[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/22506714/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/22555002/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 
32 25 15 
 1  2  3 
32 25 15 
[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   4   5   6 
 61  80 156  82  80  69 
  1   2   3   4   5   6 
 61  80 156  82  80  69 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
69 70 97 83 
 1  2  3  4 
69 70 97 83 
[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   4   5 
 85 172  82 154  40 
  1   2   3   4   5 
 85 172  82 154  40 
[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   4   5 
 91  58 187 121  59 
  1   2   3   4   5 
 91  58 187 121  59 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
175 210 131 
  1   2   3 
175 210 131 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
39 22 45 38 
 1  2  3  4 
39 22 45 38 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
41 52 28 23 
 1  2  3  4 
41 52 28 23 
[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=340,	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=27,	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   "142"   "2"    
freq.contrast "2"     "142"  
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 27  5
  subtype2 16  9
  subtype3 14  1
subtype1 subtype2 subtype3 
      32       25       15 
subtype1 subtype2 subtype3 
       5        9        1 
$subtype1
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3455 
       47.21        38.47        53.39        31.07        82.32        22.45 
TCGA-BP-4164 TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 
       32.61        36.82        49.58        48.59        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3372 TCGA-A3-3380 
       48.82        45.53        18.44        51.25        24.16        18.64 
TCGA-A3-3383 TCGA-AK-3444 TCGA-AS-3778 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 
       28.31        48.36         1.41        35.90        31.96        31.30 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4634 TCGA-CJ-4639 
       42.71        45.37        17.19       101.06       115.00       106.16 
TCGA-CJ-4643 TCGA-CJ-4644 
       58.95        11.05 

$subtype2
TCGA-CJ-4636 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       63.25         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3374 
       36.36        62.01         4.50        52.93        29.92        43.20 
TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3426 TCGA-B2-4098 TCGA-B8-4143 TCGA-B8-4620 
       20.71        18.87        29.10         1.68        23.31        25.55 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 
       90.28        93.34        89.36        73.22        14.17       114.41 
TCGA-CJ-4641 
       54.61 

$subtype3
TCGA-A3-3328 TCGA-A3-3336 TCGA-A3-3313 TCGA-A3-3363 TCGA-A3-3365 TCGA-AK-3427 
       45.53        34.29        24.16        10.49        28.70       117.80 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       94.19        46.78        40.01        83.21        37.58        12.13 
TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 
       40.70        32.61        49.97 

subtype1 subtype2 subtype3 
    1.41     0.53    10.49 
subtype1 subtype2 subtype3 
  115.00   114.41   117.80 
subtype1 subtype2 subtype3 
   38.73    39.16    40.01 
[1] "1.4 - 115.0 (38.7)"  "0.5 - 114.4 (39.2)"  "10.5 - 117.8 (40.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      22        3         6        1
  subtype2       9        4         8        4
  subtype3       9        6         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         22        9        9
  STAGE II         3        4        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 22  3  7
  subtype2 10  5 10
  subtype3  9  6  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       10        9
  T2        3        5        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 17  0
  subtype2 11  3
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    0
  subtype2   11    3
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0       17       11        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 31  1
  subtype2 21  4
  subtype3 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    1
  subtype2   21    4
  subtype3   15    0
   clus
vv  subtype1 subtype2 subtype3
  0       31       21       15
  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 17
  subtype2 10 15
  subtype3  4 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   17
  subtype2   10   15
  subtype3    4   11
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       10        4
  MALE         17       15       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"
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    30
  subtype2     0                         2    21
  subtype3     1                         3    11
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN        0        2        3
  WHITE                           30       21       11
[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  4 19
  subtype2  3 11
  subtype3  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   19
  subtype2    3   11
  subtype3    0   12
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        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-A3-3307 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3306 TCGA-A3-3324 TCGA-A3-3326 
       47.21        53.39        31.07        36.82        38.99        37.38 
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-CJ-4636 TCGA-A3-3317 TCGA-A3-3347 TCGA-AK-3426 TCGA-B8-4143 TCGA-BP-4163 
       63.25        49.02        52.93        29.10        23.31        93.34 
TCGA-BP-4167 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       89.36        73.22        14.17       114.41        54.61 

$subtype5
TCGA-A3-3359 TCGA-AK-3455 TCGA-BP-4164 TCGA-A3-3320 TCGA-A3-3331 TCGA-AK-3444 
       82.32        22.45        32.61        49.58        48.82        48.36 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4639 TCGA-CJ-4643 
       42.71        45.37        17.19       101.06       106.16        58.95 
TCGA-CJ-4644 
       11.05 

$subtype6
TCGA-A3-3325 TCGA-A3-3322 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 
       38.47        48.59        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        49.97 

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 
   53.39    90.28    37.58   114.41   106.16   115.00   117.80 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  33.930   36.755   17.325   54.610   48.360   38.470   45.530 
[1] "18.4 - 53.4 (33.9)"  "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 (45.5)"
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 47 14
  subtype2 51 28
  subtype3 84 72
  subtype4 66 16
  subtype5 51 28
  subtype6 52 17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      61       79      156       82       79       69 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      14       28       72       16       28       17 
$subtype1
TCGA-A3-3307 TCGA-A3-3358 TCGA-B0-5698 TCGA-B8-A54H TCGA-BP-4160 TCGA-BP-5168 
       47.21        42.97       119.38         8.42        94.72        48.10 
TCGA-CJ-4636 TCGA-CJ-4904 TCGA-DV-5568 TCGA-3Z-A93Z TCGA-A3-3322 TCGA-A3-3324 
       63.25       108.56        12.16        12.66        48.59        38.99 
TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 TCGA-A3-A6NL TCGA-AK-3436 TCGA-AK-3444 
       88.37        24.16        20.28        22.65       109.51        48.36 
TCGA-AK-3458 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4833 TCGA-B0-4841 TCGA-B0-5077 
       38.40        57.70         3.25        78.44         6.71        43.30 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B8-4146 TCGA-B8-A54J TCGA-BP-4159 TCGA-BP-4162 
       89.49        91.46        16.80        17.36        85.51       101.06 
TCGA-BP-4174 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4758 
       61.78        15.62        93.99        62.86        31.89        72.59 
TCGA-BP-4759 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5185 
       77.98        14.93         3.88        79.30         2.04        37.22 
TCGA-BP-5200 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4875 TCGA-CJ-4886 TCGA-CJ-4887 
       34.95       106.16        11.05       116.84        64.18        30.64 
TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-5672 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       50.01       109.84        72.00       122.83        62.10        73.35 
TCGA-CW-5587 TCGA-CW-5591 TCGA-CZ-5451 TCGA-CZ-5454 TCGA-CZ-5464 TCGA-EU-5905 
       73.18        74.66        63.42        23.74        69.96         3.91 
TCGA-GK-A6C7 
        2.01 

$subtype2
TCGA-B0-4815 TCGA-B0-5691 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4353 
       52.21       112.80        24.82        25.91         1.18        12.33 
TCGA-BP-4782 TCGA-BP-4799 TCGA-BP-4976 TCGA-BP-4988 TCGA-CJ-4891 TCGA-CJ-5689 
       11.64        37.25        53.65        27.22        26.93        53.26 
TCGA-DV-5574 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3362 TCGA-A3-3363 
       66.28        11.90         0.53        24.16        51.25        10.49 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3453 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4697 
       55.76        65.52        83.21        40.70         3.32        19.00 
TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4839 TCGA-B0-5080 
       46.59        33.50         6.02        36.53        53.88        11.24 
TCGA-B0-5095 TCGA-B0-5106 TCGA-B0-5400 TCGA-B0-5702 TCGA-B2-4098 TCGA-B2-4101 
        8.05        52.54        56.98        71.41         1.68        21.30 
TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 
        5.75        17.19        27.02         0.85        16.60        48.53 
TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A8YJ TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4337 
       14.30        29.88        14.17        62.24        54.90         0.07 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4790 
       33.99        31.33        61.68        10.82         5.33        36.53 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4967 TCGA-BP-4971 TCGA-BP-4983 
       47.97        71.41        63.62         6.74        48.89        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5198 TCGA-CJ-4882 TCGA-CJ-4884 
       16.47        43.00        30.64        19.82        61.91        57.83 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4912 
       51.52        63.98       115.69        49.97        51.29        54.48 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CW-6087 TCGA-CZ-4863 TCGA-CZ-5466 
       18.81       131.08       133.71         1.35        63.39        22.52 
TCGA-DV-A4VZ 
       12.00 

$subtype3
TCGA-A3-3336 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4712 
       34.29       109.91        58.49        28.73        19.73        43.96 
TCGA-B0-5694 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4986 
       15.78        32.61         3.58        80.68        74.17        25.81 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 
        5.82        45.07        62.86        27.02        31.79        31.27 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5573 
      118.85        75.58        46.16        43.69        45.96        37.15 
TCGA-DV-5575 TCGA-G6-A8L7 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       56.84        70.13        36.82        39.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       37.15        49.58        62.01         4.50        52.93        18.44 
TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3445 TCGA-AK-3447 
       18.87        29.10        15.78        68.61        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3461 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4700 TCGA-B0-4701 
       94.29        72.89         1.41         3.48        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4824 TCGA-B0-4828 
        5.98         6.64        15.72         0.59        54.48        10.09 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4842 TCGA-B0-4848 TCGA-B0-4849 
       40.70        45.30        27.42        56.68        29.03         2.27 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5108 
        7.30        10.95         2.24        21.86        52.08        58.59 
TCGA-B0-5109 TCGA-B0-5119 TCGA-B0-5402 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       19.30        51.02        42.41        21.57        12.00         5.10 
TCGA-B4-5835 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 
        0.53         0.36        23.31        49.97        25.55        40.04 
TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 
        0.53         1.74         4.93        90.28        89.36        64.27 
TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4761 
       97.45        27.78        49.08        11.31        12.30         5.98 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 
       48.07        13.15        68.38        36.39        10.98         6.71 
TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4974 TCGA-BP-4987 TCGA-BP-5000 
       87.45        58.68        60.30         6.94        36.95        18.51 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
       28.87         6.35        74.20        30.64         9.63        74.40 
TCGA-BP-5195 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4641 
       24.62       115.00        46.55        73.22       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 
       58.95        21.24        83.97        74.27        64.27        66.21 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4913 TCGA-CJ-5675 
       24.66        39.45        56.35        47.67        38.56       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-6028 TCGA-CJ-6032 
       25.71        18.87        22.32        25.25        53.42       119.64 
TCGA-CJ-6033 TCGA-CW-5584 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 
        7.36         5.39        18.77        25.45        69.21        58.75 
TCGA-CZ-4864 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 
       93.04        58.82        79.53        10.85        10.22        84.30 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        1.94        31.10        80.19        67.96        65.65        14.63 
TCGA-DV-A4VX TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MW-A4EC 
       53.46         4.18         7.96        35.87        19.43        16.37 

$subtype4
TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3455 TCGA-B0-5693 TCGA-B8-A54K TCGA-BP-4158 
       31.07        82.32        22.45       133.94        15.42       111.02 
TCGA-BP-4344 TCGA-BP-4965 TCGA-BP-5199 TCGA-CJ-4642 TCGA-DV-5567 TCGA-DV-5569 
       54.77        61.51        44.55       105.37        65.88        11.67 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-A3-3323 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3365 
       23.90        81.21        36.36        45.53        29.92        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3378 TCGA-A3-A6NJ TCGA-A3-A6NN TCGA-AK-3456 
       74.63        74.76        20.71        15.39         0.10        37.58 
TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4706 TCGA-B0-4818 TCGA-B0-4821 
       82.45         1.41         2.53         2.14        16.77        40.44 
TCGA-B0-4845 TCGA-B0-4945 TCGA-B0-5092 TCGA-B0-5100 TCGA-B0-5110 TCGA-B0-5113 
       65.29        70.52        15.09        62.89        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5697 
       52.73        41.88        38.43        46.39       129.67        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B2-5633 
      126.28        80.91       105.37       130.65        79.89        31.66 
TCGA-B2-5639 TCGA-B4-5844 TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4165 TCGA-BP-4169 
       32.98         0.23         6.38        27.29        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4332 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4763 TCGA-BP-4774 
       77.03        37.25        44.94        12.23        41.75        61.97 
TCGA-BP-4776 TCGA-BP-4985 TCGA-BP-4991 TCGA-BP-5004 TCGA-BP-5008 TCGA-BP-5183 
       13.51        31.30        46.45        37.02        35.21        42.44 
TCGA-BP-5187 TCGA-BP-5194 TCGA-CJ-4885 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 
       13.35        13.41       113.46        49.18        50.33        45.14 
TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5589 TCGA-CW-6090 TCGA-CZ-5459 
       62.66        64.57        81.83        78.18        83.90        55.33 
TCGA-CZ-5463 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-MM-A564 
       21.76        12.26        62.63        19.96 

$subtype5
TCGA-A3-3325 TCGA-B0-5088 TCGA-B0-5695 TCGA-B0-5812 TCGA-BP-4762 TCGA-BP-4775 
       38.47        18.51        70.68       126.05        44.15        60.59 
TCGA-BP-5009 TCGA-CW-6093 TCGA-MM-A84U TCGA-A3-3326 TCGA-A3-A6NI TCGA-AK-3428 
       35.90       103.43        23.01        37.38        33.47       122.56 
TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4814 TCGA-B0-4844 TCGA-B0-4847 
        4.57         1.38         3.62         5.52        10.29        26.07 
TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5107 TCGA-B0-5121 
       36.85        20.94        11.90        25.32        30.48        48.82 
TCGA-B0-5696 TCGA-B0-5705 TCGA-B0-5711 TCGA-B2-4099 TCGA-B2-4102 TCGA-B4-5836 
       85.78       149.16       131.15        31.96        31.30         4.64 
TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 
        5.46        42.71        25.05        45.37        50.14        23.74 
TCGA-B8-A7U6 TCGA-BP-4163 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4341 
       16.27        93.34        53.42        62.07        21.21        52.24 
TCGA-BP-4765 TCGA-BP-4787 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       71.80        15.78        61.22        57.40        58.98        14.24 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-5001 TCGA-BP-5007 
       49.38        45.50        36.07        33.34        38.70        37.48 
TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4638 TCGA-CJ-4871 
       22.78        23.47        33.47         0.95        14.17        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4907 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5686 
       47.18        75.06        49.28         3.06         4.57        67.00 
TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 
       92.02        85.78        66.31        47.08         6.77        14.66 
TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5470 
      107.41        18.44        79.63        94.45         2.40        12.69 
TCGA-EU-5904 
       18.12 

$subtype6
TCGA-BP-4760 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5181 
       77.62        20.38         6.94        41.62        27.62        49.15 
TCGA-CJ-4894 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-A3-3331 TCGA-A3-3373 
       27.65         0.59       107.54         5.46        48.82        53.29 
TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       43.20        18.64        28.31         0.10        11.18        10.62 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
      117.80       109.41        73.68       112.08        94.19        46.78 
TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4827 
       12.13        28.47        58.45        45.07        14.93        29.10 
TCGA-B0-4834 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       68.71        10.52        39.45        15.95        90.87        90.48 
TCGA-B0-5117 TCGA-B0-5690 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-A4SR 
       52.87       111.52        73.84        32.61        35.90        16.67 
TCGA-B4-5834 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5552 TCGA-B8-A54F TCGA-BP-4166 
        1.25        24.23        50.14        34.39        17.06         0.43 
TCGA-BP-4340 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4975 
       18.48        56.91        60.95        48.95        36.95        47.11 
TCGA-BP-5176 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5190 TCGA-CJ-4870 TCGA-CJ-4878 
       52.27        38.30        37.25        33.24        49.25        71.87 
TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-6088 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5988 
       50.24        18.15       105.93        90.54        91.69        22.78 
TCGA-EU-5906 TCGA-G6-A8L6 TCGA-T7-A92I 
        6.77        10.29        11.70 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    2.01     0.07     0.36     0.10     0.95     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  122.83   133.71   129.40   133.94   149.16   117.80 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  50.010   33.990   36.885   44.745   36.850   38.300 
[1] "2.0 - 122.8 (50.0)" "0.1 - 133.7 (34.0)" "0.4 - 129.4 (36.9)"
[4] "0.1 - 133.9 (44.7)" "0.9 - 149.2 (36.9)" "0.1 - 117.8 (38.3)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      29        7        12       13
  subtype2      38        8        23       11
  subtype3      63       18        41       32
  subtype4      47       12        17        6
  subtype5      38        5        19       18
  subtype6      47        7        12        3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         29       38       63       47       38       47
  STAGE II         7        8       18       12        5        7
  STAGE III       12       23       41       17       19       12
  STAGE IV        13       11       32        6       18        3
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 29 11 21  0
  subtype2 38  8 31  3
  subtype3 67 22 63  4
  subtype4 48 13 21  0
  subtype5 39  7 30  4
  subtype6 47  8 14  0
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       29       38       67       48       39       47
  T2       11        8       22       13        7        8
  T3       21       31       63       21       30       14
  T4        0        3        4        0        4        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"
D3V5, binary
          cls
clus        0  1
  subtype1 31  0
  subtype2 38  2
  subtype3 64 12
  subtype4 36  0
  subtype5 36  3
  subtype6 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    0
  subtype2   38    2
  subtype3   64   12
  subtype4   36    0
  subtype5   36    3
  subtype6   29    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       31       38       64       36       36       29
  1        0        2       12        0        3        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"
D3V6, binary
          cls
clus         0   1
  subtype1  44  13
  subtype2  65  10
  subtype3 118  31
  subtype4  70   6
  subtype5  60  16
  subtype6  61   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   13
  subtype2   65   10
  subtype3  118   31
  subtype4   70    6
  subtype5   60   16
  subtype6   61    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       44       65      118       70       60       61
  1       13       10       31        6       16        2
[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"
D3V7, binary
          cls
clus         0   1
  subtype1  21  40
  subtype2  27  53
  subtype3  50 106
  subtype4  31  51
  subtype5  34  46
  subtype6  26  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   40
  subtype2   27   53
  subtype3   50  106
  subtype4   31   51
  subtype5   34   46
  subtype6   26   43
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       21       27       50       31       34       26
  MALE         40       53      106       51       46       43
[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"
D3V8, continuous
D3V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype6 
       1        5        8        1        6 
 [1] "subtype2" "subtype3" "subtype6" "subtype6" "subtype6" "subtype3"
 [7] "subtype3" "subtype6" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype6" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[19] "subtype6"
D3V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
[4] "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 subtype6 
       1        5        1        1        4 
[1] "subtype3" "subtype6" "subtype6" "subtype3" "subtype3" "subtype6" "subtype3"
[8] "subtype3" "subtype6"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         7    53
  subtype2     3                        11    65
  subtype3     2                        11   140
  subtype4     1                        10    71
  subtype5     1                         5    73
  subtype6     1                        12    55
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        3        2        1        1
  BLACK OR AFRICAN AMERICAN        7       11       11       10        5
  WHITE                           53       65      140       71       73
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN       12
  WHITE                           55
[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"
D3V12, binary
          cls
clus         0   1
  subtype1   3  35
  subtype2   5  49
  subtype3   9 106
  subtype4   3  56
  subtype5   4  51
  subtype6   2  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   35
  subtype2    5   49
  subtype3    9  106
  subtype4    3   56
  subtype5    4   51
  subtype6    2   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        5        9        3        4        2
  NOT HISPANIC OR LATINO       35       49      106       56       51       53
[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(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 59 10
  subtype2 43 26
  subtype3 47 50
  subtype4 63 19
subtype1 subtype2 subtype3 subtype4 
      69       69       97       82 
subtype1 subtype2 subtype3 subtype4 
      10       26       50       19 
$subtype1
TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5812 TCGA-B2-5635 
       58.49        28.73       112.80       133.94       126.05        24.82 
TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-BP-5181 TCGA-BP-5199 TCGA-CZ-4856 
       15.42        77.62        20.38        49.15        44.55         0.59 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-3Z-A93Z TCGA-A3-3370 
       65.88        11.67        56.84        23.90        12.66        74.76 
TCGA-A3-3376 TCGA-A3-A8OW TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-AK-3461 
       55.76        10.62       112.08        94.19        83.21        72.89 
TCGA-B0-4699 TCGA-B0-4823 TCGA-B0-4945 TCGA-B0-5083 TCGA-B0-5100 TCGA-B0-5102 
        3.62        14.93        70.52        34.36        62.89        90.87 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5702 TCGA-B0-5711 TCGA-B2-5633 TCGA-B2-5636 
       52.87        38.43        71.41       131.15        31.66        30.21 
TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5843 TCGA-B8-5159 TCGA-B8-5165 
       16.67         5.75         1.25         0.36        23.74        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F 
       50.14        16.60         6.38        34.39        14.30        17.06 
TCGA-BP-4177 TCGA-BP-5177 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5681 
       54.90         9.63       109.84        49.28        50.33        18.15 
TCGA-CJ-5684 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CZ-5458 
       73.35        81.83        73.18        66.31        78.18        91.69 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5984 TCGA-CZ-5988 TCGA-CZ-5989 
       55.33        21.76         2.40        67.96        22.78        62.63 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       12.00        18.12         3.91 

$subtype2
TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4815 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4782 
       42.97       109.91        52.21        25.91         1.18        11.64 
TCGA-BP-5191 TCGA-CZ-4865 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-G6-A8L7 
       31.79         5.46        12.16        37.15        66.28        70.13 
TCGA-MM-A84U TCGA-6D-AA2E TCGA-A3-A6NJ TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 
       23.01        11.90        15.39         1.41         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4819 
       19.00         1.38        65.10        45.07        33.50         6.02 
TCGA-B0-4842 TCGA-B0-5080 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       56.68        11.24        15.09         8.05         2.24        52.08 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5709 
       58.59        19.30        56.98       129.67        86.47       130.65 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 
       21.57         5.10         0.53        40.04        27.02         0.85 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A8YJ 
       48.53         0.53        29.88         1.74         4.93        14.17 
TCGA-BP-4770 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5195 
       10.82         6.35        79.30        38.30        13.35        24.62 
TCGA-BP-5196 TCGA-CJ-4869 TCGA-CJ-4882 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       33.47        83.97        61.91        45.14         3.06        18.81 
TCGA-CJ-5672 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4863 
       72.00        67.00        53.42         1.35        18.77        63.39 
TCGA-CZ-5452 TCGA-CZ-5462 TCGA-CZ-5466 
       58.82        10.22        22.52 

$subtype3
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5694 TCGA-B0-5698 TCGA-BP-5178 TCGA-BP-5189 
       19.73        43.96        15.78       119.38        62.86        27.02 
TCGA-BP-5201 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-DV-A4W0 TCGA-A3-3357 
       31.27        53.26       118.85        75.58        81.21        88.37 
TCGA-A3-3367 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-4688 TCGA-B0-4691 
       74.63        20.28        68.61        78.64         3.32         4.57 
TCGA-B0-4696 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       28.47         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4821 
       58.45        15.72        46.59         0.59         5.52        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-B0-5097 TCGA-B0-5099 TCGA-B0-5106 TCGA-B0-5107 
       29.03        10.95        21.86        15.95        52.54        30.48 
TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5710 
       41.88        42.41        85.78        80.91       105.37        79.89 
TCGA-B0-5712 TCGA-B2-4101 TCGA-B4-5838 TCGA-B8-4153 TCGA-B8-4622 TCGA-B8-A54D 
       89.49        21.30         5.46        25.05        50.14        27.29 
TCGA-BP-5010 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5190 TCGA-BP-5198 TCGA-CJ-4901 
       28.87        30.64        74.40        33.24        19.82        47.67 
TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5675 
       49.97        54.48        38.56         4.57       131.08       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      133.71        25.71        18.87        22.32        25.25       122.83 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5590 TCGA-CW-5591 
       62.66         7.36        64.57         5.39        35.34        74.66 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 
       83.90        25.45       107.41        18.44        79.63        94.45 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       10.85        69.96        84.30         1.94        31.10        12.69 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-EU-5907 TCGA-G6-A5PC TCGA-MM-A563 
       65.65        14.63        53.46         4.18         7.96        19.43 
TCGA-MM-A564 
       19.96 

$subtype4
TCGA-B0-5695 TCGA-B8-A54H TCGA-BP-4993 TCGA-BP-5168 TCGA-CJ-4904 TCGA-CW-6093 
       70.68         8.42         5.82        48.10       108.56       103.43 
TCGA-DV-5565 TCGA-DV-5566 TCGA-A3-3373 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NL 
       43.69        45.96        53.29        65.52        33.47        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3458 
        0.10         0.10        11.18       122.56        73.68        38.40 
TCGA-AK-3460 TCGA-B0-4714 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4841 TCGA-B0-4846 
       82.45         3.25        16.77        54.48         6.71        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 
       26.07         2.27        36.85        90.48        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5699 
       52.73        51.02        48.82        46.39       111.52       126.28 
TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5707 TCGA-B0-5713 TCGA-B2-3924 
       58.85        73.84       149.16       123.09        91.46        35.90 
TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-A54J 
       32.98        12.00         4.64         0.23        16.80        17.36 
TCGA-B8-A7U6 TCGA-BP-4801 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5183 
       16.27        36.95         2.04        74.20        52.27        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 
       37.25        37.22        22.78        23.47        13.41        34.95 
TCGA-BP-5202 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-5683 TCGA-CJ-6032 TCGA-CW-5581 
        0.95        51.29        49.18        62.10       119.64        92.02 
TCGA-CW-5585 TCGA-CW-6088 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 
       85.78       105.93        58.75        93.04        63.42        79.53 
TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-EU-5906 TCGA-G6-A8L6 
       23.74        90.54        80.19        12.26         6.77        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        16.37        11.70 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.53     0.59     0.10 
subtype1 subtype2 subtype3 subtype4 
  133.94   130.65   133.71   149.16 
subtype1 subtype2 subtype3 subtype4 
  44.550   23.010   31.270   40.945 
[1] "0.4 - 133.9 (44.5)" "0.5 - 130.7 (23.0)" "0.6 - 133.7 (31.3)"
[4] "0.1 - 149.2 (40.9)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      51        6        10        2
  subtype2      30        3        24       13
  subtype3      20       11        32       33
  subtype4      54       11         7       11
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         51       30       20       54
  STAGE II         6        3       11       11
  STAGE III       10       24       32        7
  STAGE IV         2       13       33       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 51  6 11  1
  subtype2 32  4 30  4
  subtype3 22 16 56  3
  subtype4 54 15 14  0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       51       32       22       54
  T2        6        4       16       15
  T3       11       30       56       14
  T4        1        4        3        0
[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"
D4V5, binary
          cls
clus        0  1
  subtype1 30  0
  subtype2 30  5
  subtype3 40  3
  subtype4 33  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2   30    5
  subtype3   40    3
  subtype4   33    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       30       30       40       33
  1        0        5        3        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 63  2
  subtype2 50 11
  subtype3 62 30
  subtype4 59 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2   50   11
  subtype3   62   30
  subtype4   59   10
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       63       50       62       59
  1        2       11       30       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"
D4V7, binary
          cls
clus        0  1
  subtype1 30 39
  subtype2 28 42
  subtype3 19 78
  subtype4 37 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   39
  subtype2   28   42
  subtype3   19   78
  subtype4   37   46
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       30       28       19       37
  MALE         39       42       78       46
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        4        3        2 
[1] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        13    56
  subtype2     0                        13    56
  subtype3     1                         9    85
  subtype4     0                        14    69
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        0
  BLACK OR AFRICAN AMERICAN       13       13        9       14
  WHITE                           56       56       85       69
[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"
D4V12, binary
          cls
clus        0  1
  subtype1  1 57
  subtype2  2 58
  subtype3  4 83
  subtype4  3 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   57
  subtype2    2   58
  subtype3    4   83
  subtype4    3   62
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        4        3
  NOT HISPANIC OR LATINO       57       58       83       62
[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(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-B0-5691 TCGA-B8-4621 TCGA-BP-4353 TCGA-BP-4799 TCGA-BP-4988 TCGA-BP-4993 
      112.80        25.91        12.33        37.25        27.22         5.82 
TCGA-BP-5178 TCGA-CZ-4865 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3322 
       62.86         5.46        12.66        11.90        24.16        48.59 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3357 TCGA-A3-3362 
       38.99        37.38        62.01         4.50        88.37        51.25 
TCGA-A3-3363 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3427 
       10.49        53.29        43.20        20.71        18.87       117.80 
TCGA-AK-3428 TCGA-AK-3444 TCGA-AK-3456 TCGA-B0-4699 TCGA-B0-4714 TCGA-B0-4817 
      122.56        48.36        37.58         3.62         3.25        33.50 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4945 TCGA-B0-5084 TCGA-B0-5096 
       78.44        68.71        45.30        70.52         7.30         2.24 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5696 TCGA-B0-5700 
       90.87        19.30        52.87        56.98        85.78        58.85 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       71.41        73.84        32.61        35.90         1.68        31.96 
TCGA-B2-4102 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54E 
       31.30        16.80        25.55         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-4756 TCGA-BP-4777 TCGA-BP-4964 TCGA-BP-4967 
       21.21        52.24        12.30        56.91        61.22         6.74 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 
       58.98        49.38         3.88        43.00        37.02         6.35 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5194 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4874 
       37.22        13.35        13.41        19.82       115.00        75.06 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4902 TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6033 
      113.46        64.18        49.97        18.15        62.66         7.36 
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-A3-3329 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
       53.39       133.94        15.78        70.68       119.38       126.05 
TCGA-BP-4327 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5181 TCGA-CW-6093 TCGA-DV-5565 
        3.58        45.07        41.62        49.15       103.43        43.69 
TCGA-DV-5566 TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3385 TCGA-AK-3434 TCGA-B0-4706 
       45.96        36.82        49.58        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-B0-5699 
       51.02        48.82        46.39        42.41       111.52       126.28 
TCGA-B0-5711 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-5553 
      131.15         4.64         0.36         0.23        25.05        14.30 
TCGA-B8-A54J TCGA-BP-4161 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 
       17.36        90.28        97.45        27.78        62.07        15.62 
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-5001 TCGA-BP-5007 
       36.07        33.34        36.95        46.45        38.70        37.48 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5192 
       79.30        74.20        52.27        74.40        42.44        23.47 
TCGA-CJ-4635 TCGA-CJ-4870 TCGA-CJ-4878 TCGA-CJ-4897 TCGA-CJ-4916 TCGA-CJ-5675 
       46.55        49.25        71.87       109.84        45.14       129.40 
TCGA-CJ-5680 TCGA-CJ-5683 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-4859 
       25.25        62.10       119.64        81.83        85.78        58.75 
TCGA-CZ-5451 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-G6-A8L6 
       63.42        84.30        80.19        65.65        12.26        10.29 
TCGA-G6-A8L8 TCGA-MM-A564 TCGA-MW-A4EC 
       35.87        19.96        16.37 

$subtype3
TCGA-A3-3336 TCGA-B0-4707 TCGA-B0-4712 TCGA-BP-4342 TCGA-BP-5009 TCGA-BP-5199 
       34.29        19.73        43.96        74.17        35.90        44.55 
TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-G6-A8L7 TCGA-A3-3308 
       26.93        53.26       118.85        46.16        70.13         0.53 
TCGA-A3-3347 TCGA-A3-3387 TCGA-AK-3436 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       52.93        20.28       109.51         3.32         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4718 
        3.48        28.47         1.38        57.70         6.64        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 
       15.72         0.59         5.52        40.44        36.53        29.10 
TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5092 
       10.09        56.68        10.52        10.29        29.03        15.09 
TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5707 TCGA-B0-5709 TCGA-B4-5832 
       10.95        52.08        30.48       123.09       130.65         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-A54F TCGA-BP-4173 
        5.46        23.31        50.14        40.04        17.06        62.24 
TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 
       53.42        93.99        62.86        11.31        33.99         5.98 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4960 TCGA-BP-4983 
       10.82         5.33        15.78        10.98        71.41        46.45 
TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5175 TCGA-CJ-4638 TCGA-CJ-4869 
       31.30        16.47        18.51        30.64        14.17        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4895 TCGA-CJ-4901 
       79.66        74.27       116.84        66.21        39.45        47.67 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 
       54.48        38.56         4.57        25.71        22.32        53.42 
TCGA-CW-5588 TCGA-CW-6087 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 
       66.31         1.35        47.08        69.21         6.77        14.66 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5987 TCGA-DV-A4VX 
       79.63        94.45        69.96         1.94        14.63        53.46 
TCGA-G6-A5PC 
        7.96 

$subtype4
TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-5189 TCGA-BP-5191 
       24.82       111.02        32.61        80.68        27.02        31.79 
TCGA-BP-5201 TCGA-CJ-4904 TCGA-CZ-4862 TCGA-DV-5573 TCGA-A3-3311 TCGA-A3-3317 
       31.27       108.56       107.54        37.15        39.16        49.02 
TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3372 
       37.15        36.36        29.92        18.44        74.63        24.16 
TCGA-A3-3383 TCGA-B0-4811 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4847 TCGA-B0-5075 
       28.31        46.59        27.42        53.88        26.07        20.94 
TCGA-B0-5081 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5705 TCGA-B0-5712 
       11.90       129.67        86.47        80.91       149.16        89.49 
TCGA-B0-5713 TCGA-B2-4101 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5835 
       91.46        21.30        32.98        21.57        12.00         0.53 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-A54G TCGA-BP-4346 
       23.74         0.85        16.60        48.53         1.74        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-5190 TCGA-BP-5195 TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4884 
       45.50        33.24        24.62       114.41        64.27        57.83 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4893 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5672 
       30.64        51.52        24.66        51.29        49.28        72.00 
TCGA-CJ-5678 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 
       18.87        64.57        92.02         5.39        73.18        78.18 
TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6096 TCGA-CZ-4853 TCGA-CZ-4863 TCGA-CZ-4864 
       35.34        74.66        88.80        25.45        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5463 TCGA-CZ-5467 
      107.41        58.82        18.44        91.69        21.76         2.40 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-EU-5905 TCGA-EU-5907 TCGA-MM-A563 
       12.69        67.96        62.63         3.91         4.18        19.43 

$subtype5
TCGA-B0-4815 TCGA-B0-5088 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4762 
       52.21        18.51         1.18         8.42        15.42        44.15 
TCGA-BP-5168 TCGA-CJ-4894 TCGA-CJ-6030 TCGA-CZ-4856 TCGA-DV-5567 TCGA-DV-5574 
       48.10        27.65        75.58         0.59        65.88        66.28 
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-B0-4819 TCGA-B0-4823 
       19.00        65.10         7.82         5.98         6.02        14.93 
TCGA-B0-4836 TCGA-B0-5080 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 
       40.70        11.24         8.05        21.86        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5706 
       52.54        58.59        38.63        52.73        38.43       105.37 
TCGA-B0-5710 TCGA-B2-5633 TCGA-B2-5636 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 
       79.89        31.66        30.21        16.67         5.75         1.25 
TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-A54D TCGA-BP-4169 TCGA-BP-4337 TCGA-BP-4345 
       27.02        50.14        27.29        23.05         0.07        49.84 
TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4784 
       12.23        31.33        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-5177 TCGA-BP-5182 
        6.94        30.64        35.21        28.87         9.63        38.30 
TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4882 TCGA-CJ-4889 
       33.47        34.95        21.24        47.18        61.91        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4905 TCGA-CJ-4908 
      115.69        50.01        50.24        56.35        49.18        50.33 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5684 
        3.06        18.81       131.08       133.71       122.83        73.35 
TCGA-CJ-5686 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-5454 TCGA-CZ-5461 
       67.00       105.93        83.90        18.77        23.74        10.85 
TCGA-CZ-5466 TCGA-CZ-5469 TCGA-DV-A4VZ TCGA-GK-A6C7 
       22.52        31.10        12.00         2.01 

$subtype6
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4775 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       54.77        77.62        60.59         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-5006 TCGA-CJ-4642 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 
       25.81        27.62       105.37        12.16        11.67        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-A3-3331 TCGA-A3-3370 TCGA-B0-4693 TCGA-B0-5110 
       23.90        81.21        48.82        74.76         2.53        66.05 
TCGA-B8-5165 TCGA-B8-5552 TCGA-B8-A7U6 TCGA-BP-4758 TCGA-BP-4766 TCGA-BP-4781 
       24.23        34.39        16.27        72.59        48.07        68.38 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-5173 TCGA-BP-5184 TCGA-BP-5186 
       48.95        36.39        36.95         2.04        37.25        22.78 
TCGA-BP-5202 TCGA-CZ-5988 TCGA-EU-5906 
        0.95        22.78         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 
  122.56   133.94   130.65   149.16   133.71   105.37 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  37.250   45.960   31.300   38.155   38.365   36.950 
[1] "0.5 - 122.6 (37.2)" "0.2 - 133.9 (46.0)" "0.5 - 130.7 (31.3)"
[4] "0.5 - 149.2 (38.2)" "0.1 - 133.7 (38.4)" "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        29       35
  subtype4      35        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       35       47       29
  STAGE II         7       12        9        9       10        1
  STAGE III       18       17       29       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" "subtype3" "subtype1" "subtype3" "subtype4" "subtype4"
 [7] "subtype1" "subtype3" "subtype4" "subtype1" "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-B0-4815 TCGA-B0-5088 TCGA-B0-5693 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
       52.21        18.51       133.94         1.18         8.42        15.42 
TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4799 
       80.68        54.77        77.62        44.15        60.59        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4993 TCGA-BP-5168 TCGA-CJ-4642 TCGA-CJ-4894 
        6.94        61.51         5.82        48.10       105.37        27.65 
TCGA-CJ-4904 TCGA-CJ-6030 TCGA-CZ-4856 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
      108.56        75.58         0.59        65.88        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5576 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3322 TCGA-A3-3349 
       66.28        23.90        12.66        11.90        48.59        45.53 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
       51.25        10.49        28.70        74.76        53.29        55.76 
TCGA-A3-3380 TCGA-AK-3451 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4819 
       18.64        94.29        19.00         7.82         5.98         6.02 
TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4945 TCGA-B0-5080 
       14.93        40.70        27.42        53.88        70.52        11.24 
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-B0-5697 TCGA-B0-5702 TCGA-B0-5706 
       38.63        52.73        38.43        86.47        71.41       105.37 
TCGA-B0-5707 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-4099 
      123.09        79.89       131.15        89.49        35.90        31.96 
TCGA-B2-5633 TCGA-B2-5636 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       31.66        30.21        16.67         5.75         1.25         0.53 
TCGA-B8-4143 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-A54D 
       23.31        50.14         6.38        48.53        34.39        27.29 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4169 TCGA-BP-4170 
        4.93        17.36        16.27        14.17        23.05        77.03 
TCGA-BP-4332 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 
       37.25        12.23        31.33        41.75        71.80        61.68 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 
       56.91        60.95        36.53        36.95        47.97        87.45 
TCGA-BP-4964 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4998 
       61.22        14.24        48.89        49.38         6.94        30.64 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5194 
       35.21        28.87        79.30         9.63        38.30        13.41 
TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4886 TCGA-CJ-4889 
       33.47        34.95        21.24        47.18        64.18        63.98 
TCGA-CJ-4890 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
      115.69        50.24        56.35        49.97        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5681 
       50.33         3.06       131.08        72.00       133.71        18.15 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-6088 TCGA-CW-6097 TCGA-CZ-5454 TCGA-CZ-5461 
      122.83        73.35       105.93        18.77        23.74        10.85 
TCGA-CZ-5466 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-GK-A6C7 TCGA-MM-A563 
       22.52        12.00        18.12         2.01        19.43 

$subtype2
TCGA-A3-3336 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-BP-4158 
       34.29        15.78        70.68       119.38       126.05       111.02 
TCGA-BP-4327 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4986 TCGA-BP-5178 TCGA-BP-5191 
        3.58        74.17        12.33        25.81        62.86        31.79 
TCGA-BP-5199 TCGA-CJ-6027 TCGA-DV-5565 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-A3-3306 
       44.55       118.85        43.69        12.16        70.13        36.82 
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-A3-3347 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       52.93        18.44        74.63        18.87        28.31        65.52 
TCGA-AK-3434 TCGA-B0-4691 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4821 TCGA-B0-4822 
       68.61         4.57         2.14        58.45        40.44        36.53 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       54.48        29.10         6.71        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5092 
       39.45        36.85        20.94        43.30        11.90        15.09 
TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5699 TCGA-B0-5701 TCGA-B2-5641 
       51.02        46.39       111.52       126.28        80.91        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        40.04 
TCGA-B8-5163 TCGA-BP-4161 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       27.02        90.28        62.24        97.45        53.42        27.78 
TCGA-BP-4335 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4768 TCGA-BP-4803 TCGA-BP-4960 
       15.62        62.86        49.84        13.15         6.71        71.41 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-5000 
       60.30         6.74        14.93        31.30        16.47        18.51 
TCGA-BP-5180 TCGA-BP-5195 TCGA-CJ-4635 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
       74.40        24.62        46.55        83.97        79.66        74.27 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4920 
       66.21        57.83        30.64        47.67        54.48         4.57 
TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5580 
       18.81        25.71        22.32        62.10        53.42        64.57 
TCGA-CW-5588 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4857 
       66.31        35.34        74.66        83.90        25.45        47.08 
TCGA-CZ-5451 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5468 TCGA-CZ-5469 
       63.42        79.63        55.33        94.45         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-G6-A8L8 
       12.69        67.96        65.65        14.63        53.46        35.87 

$subtype3
TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4988 TCGA-CJ-4891 TCGA-CJ-5689 
       19.73        43.96        25.91        27.22        26.93        53.26 
TCGA-CZ-4854 TCGA-A3-3313 TCGA-A3-3324 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3378 
       46.16        24.16        38.99         4.50        43.20        20.71 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3436 TCGA-AK-3456 TCGA-B0-4688 TCGA-B0-4690 
      117.80       122.56       109.51        37.58         3.32         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4713 
        3.48        28.47         1.38         3.62        65.10         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4828 
        3.25        15.72         0.59         5.52        33.50        10.09 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4848 TCGA-B0-5084 TCGA-B0-5094 
       68.71        45.30        56.68        29.03         7.30        10.95 
TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 
        8.05        52.08        30.48        19.30        52.87        56.98 
TCGA-B0-5703 TCGA-B0-5709 TCGA-B2-3923 TCGA-B4-5836 TCGA-B4-5838 TCGA-B8-4620 
       73.84       130.65        32.61         4.64         5.46        25.55 
TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-A54E TCGA-BP-4334 TCGA-BP-4337 TCGA-BP-4338 
       16.60         0.53        29.88        21.21         0.07        93.99 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4771 
       11.31        33.99        12.30         5.98        10.82         5.33 
TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-4994 
       15.78        10.98        58.68        46.45         3.88        43.00 
TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4885 
        6.35        19.82        14.17       116.84        61.91       113.46 
TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4913 TCGA-CJ-5675 TCGA-CJ-5680 
       51.52        50.01        39.45        38.56       129.40        25.25 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-6087 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 
       62.66         7.36         1.35        69.21         6.77        14.66 
TCGA-CZ-5464 
       69.96 

$subtype4
TCGA-A3-3329 TCGA-B0-5691 TCGA-B2-5635 TCGA-BP-4164 TCGA-BP-4976 TCGA-BP-4995 
       53.39       112.80        24.82        32.61        53.65        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5201 
       41.62        27.62        35.90        49.15        27.02        31.27 
TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5575 TCGA-DV-A4W0 
      103.43       107.54         5.46        45.96        56.84        81.21 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3351 TCGA-A3-3357 
       49.02        49.58        37.38        48.82        29.92        88.37 
TCGA-A3-3372 TCGA-A3-3387 TCGA-AK-3444 TCGA-B0-4693 TCGA-B0-4710 TCGA-B0-4811 
       24.16        20.28        48.36         2.53        57.70        46.59 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4833 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-5085 
       45.07        16.77        78.44        26.07         2.27        25.32 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 
       15.95        90.87        66.05        41.88        48.82        42.41 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5713 TCGA-B2-4098 
      129.67        85.78        58.85       149.16        91.46         1.68 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B4-5377 TCGA-B8-4146 TCGA-B8-5159 
       21.30        31.30        32.98        12.00        16.80        23.74 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4165 
        0.85        24.23        14.30        17.06         1.74        99.85 
TCGA-BP-4174 TCGA-BP-4330 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 
       61.78        62.07        52.24        49.08        44.94        31.89 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4781 
       72.59        77.98        48.07        61.97        13.51        68.38 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4961 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4973 
       48.95        36.39        63.62        57.40        58.98        45.50 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-5001 
       47.11        36.07        33.34        36.95        46.45        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       37.02        37.48         2.04        74.20        30.64        52.27 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4870 TCGA-CJ-4874 
       23.47         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-6096 TCGA-CZ-4859 TCGA-CZ-4863 
       85.78        73.18        78.18        88.80        58.75        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 
       93.04       107.41        58.82        79.53        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       91.69        10.22        21.76        84.30         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.26        22.78        62.63         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 
   38.30    41.87    25.91    45.32 
[1] "0.5 - 133.9 (38.3)" "0.2 - 126.3 (41.9)" "0.1 - 130.7 (25.9)"
[4] "0.8 - 149.2 (45.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      85       10        22       19
  subtype2      46       16        30       22
  subtype3      25        6        24       29
  subtype4      78       16        37       11
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         85       46       25       78
  STAGE II        10       16        6       16
  STAGE III       22       30       24       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] "subtype4" "subtype2" "subtype1" "subtype1" "subtype4" "subtype2"
 [7] "subtype4" "subtype1" "subtype4" "subtype4" "subtype1" "subtype2"
[13] "subtype4" "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  62  22
  subtype2 141  30
  subtype3  57  25
  subtype4  78  76
  subtype5  18  22
subtype1 subtype2 subtype3 subtype4 subtype5 
      84      171       82      154       40 
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       30       25       76       22 
$subtype1
TCGA-A3-3328 TCGA-B0-5691 TCGA-B8-4621 TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4762 
       45.53       112.80        25.91        15.42        77.62        44.15 
TCGA-BP-4795 TCGA-BP-4995 TCGA-CJ-4642 TCGA-CJ-5689 TCGA-DV-5566 TCGA-DV-5567 
       20.38        45.07       105.37        53.26        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 TCGA-MM-A84U TCGA-3Z-A93Z 
       11.67        37.15        66.28        23.90        23.01        12.66 
TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       11.90        24.16        49.02        51.25        10.49        28.70 
TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
       43.20       117.80       122.56       112.08        94.19        46.78 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 
       40.01        94.29        83.21        37.58        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-4834 TCGA-B0-4841 
       40.70        28.47         3.62         6.02        68.71         6.71 
TCGA-B0-4945 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5109 
       70.52        34.36         7.30        52.08        62.89        19.30 
TCGA-B0-5117 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5707 TCGA-B0-5709 TCGA-B2-3923 
       52.87        86.47        71.41       123.09       130.65        32.61 
TCGA-B2-4098 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 
        1.68        30.21         5.75         0.53         5.46        17.19 
TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-A54E TCGA-BP-4163 TCGA-BP-4177 TCGA-BP-4334 
       24.23        16.60        29.88        93.34        54.90        21.21 
TCGA-BP-4337 TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4804 
        0.07        12.30        41.75        61.68        60.95        47.97 
TCGA-BP-4994 TCGA-BP-5008 TCGA-BP-5182 TCGA-CJ-4907 TCGA-CJ-5680 TCGA-CJ-5681 
       43.00        35.21        38.30        49.28        25.25        18.15 
TCGA-CJ-5683 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-DV-A4VZ TCGA-T7-A92I 
       62.10        78.18        74.66         1.35        12.00        11.70 

$subtype2
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 
       47.21        38.47        53.39        31.07        82.32        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B2-5635 
       28.73        22.45       133.94        70.68       119.38        24.82 
TCGA-B8-A54H TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4775 TCGA-BP-4807 
        8.42        94.72        32.61        80.68        60.59         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5201 
       61.51        53.65        27.62        48.10        49.15        31.27 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5575 TCGA-A3-3306 
       27.65       108.56       103.43         0.59        56.84        36.82 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3352 
       49.58        48.59        38.99        37.38        48.82        18.44 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3385 TCGA-A3-A6NI 
       74.63        74.76        53.29        18.64        65.52        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3429 
       15.39        22.65         0.10        11.18        10.62       109.41 
TCGA-AK-3444 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 
       48.36         1.41         2.53        16.77        54.48        78.44 
TCGA-B0-4838 TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       27.42        39.45        36.85        15.95        90.87        90.48 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 
       66.05        52.73        51.02        48.82        46.39        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 
      111.52       129.67        85.78       126.28        58.85        73.84 
TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
      149.16       131.15        89.49        91.46        35.90        31.96 
TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5843 
       31.30        32.98        16.67        12.00         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4162 
       23.74         0.85         6.38        14.30        17.36       101.06 
TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4340 TCGA-BP-4346 
       99.85        77.03        97.45        62.07        18.48        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4774 
       44.94        12.23        72.59        71.80        48.07        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4973 
       13.51        56.91        61.22        57.40        58.98        45.50 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5173 
       33.34        36.95        38.70        37.02        37.48         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.20        52.27        42.44        37.25        37.22        22.78 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5202 TCGA-CJ-4639 TCGA-CJ-4643 
       33.24        23.47        13.41         0.95       106.16        58.95 
TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4885 TCGA-CJ-4886 
       11.05        49.25        75.06        64.27       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4916 
       30.64        50.01        24.66       109.84        51.29        45.14 
TCGA-CJ-5675 TCGA-CJ-5684 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      129.40        73.35       119.64        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4863 
       85.78        73.18       105.93        25.45        58.75        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       93.04        63.42        79.53        18.44        90.54        91.69 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 
       21.76        84.30        80.19        12.26        62.63        18.12 
TCGA-EU-5906 TCGA-GK-A6C7 TCGA-MW-A4EC 
        6.77         2.01        16.37 

$subtype3
TCGA-B0-5812 TCGA-B8-5162 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4993 TCGA-BP-4999 
      126.05         1.18        74.17        54.77         5.82        41.62 
TCGA-BP-5199 TCGA-DV-5565 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3323 TCGA-A3-3349 
       44.55        43.69         0.53        49.08        36.36        45.53 
TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3431 TCGA-B0-4688 
       24.16        55.76        20.28         0.10        73.68         3.32 
TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4823 TCGA-B0-4837 TCGA-B0-5080 TCGA-B0-5095 
        5.98        15.72        14.93        45.30        11.24         8.05 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5710 
       21.86        58.59        38.63        41.88        38.43        79.89 
TCGA-B4-5834 TCGA-B8-4620 TCGA-B8-5545 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A8YJ 
        1.25        25.55        50.14        34.39        17.06        14.17 
TCGA-BP-4159 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4332 
       85.51         0.43        23.05        53.42        27.78        37.25 
TCGA-BP-4345 TCGA-BP-4759 TCGA-BP-4770 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 
       49.84        77.98        10.82        48.95        36.53        36.95 
TCGA-BP-4803 TCGA-BP-4961 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
        6.71        63.62        14.24        49.38         6.94        47.11 
TCGA-BP-4998 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5187 TCGA-BP-5195 
       30.64        28.87        79.30         9.63        13.35        24.62 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4872 
       19.82        34.95       115.00        21.24        79.66        47.18 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       63.98       115.69        50.24        49.97        49.18        50.33 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CW-5580 TCGA-CW-6090 
        3.06         4.57       131.08       122.83        64.57        83.90 
TCGA-CZ-4858 TCGA-CZ-5461 TCGA-CZ-5467 TCGA-MM-A563 
       69.21        10.85         2.40        19.43 

$subtype4
TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       42.97       109.91        19.73        43.96        52.21        18.51 
TCGA-B0-5694 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4799 TCGA-BP-4986 TCGA-BP-5009 
       15.78        12.33        11.64        37.25        25.81        35.90 
TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-6027 
       62.86        27.02        31.79        63.25        26.93       118.85 
TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5568 TCGA-G6-A8L7 
       75.58        46.16       107.54         5.46        12.16        70.13 
TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 
       39.16        37.15        62.01         4.50        52.93        88.37 
TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4690 
       20.71        18.87        29.10       109.51        78.64         1.41 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4713 TCGA-B0-4817 
        4.57         3.48         1.38        65.10         6.64        33.50 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4839 TCGA-B0-4842 
       40.44        36.53        29.10        40.70        53.88        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 
       10.52        10.29        29.03        20.94        43.30        11.90 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5400 
       15.09        10.95         2.24        52.54        30.48        56.98 
TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4143 
       80.91       105.37        31.66        21.57         5.10        23.31 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D TCGA-B8-A54G 
       40.04        27.02        48.53         0.53        27.29         1.74 
TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        4.93        90.28        89.36        62.24        61.78        64.27 
TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4768 
       93.99        62.86        11.31        33.99         5.98        13.15 
TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4959 
        5.33        68.38        15.78        36.39        10.98        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4977 TCGA-BP-4983 
       71.41        58.68        60.30         6.74        14.93        46.45 
TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 
       31.30        16.47        18.51         6.35        30.64        74.40 
TCGA-BP-5196 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       33.47        46.55        73.22        14.17       114.41        54.61 
TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4888 
       83.97        74.27        66.21        61.91        57.83        51.52 
TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5672 
       39.45        56.35        47.67        54.48        18.81        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5686 TCGA-CJ-6028 
      133.71        25.71        18.87        22.32        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5590 TCGA-CW-6097 TCGA-CZ-4857 
       62.66         7.36        66.31        35.34        18.77        47.08 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5456 
        6.77        14.66       107.41        58.82        23.74        79.63 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
       55.33        94.45        10.22        69.96        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 
       31.10        12.69        67.96        65.65        14.63        22.78 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46         3.91         4.18         7.96 

$subtype5
TCGA-BP-4158 TCGA-BP-4327 TCGA-BP-4988 TCGA-DV-A4W0 TCGA-A3-3351 TCGA-A3-3383 
      111.02         3.58        27.22        81.21        29.92        28.31 
TCGA-AK-3434 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4706 
       68.61        38.40        82.45        19.00         7.82         2.14 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
       57.70         3.25        58.45        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4828 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-5085 
       45.07        10.09        65.29        26.07         2.27        25.32 
TCGA-B2-4101 TCGA-B8-4622 TCGA-B8-A7U6 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4351 
       21.30        50.14        16.27        15.62        52.24        31.89 
TCGA-BP-4355 TCGA-BP-4971 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4991 TCGA-CJ-4875 
       31.33        48.89        36.07         3.88        46.45       116.84 
TCGA-CJ-4878 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-MM-A564 
       71.87        10.29        35.87        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.10     0.10     0.53     0.59 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.65   149.16   131.08   133.71   116.84 
subtype1 subtype2 subtype3 subtype4 subtype5 
  40.355   48.360   37.100   36.145   30.625 
[1] "0.1 - 130.7 (40.4)" "0.1 - 149.2 (48.4)" "0.1 - 131.1 (37.1)"
[4] "0.5 - 133.7 (36.1)" "0.6 - 116.8 (30.6)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      57       10         9        9
  subtype2     108       19        32       13
  subtype3      41        8        20       12
  subtype4      51       15        48       39
  subtype5      10        5        14       11
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         57      108       41       51       10
  STAGE II        10       19        8       15        5
  STAGE III        9       32       20       48       14
  STAGE IV         9       13       12       39       11
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  57  11  16   1
  subtype2 108  21  42   1
  subtype3  43   8  29   2
  subtype4  55  22  71   6
  subtype5  10   7  22   1
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       57      108       43       55       10
  T2       11       21        8       22        7
  T3       16       42       29       71       22
  T4        1        1        2        6        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 36  4
  subtype2 81  1
  subtype3 37  2
  subtype4 71  9
  subtype5 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    4
  subtype2   81    1
  subtype3   37    2
  subtype4   71    9
  subtype5   15    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       36       81       37       71       15
  1        4        1        2        9        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1  70   8
  subtype2 149  12
  subtype3  67  11
  subtype4 111  38
  subtype5  25  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    8
  subtype2  149   12
  subtype3   67   11
  subtype4  111   38
  subtype5   25   10
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       70      149       67      111       25
  1        8       12       11       38       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  31  54
  subtype2  84  88
  subtype3  22  60
  subtype4  39 115
  subtype5  12  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   54
  subtype2   84   88
  subtype3   22   60
  subtype4   39  115
  subtype5   12   28
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       31       84       22       39       12
  MALE         54       88       60      115       28
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        6        3        7        1 
 [1] "subtype1" "subtype4" "subtype2" "subtype2" "subtype2" "subtype4"
 [7] "subtype1" "subtype2" "subtype2" "subtype4" "subtype2" "subtype4"
[13] "subtype1" "subtype3" "subtype4" "subtype3" "subtype4" "subtype4"
[19] "subtype3" "subtype1"
D7V10, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        3        1        4        1 
 [1] "subtype4" "subtype1" "subtype2" "subtype2" "subtype4" "subtype1"
 [7] "subtype2" "subtype4" "subtype4" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        20    62
  subtype2     1                        16   152
  subtype3     3                         6    73
  subtype4     2                         9   140
  subtype5     0                         5    35
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        3        2        0
  BLACK OR AFRICAN AMERICAN       20       16        6        9        5
  WHITE                           62      152       73      140       35
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
          cls
clus         0   1
  subtype1   2  69
  subtype2  14 108
  subtype3   1  51
  subtype4   7 101
  subtype5   2  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   69
  subtype2   14  108
  subtype3    1   51
  subtype4    7  101
  subtype5    2   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2       14        1        7        2
  NOT HISPANIC OR LATINO       69      108       51      101       26
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

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-B0-5088 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-BP-4160 TCGA-BP-4344 
       18.51       119.38       126.05        24.82        94.72        54.77 
TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-5189 TCGA-BP-5201 TCGA-CJ-4642 
       44.15        11.64         6.94        27.02        31.27       105.37 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-A4W0 TCGA-3Z-A93Z 
      107.54         5.46        43.69        12.16        81.21        12.66 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3351 TCGA-A3-3365 
       36.82        39.16        36.36        62.01        29.92        28.70 
TCGA-A3-3380 TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 
       18.64        20.28         0.10       122.56        73.68        68.61 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 
       38.40        82.45        72.89         1.41         2.14        58.45 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4841 
       46.59         5.52        45.07        14.93        10.09         6.71 
TCGA-B0-4848 TCGA-B0-5077 TCGA-B0-5106 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5402 
       29.03        43.30        52.54        41.88        38.43        42.41 
TCGA-B0-5696 TCGA-B0-5702 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-A4SR TCGA-B8-4622 
       85.78        71.41        21.30        31.66        16.67        50.14 
TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54F TCGA-BP-4159 TCGA-BP-4161 
       50.14         6.38        34.39        17.06        85.51        90.28 
TCGA-BP-4166 TCGA-BP-4173 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4351 
        0.43        62.24        27.78        37.25        15.62        31.89 
TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 
       77.98        41.75        13.15        36.53        36.95         6.71 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4977 
       63.62        60.30         6.74        57.40        14.24        14.93 
TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5007 
       36.07         3.88        46.45        16.47        30.64        37.48 
TCGA-BP-5008 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5187 TCGA-BP-5190 
       35.21        74.40        38.30        42.44        13.35        33.24 
TCGA-BP-5195 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4899 
       24.62        79.66       116.84        30.64        63.98        50.24 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CW-5580 TCGA-CW-5590 
       49.28        50.33        18.87       122.83        64.57        35.34 
TCGA-CZ-4861 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       14.66        23.74        18.44        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-CZ-5988 
       10.85        22.52         2.40        12.69        14.63        22.78 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-MM-A563 TCGA-MM-A564 
        4.18        10.29        19.43        19.96 

$subtype2
TCGA-B0-5691 TCGA-B0-5695 TCGA-B8-4621 TCGA-CJ-5689 TCGA-DV-5566 TCGA-DV-5569 
      112.80        70.68        25.91        53.26        45.96        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3362 TCGA-A3-3363 
       37.15        66.28        11.90        24.16        51.25        10.49 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-B0-5697 TCGA-B0-5700 TCGA-B0-5707 
       83.21        37.58        12.13        86.47        58.85       123.09 
TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5835 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-A54E 
        1.68        32.98         0.53        24.23        16.60        29.88 
TCGA-BP-4756 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 
       12.30       129.40        18.15        62.10        73.35        92.02 
TCGA-CW-5584 TCGA-CW-5589 TCGA-CW-5591 TCGA-T7-A92I 
        5.39        78.18        74.66        11.70 

$subtype3
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3329 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        53.39        31.07        42.97        82.32 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5693 TCGA-B8-A54H TCGA-BP-4158 
       58.49        28.73        22.45       133.94         8.42       111.02 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4775 TCGA-BP-4965 TCGA-BP-4976 
       32.61         3.58        80.68        60.59        61.51        53.65 
TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-CJ-4894 
        5.82        41.62        27.62        48.10        49.15        27.65 
TCGA-CJ-4904 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5575 TCGA-A3-3320 TCGA-A3-3322 
      108.56       103.43         0.59        56.84        49.58        48.59 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3352 TCGA-A3-3367 
       38.99        37.38        48.82        45.53        18.44        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3383 TCGA-A3-3385 
       74.76        24.16        53.29        55.76        28.31        65.52 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3429 TCGA-AK-3444 TCGA-AS-3777 TCGA-B0-4693 TCGA-B0-4701 TCGA-B0-4710 
      109.41        48.36        40.70         2.53         7.82        57.70 
TCGA-B0-4714 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 
        3.25        16.77        54.48        78.44        27.42        53.88 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5110 TCGA-B0-5113 
       25.32        15.95        90.87        90.48        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 
       52.73        51.02        48.82        46.39       111.52       129.67 
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         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5553 TCGA-B8-A54J 
       25.05        45.37        23.74         0.85        14.30        17.36 
TCGA-B8-A7U6 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4325 
       16.27       101.06        99.85        77.03        61.78        97.45 
TCGA-BP-4330 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 
       62.07        18.48        52.24        44.94        12.23        31.33 
TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       72.59        71.80        48.07        61.97        13.51        56.91 
TCGA-BP-4789 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       48.95        61.22        58.98        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5173 
       47.11        33.34        36.95        38.70        37.02         2.04 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 
       52.27         9.63        37.25        37.22        22.78        23.47 
TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 
       13.41        34.95         0.95       115.00       106.16       114.41 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       58.95        11.05        49.25        75.06        64.27        71.87 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4903 
      113.46        64.18        50.01        24.66       109.84        51.29 
TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5686 TCGA-CJ-6032 
       49.18        45.14         4.57        72.00        67.00       119.64 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4859 
       81.83        85.78        73.18       105.93        25.45        58.75 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 
       63.39        93.04        63.42        79.53        90.54        21.76 
TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5906 
       84.30        80.19        12.26        62.63        18.12         6.77 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MW-A4EC 
       35.87         2.01        16.37 

$subtype4
TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5694 TCGA-B8-5162 
      109.91        19.73        43.96        52.21        15.78         1.18 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4799 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-5009 
       74.17        12.33        37.25        25.81        27.22        35.90 
TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4891 TCGA-CJ-6027 TCGA-CJ-6030 
       62.86        31.79        44.55        26.93       118.85        75.58 
TCGA-CZ-4854 TCGA-G6-A8L7 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 
       46.16        70.13         0.53        49.08        37.15         4.50 
TCGA-A3-3347 TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       52.93        20.71        18.87        29.10       109.51        78.64 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        3.32         1.41         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4819 
       65.10         5.98        15.72         0.59        33.50         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 
       40.44        36.53        29.10        40.70        45.30        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 
       10.52        10.29        11.24        11.90         7.30        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5108 TCGA-B0-5109 
        8.05         2.24        21.86        52.08        58.59        19.30 
TCGA-B0-5400 TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4143 
       56.98        80.91       105.37        21.57         5.10        23.31 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-B8-A8YJ 
       25.55        40.04        27.02         0.53         4.93        14.17 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4343 
       89.36        23.05        64.27        53.42        93.99        62.86 
TCGA-BP-4345 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4781 
       49.84        11.31        33.99         5.98        10.82        68.38 
TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4985 
       15.78        10.98        47.97        71.41        46.45        31.30 
TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5196 
       18.51        28.87         6.35        79.30        30.64        33.47 
TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4873 
       19.82        46.55        73.22        21.24        47.18        74.27 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4901 
       66.21        61.91        51.52       115.69        39.45        47.67 
TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 
       49.97        54.48         3.06        18.81       131.08       133.71 
TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-6087 
       22.32        53.42        62.66         7.36        66.31         1.35 
TCGA-CW-6090 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5462 
       83.90        47.08        69.21         6.77        79.63        10.22 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-A4VX 
       69.96         1.94        31.10        67.96        65.65        53.46 
TCGA-EU-5905 
        3.91 

$subtype5
TCGA-CJ-4636 TCGA-MM-A84U TCGA-A3-3317 TCGA-A3-3357 TCGA-AK-3451 TCGA-B0-4691 
       63.25        23.01        49.02        88.37        94.29         4.57 
TCGA-B0-4713 TCGA-B0-5075 TCGA-B0-5092 TCGA-B0-5107 TCGA-B0-5709 TCGA-B4-5838 
        6.64        20.94        15.09        30.48       130.65         5.46 
TCGA-B8-5550 TCGA-B8-A54D TCGA-B8-A54G TCGA-BP-4163 TCGA-BP-4337 TCGA-BP-4346 
       48.53        27.29         1.74        93.34         0.07        49.08 
TCGA-BP-4771 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-5174 
        5.33        36.39        87.45        58.68        48.89        74.20 
TCGA-CJ-4638 TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4884 TCGA-CJ-4900 TCGA-CJ-5677 
       14.17        54.61        83.97        57.83        56.35        25.71 
TCGA-CJ-5680 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-G6-A5PC 
       25.25        18.77       107.41        58.82         7.96 

$subtype6
TCGA-A3-3328 TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-BP-4995 TCGA-DV-5567 
       45.53        15.42        77.62        20.38        45.07        65.88 
TCGA-DV-5576 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
       23.90        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-BP-4177 TCGA-BP-4334 
       32.61        30.21         5.75        17.19        54.90        21.21 
TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4994 TCGA-DV-A4VZ 
       61.68        60.95        43.00        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 
  35.705   37.365   48.100   33.500   48.530   44.135 
[1] "0.1 - 126.0 (35.7)" "0.5 - 129.4 (37.4)" "0.1 - 149.2 (48.1)"
[4] "0.5 - 133.7 (33.5)" "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      61       12        24       20
  subtype2      26        4         2        3
  subtype3     117       19        35       13
  subtype4      37       13        46       36
  subtype5       5        5        14       11
  subtype6      21        4         2        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         61       26      117       37        5       21
  STAGE II        12        4       19       13        5        4
  STAGE III       24        2       35       46       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 
      11        7       17       13        1        4 
 [1] "subtype4" "subtype3" "subtype1" "subtype1" "subtype2" "subtype6"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype6"
[13] "subtype1" "subtype4" "subtype1" "subtype3" "subtype3" "subtype3"
[19] "subtype4" "subtype1" "subtype3" "subtype2" "subtype3" "subtype6"
[25] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[31] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
[37] "subtype1" "subtype4" "subtype3" "subtype1" "subtype3" "subtype4"
[43] "subtype3" "subtype4" "subtype6" "subtype3" "subtype4" "subtype3"
[49] "subtype1" "subtype1" "subtype3" "subtype2"
D8V9, continuous
D8V10, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        1        2        3        3 
[1] "subtype1" "subtype4" "subtype5" "subtype4" "subtype5" "subtype1" "subtype4"
[8] "subtype5" "subtype1"
          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  70  20
  subtype2  35  23
  subtype3 144  42
  subtype4  58  63
  subtype5  35  24
subtype1 subtype2 subtype3 subtype4 subtype5 
      90       58      186      121       59 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       23       42       63       24 
$subtype1
TCGA-AK-3425 TCGA-B0-5691 TCGA-B0-5812 TCGA-B8-A54H TCGA-BP-4160 TCGA-BP-4331 
      109.91       112.80       126.05         8.42        94.72        80.68 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 
       12.33        77.62        44.15        20.38         6.94        61.51 
TCGA-BP-4986 TCGA-BP-5181 TCGA-DV-5573 TCGA-DV-5575 TCGA-G6-A8L7 TCGA-3Z-A93Z 
       25.81        49.15        37.15        56.84        70.13        12.66 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3349 
       11.90         0.53        24.16        49.08        52.93        45.53 
TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NN TCGA-A3-A8CQ 
       51.25        53.29        20.28        33.47         0.10         0.10 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4811 
       72.89        12.13         3.32        65.10         5.98        46.59 
TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5095 TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5119 
       70.52        11.24         8.05        62.89        58.59        51.02 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B4-5838 TCGA-B8-5545 TCGA-B8-5550 
       71.41       130.65        79.89         5.46        50.14        48.53 
TCGA-B8-5552 TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4167 TCGA-BP-4337 TCGA-BP-4341 
       34.39        16.27        14.17        89.36         0.07        52.24 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4804 
       71.80        61.68        10.82        36.53        36.95        47.97 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4989 TCGA-BP-5170 
       58.98        14.24        48.89        49.38         3.88        79.30 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5196 TCGA-BP-5200 
        9.63        38.30        37.25        22.78        33.47        34.95 
TCGA-CJ-4634 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4905 
      115.00        61.91        64.18        63.98       115.69        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5680 TCGA-CW-5583 
       49.28        50.33         3.06       131.08        25.25        81.83 
TCGA-CW-5588 TCGA-CW-6088 TCGA-CZ-5456 TCGA-CZ-5988 TCGA-G6-A8L8 TCGA-MM-A563 
       66.31       105.93        79.63        22.78        35.87        19.43 

$subtype2
TCGA-B0-5088 TCGA-B2-5635 TCGA-B8-4621 TCGA-BP-4342 TCGA-BP-4782 TCGA-BP-5178 
       18.51        24.82        25.91        74.17        11.64        62.86 
TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CZ-4854 TCGA-CZ-4865 TCGA-DV-A4W0 TCGA-MM-A84U 
       63.25        26.93        46.16         5.46        81.21        23.01 
TCGA-A3-3317 TCGA-AK-3451 TCGA-B0-4691 TCGA-B0-4713 TCGA-B0-4827 TCGA-B0-5077 
       49.02        94.29         4.57         6.64        29.10        43.30 
TCGA-B0-5707 TCGA-B2-3923 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54I 
      123.09        32.61        27.29        29.88         1.74         4.93 
TCGA-BP-4173 TCGA-BP-4346 TCGA-BP-4771 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       62.24        49.08         5.33        15.78        36.39        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4977 
       71.41        63.62        58.68         6.74        57.40        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4998 TCGA-BP-5008 TCGA-CJ-4638 TCGA-CJ-4640 
       36.07        33.34        30.64        35.21        14.17       114.41 
TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4900 TCGA-CJ-5677 
       54.61        83.97        66.21        30.64        56.35        25.71 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5466 
       53.42        62.66        47.08       107.41        58.82        22.52 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-A4VX TCGA-G6-A5PC 
       67.96        65.65        53.46         7.96 

$subtype3
TCGA-A3-3307 TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5693 
       47.21        42.97        58.49        28.73        22.45       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4327 
       15.78        70.68       119.38       111.02        32.61         3.58 
TCGA-BP-4775 TCGA-BP-4976 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5168 TCGA-BP-5201 
       60.59        53.65         5.82        45.07        48.10        31.27 
TCGA-CJ-4904 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-DV-5565 TCGA-DV-5566 
      108.56       103.43         0.59       107.54        43.69        45.96 
TCGA-DV-5569 TCGA-A3-3311 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       11.67        39.16        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3351 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       37.38        48.82        29.92        74.63        74.76        24.16 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8OV TCGA-A3-A8OW 
       28.31        65.52        15.39        22.65        11.18        10.62 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3460 TCGA-B0-4693 
      122.56       109.41        68.61        48.36        82.45         2.53 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 
        2.14        57.70         3.25        16.77        54.48        78.44 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       27.42        53.88         6.71        65.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
        2.27        36.85        25.32        15.95        90.87        90.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5399 
       66.05        38.63        52.73        41.88        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5700 
       42.41       111.52       129.67        86.47       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-B2-5633 TCGA-B2-5639 TCGA-B4-5377 
       31.96        21.30        31.30        31.66        32.98        12.00 
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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 
       25.05        45.37        50.14        23.74         0.85        16.60 
TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 
        6.38        14.30        17.36        90.28       101.06        99.85 
TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4347 TCGA-BP-4758 
       97.45        62.07        15.62        18.48        44.94        72.59 
TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4973 TCGA-BP-4975 
       77.98        48.07        13.15        13.51        45.50        47.11 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       36.95        46.45        16.47        38.70        37.02        37.48 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 
        2.04        74.20        52.27        42.44        37.22        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5202 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 
       23.47        13.41         0.95       106.16        58.95        11.05 
TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4892 TCGA-CJ-4893 
       49.25       116.84        71.87       113.46        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4920 
      109.84        50.24        51.29        54.48        45.14         4.57 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       72.00       129.40        18.87        62.10        73.35        67.00 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CZ-4853 
      119.64        92.02         5.39        85.78        73.18        25.45 
TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       58.75        63.39        93.04        63.42        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 
       18.44        90.54        91.69        55.33        94.45        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 
       21.76        84.30        80.19        12.26        62.63        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 

$subtype4
TCGA-B0-4707 TCGA-B0-4815 TCGA-B8-5162 TCGA-BP-4799 TCGA-BP-4988 TCGA-BP-5009 
       19.73        52.21         1.18        37.25        27.22        35.90 
TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       27.02        31.79        27.65        53.26       118.85        75.58 
TCGA-DV-5567 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3357 TCGA-A3-3363 TCGA-A3-3374 
       65.88        37.15         4.50        88.37        10.49        43.20 
TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 
       20.71        18.87        29.10       117.80        15.78       112.08 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        40.01        83.21 
TCGA-AK-3456 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       37.58        40.70         1.41        19.00         1.38         3.62 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4828 
       58.45         0.59        33.50         6.02        40.44        10.09 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-5075 TCGA-B0-5081 
       68.71        45.30        56.68        10.29        20.94        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       34.36         7.30        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-B0-5701 TCGA-B0-5706 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 
       80.91       105.37         1.68        21.57         5.10         0.53 
TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5551 TCGA-BP-4163 
       23.31        17.19        25.55        40.04         0.53        93.34 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4343 
       61.78        64.27        53.42        21.21        93.99        62.86 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4777 
       11.31        33.99        12.30         5.98        41.75        56.91 
TCGA-BP-4781 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4983 TCGA-BP-4985 
       68.38        10.98         6.71        60.30        46.45        31.30 
TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5195 
       43.00        18.51         6.35        30.64        74.40        24.62 
TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4884 
       19.82        46.55        73.22        74.27        64.27        57.83 
TCGA-CJ-4888 TCGA-CJ-4895 TCGA-CJ-4901 TCGA-CJ-4923 TCGA-CJ-5679 TCGA-CJ-5681 
       51.52        39.45        47.67        18.81        22.32        18.15 
TCGA-CJ-6033 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
        7.36        35.34        74.66         1.35        83.90        18.77 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.21         6.77        14.66         1.94        31.10        12.69 
TCGA-CZ-5987 
       14.63 

$subtype5
TCGA-B0-4712 TCGA-B8-A54K TCGA-BP-4344 TCGA-BP-5199 TCGA-CJ-4642 TCGA-DV-5568 
       43.96        15.42        54.77        44.55       105.37        12.16 
TCGA-DV-5574 TCGA-DV-5576 TCGA-A3-3365 TCGA-A3-3376 TCGA-A3-3380 TCGA-AK-3431 
       66.28        23.90        28.70        55.76        18.64        73.68 
TCGA-AK-3458 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4701 TCGA-B0-4810 TCGA-B0-4814 
       38.40         3.48        28.47         7.82        15.72         5.52 
TCGA-B0-4816 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-4843 TCGA-B0-4848 
       45.07        36.53        14.93        40.70        10.52        29.03 
TCGA-B0-5120 TCGA-B0-5696 TCGA-B2-5636 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 
       38.43        85.78        30.21        16.67         5.75         1.25 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-A54F TCGA-BP-4159 TCGA-BP-4166 TCGA-BP-4169 
       27.02        24.23        17.06        85.51         0.43        23.05 
TCGA-BP-4177 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4345 TCGA-BP-4351 TCGA-BP-4355 
       54.90        27.78        37.25        49.84        31.89        31.33 
TCGA-BP-4789 TCGA-BP-4974 TCGA-BP-5010 TCGA-BP-5187 TCGA-CJ-4871 TCGA-CJ-4872 
       48.95         6.94        28.87        13.35        79.66        47.18 
TCGA-CJ-4902 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5580 TCGA-CW-5589 TCGA-CZ-5461 
       49.97       133.71       122.83        64.57        78.18        10.85 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-MM-A564 
       69.96         2.40        12.00         3.91        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     1.74     0.23     0.53     0.43 
subtype1 subtype2 subtype3 subtype4 subtype5 
  131.08   123.09   149.16   118.85   133.71 
subtype1 subtype2 subtype3 subtype4 subtype5 
  48.710   39.845   45.255   31.790   29.030 
[1] "0.1 - 131.1 (48.7)" "1.7 - 123.1 (39.8)" "0.2 - 149.2 (45.3)"
[4] "0.5 - 118.8 (31.8)" "0.4 - 133.7 (29.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      59        4        18        9
  subtype2      23        9        13       13
  subtype3     105       19        39       24
  subtype4      42       15        36       27
  subtype5      24        8        17       10
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         59       23      105       42       24
  STAGE II         4        9       19       15        8
  STAGE III       18       13       39       36       17
  STAGE IV         9       13       24       27       10
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  61   4  23   3
  subtype2  24  11  22   1
  subtype3 106  25  55   1
  subtype4  43  19  54   5
  subtype5  25   8  25   1
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       61       24      106       43       25
  T2        4       11       25       19        8
  T3       23       22       55       54       25
  T4        3        1        1        5        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 39  3
  subtype2 27  3
  subtype3 79  1
  subtype4 57  9
  subtype5 26  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    3
  subtype2   27    3
  subtype3   79    1
  subtype4   57    9
  subtype5   26    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       39       27       79       57       26
  1        3        3        1        9        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1  73   7
  subtype2  39  12
  subtype3 155  22
  subtype4  94  27
  subtype5  45  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    7
  subtype2   39   12
  subtype3  155   22
  subtype4   94   27
  subtype5   45   10
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       73       39      155       94       45
  1        7       12       22       27       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  35  56
  subtype2  16  42
  subtype3  83 104
  subtype4  34  87
  subtype5  13  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   56
  subtype2   16   42
  subtype3   83  104
  subtype4   34   87
  subtype5   13   46
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       35       16       83       34       13
  MALE         56       42      104       87       46
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        7        5        2        2 
 [1] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
D9V10, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        3        3        2        1 
[1] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
[8] "subtype1" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        18    72
  subtype2     1                         9    46
  subtype3     2                        16   166
  subtype4     4                         6   110
  subtype5     0                         7    51
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        2        4        0
  BLACK OR AFRICAN AMERICAN       18        9       16        6        7
  WHITE                           72       46      166      110       51
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus         0   1
  subtype1   3  57
  subtype2   3  36
  subtype3  11 126
  subtype4   4  84
  subtype5   3  42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   57
  subtype2    3   36
  subtype3   11  126
  subtype4    4   84
  subtype5    3   42
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        3       11        4        3
  NOT HISPANIC OR LATINO       57       36      126       84       42
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  99  75
  subtype2 161  48
  subtype3  82  49
subtype1 subtype2 subtype3 
     174      209      131 
subtype1 subtype2 subtype3 
      75       48       49 
$subtype1
TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
      109.91        19.73        43.96        52.21        18.51       112.80 
TCGA-B0-5812 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4342 
      126.05         1.18         8.42        15.42        94.72        74.17 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       12.33        77.62        44.15        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-4988 TCGA-CJ-4642 TCGA-CJ-5689 
        6.94        61.51        25.81        27.22       105.37        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5567 
      118.85        75.58        46.16         5.46        43.69        65.88 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-3Z-A93Z 
       37.15        66.28        56.84        23.90        70.13        12.66 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3362 
       11.90         0.53        49.08        49.02        52.93        51.25 
TCGA-A3-3376 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 
       55.76        18.87        29.10        73.68       109.51        78.64 
TCGA-AK-3461 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       72.89         3.32         1.41         4.57         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 
        1.38        65.10         5.98        15.72         0.59        45.07 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4836 
        6.02        40.44        36.53        14.93        29.10        40.70 
TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5080 
       45.30        10.52        10.29        29.03        70.52        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       11.90         7.30         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 
       62.89        58.59        19.30        51.02        38.43        56.98 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B2-5636 TCGA-B2-5641 TCGA-B4-5378 
       71.41       130.65        79.89        30.21        21.57         5.75 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 
        5.46        23.31        25.55        27.02        50.14        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4169 
        0.53        34.39        17.06         4.93        14.17        23.05 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4337 TCGA-BP-4343 TCGA-BP-4345 
       62.24        54.90        53.42         0.07        62.86        49.84 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 
       11.31        33.99        31.33        41.75        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       10.82        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 
       36.95        47.97        87.45        71.41         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 
       14.24        48.89        49.38        46.45        31.30         3.88 
TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5182 
       30.64        35.21        28.87         6.35        79.30        38.30 
TCGA-BP-5187 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4871 
       13.35        33.47        19.82        46.55        73.22        79.66 
TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4895 
       47.18        66.21        61.91        63.98       115.69        39.45 
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-4923 TCGA-CJ-5671 TCGA-CJ-5679 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 
       18.81       131.08        22.32        62.66         7.36        66.31 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
        1.35        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-MM-A563 
       79.63        69.96        22.78        12.00         3.91        19.43 

$subtype2
TCGA-A3-3307 TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5693 
       47.21        42.97        58.49        28.73        22.45       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4327 
       15.78        70.68       119.38        24.82       111.02         3.58 
TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4775 TCGA-BP-4976 TCGA-BP-4995 TCGA-BP-5168 
       80.68        54.77        60.59        53.65        45.07        48.10 
TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4894 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       49.15        44.55        27.65       103.43         0.59       107.54 
TCGA-DV-5566 TCGA-DV-5569 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 
       45.96        11.67        39.16        24.16        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3365 
       36.36        38.99        37.38        45.53        29.92        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       74.63        74.76        53.29        18.64        28.31        65.52 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3460 TCGA-B0-4693 
      122.56       109.41        68.61        48.36        82.45         2.53 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 
        7.82         2.14        57.70         3.25        46.59         5.52 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4846 
       16.77        54.48        78.44         6.71        65.29        39.45 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5085 TCGA-B0-5099 TCGA-B0-5102 
        2.27        36.85        43.30        25.32        15.95        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 
       90.48        52.54        66.05        38.63        52.73        48.82 
TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 
       46.39       111.52       129.67       126.28        58.85       149.16 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
      131.15        89.49        91.46        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 
       31.30        31.66        16.67        12.00         1.25         4.64 
TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.36        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J 
       23.74         0.85        24.23         6.38        14.30        17.36 
TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 
       16.27        85.51       101.06        99.85         0.43        61.78 
TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4347 TCGA-BP-4351 
       97.45        62.07        18.48        52.24        44.94        31.89 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4776 TCGA-BP-4781 
       72.59        77.98        48.07        13.15        13.51        68.38 
TCGA-BP-4961 TCGA-BP-4969 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       63.62        58.98         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5001 TCGA-BP-5004 
       33.34        36.95        46.45        16.47        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5183 
       37.48         2.04        74.20        52.27         9.63        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 
       37.25        37.22        22.78        23.47        13.41        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 
        0.95       115.00       106.16        58.95        11.05        49.25 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 
       64.27        71.87       113.46        64.18        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4920 
      109.84        50.24        51.29        54.48        45.14         4.57 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       72.00       129.40       133.71       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       67.00       119.64        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 
       78.18       105.93        25.45        58.75        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
       63.42        79.53        18.44        90.54        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       10.85        10.22        21.76        84.30         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       12.26        62.63        18.12         6.77         4.18        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.96        16.37        11.70 

$subtype3
TCGA-B8-4621 TCGA-BP-4164 TCGA-BP-4993 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5189 
       25.91        32.61         5.82        35.90        62.86        27.02 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4904 TCGA-DV-5568 
       31.79        31.27        63.25        26.93       108.56        12.16 
TCGA-DV-A4W0 TCGA-MM-A84U TCGA-A3-3319 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3357 
       81.21        23.01        37.15        48.82         4.50        88.37 
TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3387 TCGA-A3-A6NN 
       10.49        24.16        43.20        20.71        20.28         0.10 
TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
      117.80        15.78       112.08        94.19        46.78        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 
       94.29        83.21        37.58        38.40        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4817 TCGA-B0-4828 
       28.47         3.62         6.64        58.45        33.50        10.09 
TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-5075 
       68.71        27.42        53.88        56.68        26.07        20.94 
TCGA-B0-5083 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5117 
       34.36        15.09        10.95        30.48        41.88        52.87 
TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5706 
       42.41        85.78        86.47        80.91        73.84       105.37 
TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 
      123.09        32.61         1.68        32.98         5.10         0.53 
TCGA-B4-5844 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5546 TCGA-B8-A54D 
        0.23        17.19        50.14        40.04        16.60        27.29 
TCGA-B8-A54E TCGA-B8-A54G TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4176 
       29.88         1.74        90.28        93.34        89.36        64.27 
TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4346 
       27.78        37.25        21.21        15.62        93.99        49.08 
TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4803 TCGA-BP-4962 
       12.30         5.98         5.33        56.91         6.71        58.68 
TCGA-BP-4963 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5175 TCGA-BP-5180 
       60.30        45.50        43.00        18.51        30.64        74.40 
TCGA-BP-5190 TCGA-BP-5195 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 
       33.24        24.62        14.17       114.41        54.61        83.97 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4900 
       74.27       116.84        57.83        30.64        51.52        56.35 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-6028 TCGA-CW-5580 
       25.71        18.87        25.25        18.15        53.42        64.57 
TCGA-CW-5581 TCGA-CW-5590 TCGA-CW-5591 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5452 
       92.02        35.34        74.66        14.66       107.41        58.82 
TCGA-CZ-5454 TCGA-CZ-5458 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       23.74        91.69        22.52         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-G6-A5PC 
       67.96        65.65        14.63        53.46         7.96 

subtype1 subtype2 subtype3 
    0.07     0.10     0.10 
subtype1 subtype2 subtype3 
  131.08   149.16   123.09 
subtype1 subtype2 subtype3 
   37.20    45.07    35.34 
[1] "0.1 - 131.1 (37.2)" "0.1 - 149.2 (45.1)" "0.1 - 123.1 (35.3)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      80       14        48       31
  subtype2     125       24        42       19
  subtype3      48       17        33       33
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         80      125       48
  STAGE II        14       24       17
  STAGE III       48       42       33
  STAGE IV        31       19       33
[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  82  17  69   7
  subtype2 127  28  54   1
  subtype3  50  22  56   3
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       82      127       50
  T2       17       28       22
  T3       69       54       56
  T4        7        1        3
[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"
D10V5, binary
          cls
clus        0  1
  subtype1 77 10
  subtype2 88  1
  subtype3 63  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   10
  subtype2   88    1
  subtype3   63    6
   clus
vv  subtype1 subtype2 subtype3
  0       77       88       63
  1       10        1        6
[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"
D10V6, binary
          cls
clus         0   1
  subtype1 136  29
  subtype2 177  18
  subtype3  93  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  136   29
  subtype2  177   18
  subtype3   93   31
   clus
vv  subtype1 subtype2 subtype3
  0      136      177       93
  1       29       18       31
[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"
D10V7, binary
          cls
clus         0   1
  subtype1  52 123
  subtype2  92 118
  subtype3  37  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52  123
  subtype2   92  118
  subtype3   37   94
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       52       92       37
  MALE        123      118       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        20   150
  subtype2     2                        21   183
  subtype3     2                        15   112
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        2        2
  BLACK OR AFRICAN AMERICAN       20       21       15
  WHITE                          150      183      112
[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"
D10V12, binary
          cls
clus         0   1
  subtype1   6 117
  subtype2  14 133
  subtype3   4  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  117
  subtype2   14  133
  subtype3    4   95
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       14        4
  NOT HISPANIC OR LATINO      117      133       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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 29  8
  subtype2 18  4
  subtype3 34 11
  subtype4 17 21
subtype1 subtype2 subtype3 subtype4 
      37       22       45       38 
subtype1 subtype2 subtype3 subtype4 
       8        4       11       21 
$subtype1
TCGA-B2-5635 TCGA-B8-A54H TCGA-B8-A54K TCGA-CZ-4854 TCGA-MM-A84U TCGA-3Z-A93Z 
       24.82         8.42        15.42        46.16        23.01        12.66 
TCGA-6D-AA2E TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       11.90        33.47        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-5633 
       10.62        94.19        12.13        32.61        35.90        31.66 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4340 TCGA-BP-4804 TCGA-BP-4961 
       17.36        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-CZ-4857 
       36.07        33.34        49.25       116.84        66.21        47.08 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-T7-A92I 
       11.70 

$subtype2
TCGA-B0-5691 TCGA-BP-4807 TCGA-A3-3317 TCGA-A3-3387 TCGA-B0-4811 TCGA-B0-5080 
      112.80         6.94        49.02        20.28        46.59        11.24 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B2-5636 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 
       71.41       130.65        30.21        50.14        48.53        34.39 
TCGA-B8-A8YJ TCGA-BP-4770 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4970 TCGA-BP-5008 
       14.17        10.82        48.95        36.53        14.24        35.21 
TCGA-CJ-4889 TCGA-CJ-5671 TCGA-CJ-6031 TCGA-EU-5904 
       63.98       131.08        62.66        18.12 

$subtype3
TCGA-A3-3358 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-BP-4976 TCGA-BP-4995 
       42.97       133.94        15.78        70.68        53.65        45.07 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 TCGA-AK-3458 TCGA-B0-4706 
       43.69        45.96        11.67        37.15        38.40         2.14 
TCGA-B0-4710 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5696 
       57.70        36.85        25.32        46.39       129.67        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-5001 TCGA-CJ-4878 TCGA-CJ-4887 
       14.30        58.98         6.94        38.70        71.87        30.64 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5683 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 
      129.40       133.71        62.10       119.64        85.78        78.18 
TCGA-CW-6088 TCGA-CZ-4864 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 
      105.93        93.04        79.53        18.44        90.54        55.33 
TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5989 
       21.76         2.40        62.63 

$subtype4
TCGA-B0-4712 TCGA-B0-5088 TCGA-B8-4621 TCGA-BP-4988 TCGA-BP-5009 TCGA-G6-A8L7 
       43.96        18.51        25.91        27.22        35.90        70.13 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4810 TCGA-B0-4821 TCGA-B0-4836 TCGA-B0-4837 
        1.38        65.10        15.72        40.44        40.70        45.30 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4761 TCGA-BP-4787 TCGA-BP-4959 TCGA-BP-4967 
        0.53         4.93         5.98        15.78        87.45         6.74 
TCGA-BP-4968 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-CJ-4876 
       57.40        31.30         3.88        16.47        30.64        64.27 
TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CW-6087 
      115.69        39.45        56.35        18.15        67.00         1.35 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5454 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 
       69.21         6.77        23.74        10.22        69.96        22.52 
TCGA-CZ-5469 TCGA-CZ-5470 
       31.10        12.69 

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 
   22.65    41.56    53.65    28.93 
[1] "0.1 - 116.8 (22.6)" "6.9 - 131.1 (41.6)" "2.1 - 149.2 (53.6)"
[4] "0.5 - 115.7 (28.9)"
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      25        5         4        4
  subtype2      15        1         4        2
  subtype3      21        7        11        6
  subtype4      13        4         7       14
D11V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         25       15       21       13
  STAGE II         5        1        7        4
  STAGE III        4        4       11        7
  STAGE IV         4        2        6       14
[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 26  6  7  0
  subtype2 16  1  4  1
  subtype3 21  7 17  0
  subtype4 14  5 15  4
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       26       16       21       14
  T2        6        1        7        5
  T3        7        4       17       15
  T4        0        1        0        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2  9  1
  subtype3 22  0
  subtype4 17  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2    9    1
  subtype3   22    0
  subtype4   17    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        8        9       22       17
  1        0        1        0        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 16  3
  subtype2 20  1
  subtype3 39  6
  subtype4 23 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    3
  subtype2   20    1
  subtype3   39    6
  subtype4   23   13
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       16       20       39       23
  1        3        1        6       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"
D11V7, binary
          cls
clus        0  1
  subtype1 17 22
  subtype2  7 15
  subtype3 18 27
  subtype4  8 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   22
  subtype2    7   15
  subtype3   18   27
  subtype4    8   30
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17        7       18        8
  MALE         22       15       27       30
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 subtype4 
       8        1        8        4 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype4"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype3" "subtype4" "subtype4" "subtype3" "subtype4" "subtype1"
[19] "subtype1" "subtype1"
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    15
  subtype2     1                         2    18
  subtype3     0                         0    45
  subtype4     2                         4    30
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        2
  BLACK OR AFRICAN AMERICAN       24        2        0        4
  WHITE                           15       18       45       30
[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 33
  subtype2  1 12
  subtype3  4 35
  subtype4  1 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    1   12
  subtype3    4   35
  subtype4    1   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        4        1
  NOT HISPANIC OR LATINO       33       12       35       24
[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 30  9
  subtype2 31 21
  subtype3 20  8
  subtype4 17  6
subtype1 subtype2 subtype3 subtype4 
      39       52       28       23 
subtype1 subtype2 subtype3 subtype4 
       9       21        8        6 
$subtype1
TCGA-B2-5635 TCGA-B8-A54H TCGA-B8-A54K TCGA-CZ-4854 TCGA-G6-A8L7 TCGA-MM-A84U 
       24.82         8.42        15.42        46.16        70.13        23.01 
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-B2-5636 TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4173 
       31.66        30.21         4.93        17.36        16.27        62.24 
TCGA-BP-4340 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4981 TCGA-BP-4982 TCGA-CJ-4870 
       18.48        47.97        63.62        36.07        33.34        49.25 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4900 TCGA-CZ-4857 TCGA-G6-A5PC TCGA-G6-A8L6 
      116.84        66.21        56.35        47.08         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-T7-A92I 
       35.87         2.01        11.70 

$subtype2
TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-BP-4807 TCGA-BP-4988 TCGA-BP-4995 
       43.96        18.51       112.80         6.94        27.22        45.07 
TCGA-DV-5573 TCGA-A3-3317 TCGA-A3-3387 TCGA-AK-3458 TCGA-B0-4698 TCGA-B0-4700 
       37.15        49.02        20.28        38.40         1.38        65.10 
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-B0-5399 TCGA-B0-5702 TCGA-B0-5709 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 
       46.39        71.41       130.65        50.14        48.53         0.53 
TCGA-B8-5552 TCGA-B8-A8YJ TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4789 
       34.39        14.17         5.98        10.82        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4959 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4974 
       36.53        87.45         6.74        57.40        14.24         6.94 
TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 TCGA-CJ-4889 TCGA-CJ-4890 
       31.30         3.88        30.64        35.21        63.98       115.69 
TCGA-CJ-4895 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6031 TCGA-CW-6087 TCGA-CZ-4858 
       39.45       131.08       133.71        62.66         1.35        69.21 
TCGA-CZ-4860 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-MM-A563 
        6.77        69.96        31.10        19.43 

$subtype3
TCGA-A3-3358 TCGA-B8-4621 TCGA-BP-4976 TCGA-BP-5009 TCGA-DV-5569 TCGA-B0-4710 
       42.97        25.91        53.65        35.90        11.67        57.70 
TCGA-B0-4852 TCGA-B0-5692 TCGA-B0-5699 TCGA-B2-5639 TCGA-B4-5377 TCGA-B8-5553 
       36.85       129.67       126.28        32.98        12.00        14.30 
TCGA-BP-4992 TCGA-BP-5001 TCGA-CJ-4876 TCGA-CJ-4887 TCGA-CJ-5675 TCGA-CJ-5681 
       16.47        38.70        64.27        30.64       129.40        18.15 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CZ-4864 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5459 
       67.00       119.64        93.04        23.74        90.54        55.33 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5470 TCGA-CZ-5989 
       10.22        21.76        12.69        62.63 

$subtype4
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-DV-5565 TCGA-DV-5566 TCGA-B0-4706 
      133.94        15.78        70.68        43.69        45.96         2.14 
TCGA-B0-5085 TCGA-B0-5696 TCGA-B0-5700 TCGA-B0-5705 TCGA-B4-5836 TCGA-BP-4969 
       25.32        85.78        58.85       149.16         4.64        58.98 
TCGA-CJ-4878 TCGA-CJ-5683 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-5453 
       71.87        62.10        85.78        78.18       105.93        79.53 
TCGA-CZ-5455 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-EU-5904 TCGA-MM-A564 
       18.44        22.52         2.40        18.12        19.96 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.53    10.22     2.14 
subtype1 subtype2 subtype3 subtype4 
  116.84   133.71   129.67   149.16 
subtype1 subtype2 subtype3 subtype4 
  24.820   37.775   37.775   58.850 
[1] "0.1 - 116.8 (24.8)"  "0.5 - 133.7 (37.8)"  "10.2 - 129.7 (37.8)"
[4] "2.1 - 149.2 (58.9)" 
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      28        4         4        5
  subtype2      24        3        11       13
  subtype3      10        8         4        6
  subtype4      12        2         7        2
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         28       24       10       12
  STAGE II         4        3        8        2
  STAGE III        4       11        4        7
  STAGE IV         5       13        6        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 29  5  6  1
  subtype2 25  3 20  4
  subtype3 11  9  8  0
  subtype4 12  2  9  0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       29       25       11       12
  T2        5        3        9        2
  T3        6       20        8        9
  T4        1        4        0        0
[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"
D12V5, binary
          cls
clus        0  1
  subtype1  9  1
  subtype2 24  4
  subtype3 13  0
  subtype4 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    1
  subtype2   24    4
  subtype3   13    0
  subtype4   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        9       24       13       10
  1        1        4        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
          cls
clus        0  1
  subtype1 17  4
  subtype2 39 11
  subtype3 22  6
  subtype4 20  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    4
  subtype2   39   11
  subtype3   22    6
  subtype4   20    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       17       39       22       20
  1        4       11        6        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1 19 22
  subtype2  9 43
  subtype3 12 16
  subtype4 10 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   22
  subtype2    9   43
  subtype3   12   16
  subtype4   10   13
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19        9       12       10
  MALE         22       43       16       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"
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       6        3        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[8] "subtype2" "subtype1"
D12V10, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 
       5        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        24    17
  subtype2     3                         4    44
  subtype3     0                         1    26
  subtype4     0                         1    21
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        3        0        0
  BLACK OR AFRICAN AMERICAN       24        4        1        1
  WHITE                           17       44       26       21
[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"
D12V12, binary
          cls
clus        0  1
  subtype1  0 35
  subtype2  2 32
  subtype3  2 19
  subtype4  2 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   35
  subtype2    2   32
  subtype3    2   19
  subtype4    2   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        2        2
  NOT HISPANIC OR LATINO       35       32       19       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
