90        80.68        37.25 
TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4345 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
        0.07        52.24        49.84        12.33        77.62        44.15 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       71.80        61.68        10.82        48.95        36.53        20.38 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4969 
       36.95        47.97         6.94        63.62        61.51        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4982 TCGA-BP-5010 TCGA-BP-5170 
       14.24        48.89        49.38        33.34        28.87        79.30 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5196 TCGA-BP-5198 
        9.63        38.30        37.25        22.78        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4872 
       44.55        34.95       115.00        63.25       105.37        10.72 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4902 TCGA-CJ-4905 
       61.91        64.18        63.98       115.69        49.97        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5680 TCGA-CJ-6031 
       49.28        50.33         3.06       131.08        25.25        62.66 
TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4865 
       81.83        66.31       105.93        83.90         6.77         5.46 
TCGA-CZ-5988 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       22.78        12.16        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5905 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 
       81.21         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       109.41        68.61        48.36 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3460 TCGA-B0-4693 TCGA-B0-4701 
       49.28        28.73        22.45        82.45         2.53         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4824 
        2.14        57.70         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        66.05        38.63        52.73        41.88 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 
       48.82        46.39        42.41       111.52       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 
       15.78        70.68        85.78       119.38       126.28        58.85 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
       73.84       149.16       131.15        89.49        91.46        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       31.96        21.30        31.30        32.98        16.67        12.00 
TCGA-B4-5834 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.85         0.36         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 
       25.05        45.37        50.14        23.74         0.85        24.23 
TCGA-B8-5546 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         6.90        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         1.74        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       106.16 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4885 
       58.95        11.05        49.25       116.84        71.87       113.46 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 
       50.01        24.66        27.65       109.84        50.24        51.25 
TCGA-CJ-4904 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5681 
      108.56        45.14         4.57        72.00       129.40        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
      122.83        62.10        73.35        67.00       119.64        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       107.54        63.39        93.04        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       94.45        10.22        21.76        84.30         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        13.28        45.96        11.67        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC TCGA-T7-A92I 
        6.77         4.18        10.29         2.01        16.37        11.70 

$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       117.80        15.78       112.08       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        40.01        94.29        83.21 
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        58.45        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        52.87        56.98 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 
       86.47        80.91       105.37       123.09        32.61         1.68 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5835 
       31.66        24.82        21.57         5.75         5.10         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       114.41        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       133.71 
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       118.85        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        79.63        10.85        69.96        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-DV-A4VX TCGA-DV-A4VZ TCGA-G6-A5PC TCGA-MM-A564 TCGA-MM-A84U 
       53.46        12.00         7.96        19.96        23.01 

subtype1 subtype2 subtype3 
    0.07     0.23     0.53 
subtype1 subtype2 subtype3 
  131.08   149.16   133.71 
subtype1 subtype2 subtype3 
  45.530   42.425   33.500 
[1] "0.1 - 131.1 (45.5)" "0.2 - 149.2 (42.4)" "0.5 - 133.7 (33.5)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      77       11        27       11
  subtype2     111       20        45       29
  subtype3      66       24        52       43
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         77      111       66
  STAGE II        11       20       24
  STAGE III       27       45       52
  STAGE IV        11       29       43
[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  78  11  33   4
  subtype2 112  26  65   2
  subtype3  69  30  81   5
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       78      112       69
  T2       11       26       30
  T3       33       65       81
  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 88  1
  subtype3 84 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56    3
  subtype2   88    1
  subtype3   84   13
   clus
vv  subtype1 subtype2 subtype3
  0       56       88       84
  1        3        1       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  82
  subtype2  89 116
  subtype3  48 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   82
  subtype2   89  116
  subtype3   48  137
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       89       48
  MALE         82      116      137
[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
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        20   104
  subtype2     3                        16   182
  subtype3     4                        20   159
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        4
  BLACK OR AFRICAN AMERICAN       20       16       20
  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  83
  subtype2  12 134
  subtype3  10 128
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   83
  subtype2   12  134
  subtype3   10  128
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2       12       10
  NOT HISPANIC OR LATINO       83      134      128
[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  96  49
  subtype2  86  51
  subtype3 149  46
  subtype4  11  26
subtype1 subtype2 subtype3 subtype4 
     145      137      195       37 
subtype1 subtype2 subtype3 subtype4 
      49       51       46       26 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3349 
       12.66        11.90         0.53        49.08        52.93        45.53 
TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3382 TCGA-A3-A6NI 
       51.25        74.76        53.29        55.76        18.87        33.47 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3454 TCGA-AK-3461 
      109.91        29.10       109.51        78.64        28.73        72.89 
TCGA-B0-4688 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4810 
        3.32        19.00         1.38        65.10         5.98        15.72 
TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4827 TCGA-B0-4945 
        0.59        45.07         6.02        40.44        29.10        70.52 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 
       11.24        11.90         7.30        18.51         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5119 TCGA-B0-5120 
       52.08        62.89        58.59        19.30        51.02        38.43 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 
       56.98       112.80        71.41       130.65        79.89       126.05 
TCGA-B2-5636 TCGA-B2-5641 TCGA-B4-5378 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5162 
       30.21        21.57         5.75        23.31        25.55         1.18 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A54H 
       50.14        48.53         0.53        34.39        17.06         8.42 
TCGA-B8-A54I TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4169 
        4.93        15.42        16.27        14.17        94.72        23.05 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4345 
       62.24        54.90        53.42        80.68         0.07        49.84 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       11.31        12.33        31.33        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 
       71.80        61.68        10.82        68.38        11.64        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
       36.53        20.38        37.25        36.95        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       87.45        71.41        61.51         6.74        57.40        14.24 
TCGA-BP-4972 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4998 
       49.38        46.45        31.30        27.22         3.88        30.64 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5187 
       35.21        28.87         6.35        79.30         9.63        13.35 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4882 TCGA-CJ-4889 
       33.47        19.82        34.95       115.00        61.91        63.98 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4918 
       47.67        49.97        49.18        49.28        50.33         3.06 
TCGA-CJ-5671 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5583 TCGA-CW-5588 
      131.08        75.58        62.66         7.36        81.83        66.31 
TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4865 TCGA-CZ-5456 
        1.35        18.77        69.21         6.77         5.46        79.63 
TCGA-CZ-5464 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5573 TCGA-DV-5574 
       69.96        22.78        13.28        65.88        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-G6-A8L7 
       56.84        23.90        12.00        18.12         3.91        70.13 
TCGA-MM-A563 
       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       117.80 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3451 
       15.78       112.08        94.19        46.78        40.01        94.29 
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        58.45        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        41.88        52.87        42.41 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5707 
       85.78        86.47        80.91        73.84       105.37       123.09 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61         1.68        32.98         5.10         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        50.14        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       114.41        54.61        83.97        74.27 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 
      116.84        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       108.56        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        91.69        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-A4VX TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-MM-A84U 
       12.16        53.46        81.21         7.96        23.01 

$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       109.41        68.61        48.36 
TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3460 TCGA-B0-4693 TCGA-B0-4701 
       49.28        83.21        22.45        82.45         2.53         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4818 
        2.14        57.70         3.25        46.59         5.52        16.77 
TCGA-B0-4824 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        66.05        38.63        52.73        48.82        46.39 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
      111.52       129.67       133.94        15.78        70.68       119.38 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      126.28        58.85       149.16       131.15        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
       35.90        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4146 
       16.67        12.00         0.85         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        42.71        25.05        45.37        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         6.90        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         1.74        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       106.16        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       113.46        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       109.84        50.24        51.25        54.48 
TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 
       45.14         4.57       129.40       133.71       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       73.35        67.00       119.64         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 
      107.54        63.39        93.04        63.42        79.53        18.44 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
       84.30         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 TCGA-T7-A92I 
       19.96        16.37        11.70 

$subtype4
TCGA-AK-3431 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       73.68         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        10.52        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       105.37        79.66        10.72       115.69        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       118.85        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 
  131.08   123.09   149.16   118.85 
subtype1 subtype2 subtype3 subtype4 
   36.53    34.36    44.94    40.70 
[1] "0.1 - 131.1 (36.5)" "0.1 - 123.1 (34.4)" "0.1 - 149.2 (44.9)"
[4] "1.4 - 118.8 (40.7)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      83       10        36       17
  subtype2      51       17        34       35
  subtype3     111       24        42       19
  subtype4       9        4        12       12
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         83       51      111        9
  STAGE II        10       17       24        4
  STAGE III       36       34       42       12
  STAGE IV        17       35       19       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  84  11  46   5
  subtype2  53  23  58   3
  subtype3 113  28  54   1
  subtype4   9   5  21   2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       84       53      113        9
  T2       11       23       28        5
  T3       46       58       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 67  7
  subtype3 84  1
  subtype4 16  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61    8
  subtype2   67    7
  subtype3   84    1
  subtype4   16    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       61       67       84       16
  1        8        7        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  92
  subtype2  36 101
  subtype3  85 111
  subtype4   6  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   92
  subtype2   36  101
  subtype3   85  111
  subtype4    6   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       54       36       85        6
  MALE         92      101      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 
      17       16       19        1 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[19] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[25] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[31] "subtype2" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
[37] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[43] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
[49] "subtype3" "subtype1" "subtype3" "subtype3"
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        22   120
  subtype2     2                        15   117
  subtype3     2                        19   171
  subtype4     0                         0    37
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        2        0
  BLACK OR AFRICAN AMERICAN       22       15       19        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  95
  subtype2   4  99
  subtype3  14 125
  subtype4   4  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   95
  subtype2    4   99
  subtype3   14  125
  subtype4    4   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4       14        4
  NOT HISPANIC OR LATINO       95       99      125       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 27  9
  subtype2 18  4
  subtype3 36 13
  subtype4 17 18
subtype1 subtype2 subtype3 subtype4 
      36       22       49       35 
subtype1 subtype2 subtype3 subtype4 
       9        4       13       18 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       12.66        11.90        33.47        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 
       11.18        10.62        94.19        12.13        32.61        35.90 
TCGA-B2-5635 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-BP-4173 
       24.82         8.42        17.36        15.42        16.27        62.24 
TCGA-BP-4340 TCGA-BP-4961 TCGA-BP-4981 TCGA-BP-4982 TCGA-CJ-4870 TCGA-CJ-4875 
       18.48        63.62        36.07        33.34        49.25       116.84 
TCGA-CJ-4881 TCGA-CJ-4900 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.21        56.35        46.16        47.08         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        23.01        11.70 

$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        71.41 
TCGA-B0-5709 TCGA-B2-5636 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-A8YJ 
      130.65        30.21        50.14        48.53        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       131.08        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        57.70        36.85        25.32 
TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
       46.39       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 
      126.28        58.85       149.16        32.98        12.00         4.64 
TCGA-B8-5553 TCGA-BP-4969 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4995 TCGA-BP-5001 
       14.30        58.98         6.90        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       129.40       133.71        18.15        62.10 
TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4864 TCGA-CZ-5453 
      119.64        85.78        78.18       105.93        93.04        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5466 
       23.74        18.44        90.54        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        13.28        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        31.66        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 
      115.69        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        69.96        31.10        12.69        70.13 

subtype1 subtype2 subtype3 subtype4 
    0.10     6.94     2.14     0.53 
subtype1 subtype2 subtype3 subtype4 
  116.84   131.08   149.16   115.69 
subtype1 subtype2 subtype3 subtype4 
  21.305   47.280   45.960   31.100 
[1] "0.1 - 116.8 (21.3)" "6.9 - 131.1 (47.3)" "2.1 - 149.2 (46.0)"
[4] "0.5 - 115.7 (31.1)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      24        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         24       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 24  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       24       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 18 20
  subtype2  6 16
  subtype3 20 29
  subtype4  6 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   20
  subtype2    6   16
  subtype3   20   29
  subtype4    6   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18        6       20        6
  MALE         20       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 
       6        2        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
D11V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype4 
       5        1        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        24    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       24        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 32
  subtype2  1 13
  subtype3  4 37
  subtype4  1 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   32
  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       32       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 29  9
  subtype2 35 21
  subtype3 34 14
subtype1 subtype2 subtype3 
      38       56       48 
subtype1 subtype2 subtype3 
       9       21       14 
$subtype1
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       12.66        11.90        33.47        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 
       11.18        10.62        94.19        12.13        32.61        35.90 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       31.66        24.82        30.21         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4340 TCGA-BP-4804 TCGA-BP-4961 
       15.42        16.27        62.24        18.48        47.97        63.62 
TCGA-BP-4981 TCGA-BP-4982 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4900 
       36.07        33.34        49.25       116.84        66.21        56.35 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       46.16        47.08         7.96        10.29        35.87         2.01 
TCGA-MM-A84U TCGA-T7-A92I 
       23.01        11.70 

$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        46.39       112.80        85.78        71.41       130.65 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A8YJ TCGA-BP-4761 
       50.14        48.53         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         6.90        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       115.69        39.45 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6031 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
      131.08       133.71        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        69.96        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        57.70        36.85        25.32       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 
      133.94        15.78        70.68       126.28        58.85       149.16 
TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-4621 TCGA-B8-5553 TCGA-BP-4969 
       32.98        12.00         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       129.40        18.15        62.10        67.00 
TCGA-CJ-6032 TCGA-CW-5585 TCGA-CZ-4864 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      119.64        85.78        93.04        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 
       90.54        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        13.28        45.96        11.67        18.12 

subtype1 subtype2 subtype3 
    0.10     0.53     2.14 
subtype1 subtype2 subtype3 
  116.84   133.71   149.16 
subtype1 subtype2 subtype3 
  23.915   38.925   40.835 
[1] "0.1 - 116.8 (23.9)" "0.5 - 133.7 (38.9)" "2.1 - 149.2 (40.8)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      27        4         4        5
  subtype2      27        4        12       13
  subtype3      21        9        10        8
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         27       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 28  5  6  1
  subtype2 27  4 21  4
  subtype3 22 10 16  0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       28       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 18 22
  subtype2 10 46
  subtype3 22 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   22
  subtype2   10   46
  subtype3   22   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       10       22
  MALE         22       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 
       5        4        1 
[1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[8] "subtype2" "subtype1"
D12V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        23    17
  subtype2     3                         6    46
  subtype3     0                         1    45
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        3        0
  BLACK OR AFRICAN AMERICAN       23        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 34
  subtype2  3 35
  subtype3  3 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    3   35
  subtype3    3   35
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        3        3
  NOT HISPANIC OR LATINO       34       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"
