[1] "ofn"        "-oTLUSC-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/LUSC-TP/22506957/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/22552638/LUSC-TP.mergedcluster.txt"

nPatients in clinical file=504, in cluster file=504, common to both=504
[1]  12 504
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
41 50 34 29 
 1  2  3  4 
41 50 34 29 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
47 56 51 
 1  2  3 
47 56 51 
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5   6 
 43 115  29  87 169  58 
  1   2   3   4   5   6 
 43 115  29  87 169  58 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
 90  96  58 126 
  1   2   3   4 
 90  96  58 126 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
105 110  86  27 
  1   2   3   4 
105 110  86  27 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
79 68 62 60 31 28 
 1  2  3  4  5  6 
79 68 62 60 31 28 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
106 151 160  84 
  1   2   3   4 
106 151 160  84 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
179 191 131 
  1   2   3 
179 191 131 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
185  88 125  80 
  1   2   3   4 
185  88 125  80 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 89 118 201  70 
  1   2   3   4 
 89 118 201  70 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 61 116  67  93 
  1   2   3   4 
 61 116  67  93 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 37 190 110 
  1   2   3 
 37 190 110 
[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] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 504 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=203,	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=255,	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=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	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=21,	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=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=105,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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 504 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=45, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
114 295  71  24 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
114 295  71  24 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
114 295  71  24 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
114 295  71  24 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
320 133  40   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
320 133  40   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
320 133  40   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
320 133  40   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=105, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
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 24 17
  subtype2 25 24
  subtype3 16 18
  subtype4 15 13
subtype1 subtype2 subtype3 subtype4 
      41       49       34       28 
subtype1 subtype2 subtype3 subtype4 
      17       24       18       13 
$subtype1
TCGA-18-3406 TCGA-33-4589 TCGA-34-2609 TCGA-60-2721 TCGA-18-3414 TCGA-18-3419 
       12.20         1.55        31.27        32.32        23.54        92.42 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       86.96       119.54        31.73       122.43         9.34       119.80 
TCGA-22-0944 TCGA-22-1011 TCGA-22-4595 TCGA-22-4607 TCGA-33-4547 TCGA-34-2600 
        7.33         1.74        24.13        19.30        79.53        61.61 
TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-39-5029 TCGA-43-3920 TCGA-56-1622 
       16.93         4.01         0.43        24.33        33.11        28.96 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 TCGA-66-2734 
       21.93        80.45        42.64         3.19        23.57        43.10 
TCGA-66-2742 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 
       21.07        25.05         0.99         2.01         2.01        19.00 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 
       19.00        12.03         3.98        12.00        22.98 

$subtype2
TCGA-18-3407 TCGA-18-3416 TCGA-33-4532 TCGA-34-2605 TCGA-60-2711 TCGA-18-3408 
        4.47        31.99       129.01        28.96        41.42        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4086 TCGA-21-1071 TCGA-21-1072 
      117.57        11.34        92.15         2.79        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       70.16        34.78        14.10        38.17        34.75        13.12 
TCGA-33-4538 TCGA-34-2596 TCGA-34-5240 TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 
       97.94         2.63        50.66       126.58        68.58        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-46-3765 TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 
       55.56        39.12        13.32         9.83         0.39         0.39 
TCGA-51-4081 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-66-2727 
       29.95        66.54        56.91        29.85        35.90        16.96 
TCGA-66-2737 TCGA-66-2758 TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        2.01        21.01         1.02        23.01         3.02         2.01 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       24.95        40.01         5.03        30.02        54.08         4.01 
TCGA-66-2800 
       49.05 

$subtype3
TCGA-18-3409 TCGA-22-1000 TCGA-22-1017 TCGA-34-2604 TCGA-60-2696 TCGA-60-2712 
      123.19        14.93        48.82        31.50         3.58         9.01 
TCGA-60-2715 TCGA-21-1076 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       35.34        60.89        21.99         4.31        64.21        27.02 
TCGA-22-4594 TCGA-22-4596 TCGA-33-4566 TCGA-34-2608 TCGA-37-3792 TCGA-39-5030 
       48.33         0.56       173.82        32.88         0.39         1.94 
TCGA-43-2576 TCGA-43-2581 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-60-2698 
       40.21        38.66        12.16        13.02         4.44        10.22 
TCGA-60-2706 TCGA-60-2714 TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       92.71        50.33        26.83         0.99         1.02         0.92 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2785 TCGA-66-2789 
        2.01         7.07         1.97         4.04 

$subtype4
TCGA-18-3410 TCGA-18-4083 TCGA-33-4533 TCGA-43-2578 TCGA-18-3417 TCGA-21-1078 
        4.80         6.18       133.74        22.49        36.07        15.58 
TCGA-21-1083 TCGA-22-4591 TCGA-22-4613 TCGA-33-4582 TCGA-37-4129 TCGA-37-4130 
       43.23        20.48        11.77       103.53         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5034 
        7.46         7.82         6.81         0.39       133.25        36.39 
TCGA-39-5035 TCGA-60-2695 TCGA-60-2716 TCGA-60-2726 TCGA-66-2754 TCGA-66-2756 
       68.38        21.11        48.49        11.77         2.01         0.99 
TCGA-66-2757 TCGA-66-2786 TCGA-66-2790 TCGA-66-2793 
       43.99        25.97        22.98        10.06 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.39     0.39     0.39 
subtype1 subtype2 subtype3 subtype4 
  122.43   129.01   173.82   133.74 
subtype1 subtype2 subtype3 subtype4 
  22.980   31.990   13.975   18.030 
[1] "0.4 - 122.4 (23.0)" "0.4 - 129.0 (32.0)" "0.4 - 173.8 (14.0)"
[4] "0.4 - 133.7 (18.0)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  subtype1        2       21         0         8          7          1        2
  subtype2        2       23         4         9          5          7        0
  subtype3        8       12         2         4          4          3        0
  subtype4       11        4         1         6          3          2        2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          2        2        8       11
  STAGE IB         21       23       12        4
  STAGE IIA         0        4        2        1
  STAGE IIB         8        9        4        6
  STAGE IIIA        7        5        4        3
  STAGE IIIB        1        7        3        2
  STAGE IV          2        0        0        2
[1] 7 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  4 30  6  1
  subtype2  4 39  1  6
  subtype3 11 19  2  2
  subtype4 11 12  3  3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        4        4       11       11
  T2       30       39       19       12
  T3        6        1        2        3
  T4        1        6        2        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 26 10  4  1
  subtype2 27 17  4  2
  subtype3 23  6  3  2
  subtype4 20  7  2  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       26       27       23       20
  N1       10       17        6        7
  N2        4        4        3        2
  N3        1        2        2        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"
D1V6, binary
          cls
clus        0  1
  subtype1 37  2
  subtype2 48  0
  subtype3 34  0
  subtype4 27  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    2
  subtype2   48    0
  subtype3   34    0
  subtype4   27    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       37       48       34       27
  1        2        0        0        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"
D1V7, binary
          cls
clus        0  1
  subtype1  9 32
  subtype2 12 38
  subtype3 11 23
  subtype4 12 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   32
  subtype2   12   38
  subtype3   11   23
  subtype4   12   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       12       11       12
  MALE         32       38       23       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1 27  4
  subtype2 34  4
  subtype3 20  3
  subtype4 20  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27    4
  subtype2   34    4
  subtype3   20    3
  subtype4   20    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        27       34       20       20
  YES        4        4        3        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"
D1V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     1
  subtype4                                     1
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      0
  subtype3                                      0
  subtype4                                      1
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          41
  subtype2                                                          47
  subtype3                                                          33
  subtype4                                                          27
D1V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       41       47
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       33       27
[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"
D1V11, continuous
D1V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 37  0  1  1
  subtype2 45  1  1  1
  subtype3 28  2  0  3
  subtype4 29  0  0  0
D1V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       37       45       28       29
  R1        0        1        2        0
  R2        1        1        0        0
  RX        1        1        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    24
  subtype2     1                         3    27
  subtype3     1                         1    24
  subtype4     0                         1    18
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        0
  BLACK OR AFRICAN AMERICAN        2        3        1        1
  WHITE                           24       27       24       18
[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"
D1V15, binary
          cls
clus        0  1
  subtype1  3 23
  subtype2  1 25
  subtype3  0 23
  subtype4  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   23
  subtype2    1   25
  subtype3    0   23
  subtype4    0   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        0        0
  NOT HISPANIC OR LATINO       23       25       23       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"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 23 23
  subtype2 29 26
  subtype3 28 23
subtype1 subtype2 subtype3 
      46       55       51 
subtype1 subtype2 subtype3 
      23       26       23 
$subtype1
TCGA-18-3406 TCGA-33-4589 TCGA-60-2696 TCGA-60-2721 TCGA-18-3414 TCGA-18-3417 
       12.20         1.55         3.58        32.32        23.54        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       92.42        86.96       119.54        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4607 
        9.34       119.80         1.74        20.48        24.13        19.30 
TCGA-22-4613 TCGA-33-4547 TCGA-33-4582 TCGA-34-2600 TCGA-34-5241 TCGA-37-3783 
       11.77        79.53       103.53        61.61        16.93         4.01 
TCGA-37-3789 TCGA-39-5029 TCGA-43-3920 TCGA-56-1622 TCGA-60-2707 TCGA-60-2708 
        0.43        24.33        33.11        28.96        21.93        80.45 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2724 TCGA-60-2726 TCGA-66-2734 TCGA-66-2742 
       48.49        42.64        23.57        11.77        43.10        21.07 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 
        0.99         2.01         2.01        19.00        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2793 
        3.98        12.00        22.98        10.06 

$subtype2
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-33-4532 TCGA-34-2605 TCGA-60-2711 
        4.47        31.99         6.18       129.01        28.96        41.42 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4086 TCGA-21-1071 
       75.75       117.57        11.34        92.15         2.79        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-22-0944 TCGA-22-1012 
       99.16        70.16        60.89        34.78         7.33        14.10 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-33-4538 TCGA-34-2596 TCGA-34-5240 
       38.17        34.75        13.12        97.94         2.63        50.66 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 
        7.82       126.58        68.58        71.18        55.56        39.12 
TCGA-46-3765 TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-60-2710 
       13.32         9.83         0.39         0.39        29.95        66.54 
TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 
       56.91        29.85        35.90        16.96         2.01        21.01 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
       25.05         1.02         2.01        23.01         3.02         2.01 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       24.95        40.01         5.03        30.02        54.08         4.01 
TCGA-66-2800 
       49.05 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-22-1000 TCGA-22-1017 TCGA-33-4533 TCGA-34-2604 
      123.19         4.80        14.93        48.82       133.74        31.50 
TCGA-34-2609 TCGA-43-2578 TCGA-60-2712 TCGA-60-2715 TCGA-21-1083 TCGA-22-0940 
       31.27        22.49         9.01        35.34        43.23        21.99 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-33-4566 
        4.31        64.21        27.02        48.33         0.56       173.82 
TCGA-34-2608 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
       32.88         0.39         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 
        0.39       133.25         1.94        36.39        68.38        40.21 
TCGA-43-2581 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-60-2695 TCGA-60-2698 
       38.66        12.16        13.02         4.44        21.11        10.22 
TCGA-60-2706 TCGA-60-2714 TCGA-60-2720 TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 
       92.71        50.33         3.19        26.83         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 
        2.01         0.92         0.99        43.99         7.07         1.97 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
       25.97         4.04        22.98 

subtype1 subtype2 subtype3 
    0.43     0.39     0.39 
subtype1 subtype2 subtype3 
  122.43   129.01   173.82 
subtype1 subtype2 subtype3 
   21.50    29.95    21.11 
[1] "0.4 - 122.4 (21.5)" "0.4 - 129.0 (29.9)" "0.4 - 173.8 (21.1)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  subtype1        4       20         2         9          7          2        3
  subtype2        2       25         4        10          7          8        0
  subtype3       17       15         1         8          5          3        1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          4        2       17
  STAGE IB         20       25       15
  STAGE IIA         2        4        1
  STAGE IIB         9       10        8
  STAGE IIIA        7        7        5
  STAGE IIIB        2        8        3
  STAGE IV          3        0        1
[1] 7 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  6 32  7  2
  subtype2  4 44  1  7
  subtype3 20 24  4  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        6        4       20
  T2       32       44       24
  T3        7        1        4
  T4        2        7        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"
          vv
clus       N0 N1 N2 N3
  subtype1 28 14  4  1
  subtype2 30 18  5  3
  subtype3 38  8  4  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       28       30       38
  N1       14       18        8
  N2        4        5        4
  N3        1        3        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 42  3
  subtype2 54  0
  subtype3 50  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    3
  subtype2   54    0
  subtype3   50    1
   clus
vv  subtype1 subtype2 subtype3
  0       42       54       50
  1        3        0        1
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 10 37
  subtype2 13 43
  subtype3 21 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   37
  subtype2   13   43
  subtype3   21   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       13       21
  MALE         37       43       30
[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"
D2V8, binary
          cls
clus        0  1
  subtype1 34  4
  subtype2 36  5
  subtype3 31  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    4
  subtype2   36    5
  subtype3   31    4
     clus
vv    subtype1 subtype2 subtype3
  NO        34       36       31
  YES        4        5        4
[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"
D2V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     2
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      0
  subtype3                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          46
  subtype2                                                          53
  subtype3                                                          49
D2V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       46       53
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       49
[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"
D2V11, continuous
D2V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 42  0  1  2
  subtype2 51  1  1  1
  subtype3 46  2  0  2
D2V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       42       51       46
  R1        0        1        2
  R2        1        1        0
  RX        2        1        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    27
  subtype2     1                         3    31
  subtype3     1                         2    35
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        1
  BLACK OR AFRICAN AMERICAN        2        3        2
  WHITE                           27       31       35
[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"
D2V15, binary
          cls
clus        0  1
  subtype1  3 25
  subtype2  1 29
  subtype3  0 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   25
  subtype2    1   29
  subtype3    0   35
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        0
  NOT HISPANIC OR LATINO       25       29       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 25 17
  subtype2 56 58
  subtype3 10 19
  subtype4 56 30
  subtype5 96 70
  subtype6 37 20
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      42      114       29       86      166       57 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      17       58       19       30       70       20 
$subtype1
TCGA-18-3406 TCGA-22-5471 TCGA-43-2578 TCGA-43-A56V TCGA-56-8504 TCGA-98-A539 
       12.20        60.66        22.49        12.03        16.77         5.69 
TCGA-NC-A5HM TCGA-18-3412 TCGA-18-5592 TCGA-21-1070 TCGA-21-5782 TCGA-33-AASI 
       39.85        11.34        49.94       119.54        31.63        44.19 
TCGA-37-3783 TCGA-37-5819 TCGA-39-5029 TCGA-39-5036 TCGA-56-1622 TCGA-56-8304 
        4.01         3.39        24.33        71.18        28.96         3.48 
TCGA-56-A49D TCGA-56-A62T TCGA-58-8386 TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 
       20.94        14.47         0.03        92.71        80.45        50.33 
TCGA-60-2726 TCGA-63-7020 TCGA-66-2763 TCGA-66-2780 TCGA-66-2782 TCGA-77-7337 
       11.77        70.13         0.99        12.03        12.00       106.95 
TCGA-77-8144 TCGA-77-A5G8 TCGA-85-6561 TCGA-85-A4JB TCGA-85-A4QQ TCGA-94-A4VJ 
       27.39        61.94        40.24        30.97        30.48        14.14 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HQ TCGA-O2-A52Q 
       13.41         4.54        64.54        57.30        14.73         3.72 

$subtype2
TCGA-18-3407 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4589 TCGA-34-2604 
        4.47        27.19        14.93        48.82         1.55        31.50 
TCGA-39-5039 TCGA-43-5668 TCGA-56-8201 TCGA-56-A4ZJ TCGA-60-2715 TCGA-77-A5GB 
       17.88        18.38        13.05        21.04        35.34        30.81 
TCGA-98-A53D TCGA-NC-A5HE TCGA-21-1076 TCGA-21-1078 TCGA-21-5784 TCGA-22-0940 
       21.21        76.80        60.89        15.58        41.69        21.99 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 
        4.31        64.21         1.74        27.02        48.33         0.56 
TCGA-22-5479 TCGA-22-5480 TCGA-33-4566 TCGA-33-4583 TCGA-34-2608 TCGA-34-5232 
       86.30        71.34       173.82       151.27        32.88        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 
       74.66        60.30        16.93         0.39         7.96       133.25 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       55.20        82.52         1.71         1.94        60.53        36.39 
TCGA-43-2581 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U 
       38.66        24.89         5.46         3.81         9.73        14.20 
TCGA-46-3766 TCGA-46-3767 TCGA-52-7811 TCGA-52-7812 TCGA-56-7731 TCGA-56-8309 
       12.16        13.02         8.75        27.45         0.10        14.07 
TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-A5DS TCGA-58-8393 
        1.35        22.75        13.81        10.36         0.26        34.78 
TCGA-58-A46J TCGA-60-2697 TCGA-60-2709 TCGA-60-2716 TCGA-60-2720 TCGA-63-7021 
       85.12        12.23        49.48        48.49         3.19        70.42 
TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-66-2737 
       68.15        70.62        14.99        11.34        89.29         2.01 
TCGA-66-2744 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-77-7138 
        0.99         6.64         6.94        16.18        12.07        11.18 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-A5FZ 
        6.51        86.76        12.59        39.09        17.72       126.18 
TCGA-77-A5G1 TCGA-85-6175 TCGA-85-8048 TCGA-85-8049 TCGA-85-8355 TCGA-85-8481 
      132.36         9.67        25.15        19.04         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 
       38.14        12.59        22.59        24.36        27.16        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 
       29.92        24.92        20.22         2.70         5.26         2.30 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H 
       17.46        27.68        21.44        21.34        27.02        20.32 
TCGA-L3-A4E7 TCGA-NC-A5HJ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       12.89        13.74         3.65        33.07        11.18         0.20 

$subtype3
TCGA-18-3409 TCGA-43-8118 TCGA-56-7221 TCGA-98-8020 TCGA-18-3408 TCGA-18-3414 
      123.19         2.93        19.99         2.76        75.75        23.54 
TCGA-21-1079 TCGA-22-4591 TCGA-22-4593 TCGA-22-4609 TCGA-22-5478 TCGA-22-5482 
       31.73        20.48        35.08         9.57         0.79        11.74 
TCGA-33-AASD TCGA-34-8455 TCGA-34-A5IX TCGA-52-7810 TCGA-56-5898 TCGA-56-7580 
      110.99         4.04        33.90        30.35        18.25        30.41 
TCGA-56-7822 TCGA-56-8083 TCGA-56-8626 TCGA-56-A4BW TCGA-60-2707 TCGA-63-A5MV 
       17.49         4.93         9.93        19.23        21.93        36.16 
TCGA-66-2755 TCGA-77-7463 TCGA-77-8143 TCGA-77-8145 TCGA-85-A4JC 
        0.92        46.78        26.40         6.97        19.86 

$subtype4
TCGA-18-3410 TCGA-21-A5DI TCGA-22-5472 TCGA-33-6737 TCGA-34-2609 TCGA-60-2696 
        4.80        32.19        64.93        19.76        31.27         3.58 
TCGA-60-2721 TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-NK-A5CT 
       32.32         9.50        14.07        21.04         0.16        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3419 TCGA-18-4086 TCGA-22-4601 TCGA-22-4607 
       16.80         0.43        92.42         2.79        34.75        19.30 
TCGA-33-4547 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-34-5929 
       79.53        54.44         4.70         0.30         6.94         4.96 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4132 TCGA-37-4141 TCGA-39-5040 TCGA-43-7656 
       38.79         0.43         7.46         0.39        17.06        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 TCGA-56-8082 
       13.38        11.77        12.43        18.48        31.27        14.96 
TCGA-56-8307 TCGA-56-8622 TCGA-56-8628 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       26.89         1.81        20.25        13.25        13.55        29.95 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MT TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 
       23.57        26.83        16.37        43.10         1.02         2.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2783 
       25.05         2.01         2.01        19.00        19.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 
        1.97        25.97        22.98         4.04        22.98        13.35 
TCGA-77-6844 TCGA-77-7335 TCGA-77-8139 TCGA-77-8140 TCGA-77-8154 TCGA-77-A5G7 
       75.09        70.13       104.09        11.54        60.53         5.92 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8288 
       41.39        34.95         1.38        29.95        18.94        13.22 
TCGA-85-8479 TCGA-85-A50Z TCGA-85-A510 TCGA-92-8063 TCGA-94-8035 TCGA-96-7544 
       15.39        16.21        15.85         4.01         4.01        71.01 
TCGA-96-8169 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-NC-A5HK 
       18.31        30.67        27.16        18.15         2.01         4.21 
TCGA-NC-A5HT TCGA-O2-A52V 
       26.43        43.89 

$subtype5
TCGA-18-3416 TCGA-18-4083 TCGA-33-4532 TCGA-33-4533 TCGA-34-2605 TCGA-43-A474 
       31.99         6.18       129.01       133.74        28.96        11.61 
TCGA-56-8308 TCGA-60-2711 TCGA-60-2712 TCGA-77-7140 TCGA-77-A5GA TCGA-94-7943 
       17.00        41.42         9.01        20.78        42.08        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HR TCGA-18-3411 
       16.14        57.07        19.36        19.10        40.90       117.57 
TCGA-18-3415 TCGA-18-4721 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
       92.15       154.32        46.88        99.16        70.16        34.78 
TCGA-21-1082 TCGA-21-1083 TCGA-22-0944 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 
      119.80        43.23         7.33        24.13        38.17        13.12 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5483 TCGA-22-5485 
       11.77        63.55        14.63        44.25        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 TCGA-33-AAS8 
       62.86        56.32        97.94       103.53        14.07        36.62 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5236 
      118.36        27.16         2.63        61.61        65.23         9.07 
TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-4135 
       50.66        44.75         1.12        26.43         7.82         6.81 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
       37.58        21.70       126.58       111.35        68.58       102.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-3394 TCGA-43-6143 TCGA-43-6770 TCGA-46-3765 
       55.56        40.21        39.12        22.98        21.47        13.32 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-A4BX 
       28.34        14.53        19.76         6.51        33.24        13.32 
TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       18.74        71.24        16.47        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2704 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 
       29.92        10.22        37.94        66.54        56.91        29.85 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2727 
       55.30       102.67        59.97        45.57        25.28        16.96 
TCGA-66-2742 TCGA-66-2757 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 
       21.07        43.99        21.01         2.01        23.01         3.02 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        2.01         3.98        40.01         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-70-6723 
       54.08         4.01        49.05         2.73        14.73        12.33 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       73.12        23.28       140.09         0.49        73.22         0.16 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 
       32.55        55.73        37.81        53.92        66.51        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
       65.49        36.36       150.25        27.62         6.41        36.53 
TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       31.30        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL 
       10.09         3.09        32.71        36.59        18.08        30.28 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 
       34.13        19.73        15.29        12.39         3.65        11.77 
TCGA-90-A59Q TCGA-92-7341 TCGA-94-8490 TCGA-94-A5I6 TCGA-98-8021 TCGA-98-A53I 
       10.59         3.48         5.03        17.69        30.81        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HN 
       20.71        16.11        13.18        11.84         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52S 
       43.92        25.32        83.57        12.72 

$subtype6
TCGA-22-A5C4 TCGA-43-7657 TCGA-43-7658 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A5DR 
       22.06         7.76        78.18         3.45        17.85         0.13 
TCGA-63-A5MH TCGA-68-8250 TCGA-NC-A5HD TCGA-O2-A52W TCGA-18-3417 TCGA-18-3421 
       66.61         8.02         0.07         8.58        36.07        86.96 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-1012 
      122.43         9.34        88.11        33.93        10.82        14.10 
TCGA-22-4605 TCGA-22-5481 TCGA-22-5492 TCGA-33-6738 TCGA-34-5928 TCGA-37-4130 
       32.02        79.20        16.64        63.35        39.32         8.12 
TCGA-39-5035 TCGA-43-3920 TCGA-43-5670 TCGA-46-3769 TCGA-52-7809 TCGA-56-6545 
       68.38        33.11        27.91         4.44         5.46        21.90 
TCGA-56-8629 TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 TCGA-60-2723 TCGA-63-6202 
       15.81        21.11        96.82        42.64        35.90        52.67 
TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2756 TCGA-66-2766 
       58.65        78.28        53.88        34.59         0.99         1.02 
TCGA-66-2769 TCGA-77-6842 TCGA-77-8130 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-7699 
        7.07        29.56       156.66        22.29        38.86        32.91 
TCGA-85-7843 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-90-7767 
        1.15         0.76        22.45        16.77         5.29         2.93 
TCGA-90-A4EE TCGA-94-8491 TCGA-NC-A5HH 
       22.62        26.63         1.22 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.10     0.79     0.16     0.16     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  119.54   173.82   123.19   104.09   154.32   156.66 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.410   19.630   19.990   18.230   29.405   22.450 
[1] "0.0 - 119.5 (23.4)" "0.1 - 173.8 (19.6)" "0.8 - 123.2 (20.0)"
[4] "0.2 - 104.1 (18.2)" "0.2 - 154.3 (29.4)" "0.1 - 156.7 (22.4)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        6       13        0         2        10         1
  subtype2       1       25       37        0        12        24         1
  subtype3       0        6        9        0         4         3         0
  subtype4       0       15       28        1        10        16         0
  subtype5       0       26       48        1        29        33         1
  subtype6       1       11       17        0         8         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          1        1
  subtype2         12          1        0
  subtype3          4          1        2
  subtype4         11          5        1
  subtype5         19          9        2
  subtype6          8          2        1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        1        0        0        0        1
  STAGE IA          6       25        6       15       26       11
  STAGE IB         13       37        9       28       48       17
  STAGE II          0        0        0        1        1        0
  STAGE IIA         2       12        4       10       29        8
  STAGE IIB        10       24        3       16       33        9
  STAGE III         1        1        0        0        1        0
  STAGE IIIA        9       12        4       11       19        8
  STAGE IIIB        1        1        1        5        9        2
  STAGE IV          1        0        2        1        2        1
[1] 10  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   7  24  11   1
  subtype2  30  61  20   4
  subtype3   6  16   4   3
  subtype4  19  51  14   3
  subtype5  37 103  20   9
  subtype6  13  39   2   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        7       30        6       19       37       13
  T2       24       61       16       51      103       39
  T3       11       20        4       14       20        2
  T4        1        4        3        3        9        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 26  8  7  0
  subtype2 79 28  5  0
  subtype3 22  4  3  0
  subtype4 59 18  7  3
  subtype5 93 61 12  2
  subtype6 38 14  6  0
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       26       79       22       59       93       38
  N1        8       28        4       18       61       14
  N2        7        5        3        7       12        6
  N3        0        0        0        3        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"
D3V6, binary
          cls
clus         0   1
  subtype1  34   1
  subtype2  92   0
  subtype3  24   2
  subtype4  68   1
  subtype5 145   2
  subtype6  48   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    1
  subtype2   92    0
  subtype3   24    2
  subtype4   68    1
  subtype5  145    2
  subtype6   48    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       34       92       24       68      145       48
  1        1        0        2        1        2        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"
D3V7, binary
          cls
clus         0   1
  subtype1  11  32
  subtype2  43  72
  subtype3   4  25
  subtype4  22  65
  subtype5  38 131
  subtype6  12  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   32
  subtype2   43   72
  subtype3    4   25
  subtype4   22   65
  subtype5   38  131
  subtype6   12   46
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       11       43        4       22       38       12
  MALE         32       72       25       65      131       46
[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, binary
          cls
clus         0   1
  subtype1  29   8
  subtype2  94   8
  subtype3  23   3
  subtype4  64   8
  subtype5 131  21
  subtype6  43   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    8
  subtype2   94    8
  subtype3   23    3
  subtype4   64    8
  subtype5  131   21
  subtype6   43    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        29       94       23       64      131       43
  YES        8        8        3        8       21        5
[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"
D3V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     0
  subtype3                                     1
  subtype4                                     2
  subtype5                                     8
  subtype6                                     3
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      4
  subtype3                                      0
  subtype4                                      1
  subtype5                                      1
  subtype6                                      0
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       0
  subtype4                                       1
  subtype5                                       0
  subtype6                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          42
  subtype2                                                         111
  subtype3                                                          28
  subtype4                                                          83
  subtype5                                                         160
  subtype6                                                          55
D3V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       42      111
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       28       83
                                                             clus
vv                                                            subtype5 subtype6
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              8        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      160       55
[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"
D3V11, continuous
D3V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  36   1   1   1
  subtype2  88   3   0   8
  subtype3  24   1   0   1
  subtype4  66   0   2   4
  subtype5 139   5   1   8
  subtype6  46   2   0   1
D3V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       36       88       24       66      139       46
  R1        1        3        1        0        5        2
  R2        1        0        0        2        1        0
  RX        1        8        1        4        8        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         5    29
  subtype2     6                         4    84
  subtype3     1                         3    19
  subtype4     0                         8    57
  subtype5     2                         8   121
  subtype6     0                         3    39
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        6        1        0        2
  BLACK OR AFRICAN AMERICAN        5        4        3        8        8
  WHITE                           29       84       19       57      121
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           39
[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"
D3V15, binary
          cls
clus         0   1
  subtype1   1  23
  subtype2   3  83
  subtype3   1  17
  subtype4   1  57
  subtype5   2 103
  subtype6   0  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    3   83
  subtype3    1   17
  subtype4    1   57
  subtype5    2  103
  subtype6    0   34
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        3        1        1        2        0
  NOT HISPANIC OR LATINO       23       83       17       57      103       34
[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 52 35
  subtype2 54 39
  subtype3 33 25
  subtype4 69 56
subtype1 subtype2 subtype3 subtype4 
      87       93       58      125 
subtype1 subtype2 subtype3 subtype4 
      35       39       25       56 
$subtype1
TCGA-18-5595 TCGA-22-5472 TCGA-22-A5C4 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       27.19        64.93        22.06        11.61        12.03        19.99 
TCGA-56-A5DR TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        0.13        66.61         8.02         9.50        14.07        21.04 
TCGA-98-8020 TCGA-NC-A5HM TCGA-O2-A52W TCGA-18-3417 TCGA-21-5782 TCGA-22-4593 
        2.76        39.85         8.58        36.07        31.63        35.08 
TCGA-22-5478 TCGA-22-5492 TCGA-33-4587 TCGA-33-AASI TCGA-34-5231 TCGA-34-5239 
        0.79        16.64        54.44        44.19        65.23        60.30 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8455 TCGA-37-A5EL TCGA-39-5035 TCGA-43-5670 
       44.75         4.96         4.04        37.58        68.38        27.91 
TCGA-43-6143 TCGA-43-8116 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-7222 
       22.98        11.77        13.91         5.46        30.35        18.48 
TCGA-56-7580 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8622 
       30.41        17.49        33.24        14.96         4.93         1.81 
TCGA-56-A4BX TCGA-58-8386 TCGA-58-8390 TCGA-63-7020 TCGA-63-A5MI TCGA-63-A5MT 
       13.32         0.03        29.95        70.13        58.65        16.37 
TCGA-63-A5MW TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-7337 TCGA-77-7465 
       53.88        13.35        29.56        75.09       106.95        32.55 
TCGA-77-8130 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5G6 
      156.66       104.09        11.54         6.97        60.53        22.29 
TCGA-77-A5G7 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8071 
        5.92        32.91         1.38         1.15        18.94        26.79 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QQ 
       13.22        16.77         5.29        15.39        18.08        30.48 
TCGA-85-A4QR TCGA-92-7340 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8022 
       19.73         2.70         4.01        14.14        71.01        30.67 
TCGA-98-A538 TCGA-98-A53B TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       27.16         2.01         4.54        64.54         1.22        57.30 
TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CX 
       49.28        26.43         3.65 

$subtype2
TCGA-43-8118 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-77-7140 TCGA-77-A5GA 
        2.93        17.00        16.77        17.85        20.78        42.08 
TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-18-4721 TCGA-22-4599 TCGA-22-4613 
       57.07        19.36        19.10       154.32        38.17        11.77 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       63.55        44.25        86.30        11.74        18.84        30.12 
TCGA-22-5491 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASJ 
       56.32       151.27        14.07         4.70        36.62       118.36 
TCGA-34-5240 TCGA-34-8456 TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
       50.66        26.43        28.50        21.70       126.58       111.35 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-6770 
      102.18        24.33        60.53        71.18        55.56        21.47 
TCGA-43-8115 TCGA-43-A475 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       13.38         9.73        28.34        31.27        19.76         6.51 
TCGA-56-8304 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-A46M 
        3.48        18.74        14.47        71.24        16.47        35.24 
TCGA-58-A46N TCGA-63-7023 TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MY TCGA-68-7755 
       29.92        55.30        59.97        25.28        34.59         2.73 
TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
       12.33        73.12        23.28       140.09         0.49        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8009 TCGA-77-8128 TCGA-77-8143 TCGA-77-8144 
        0.16        46.78        55.73        37.81        26.40        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GF 
       66.51        54.41        65.49       150.25        61.94        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
       40.24         6.41        31.30        31.56        30.64        34.52 
TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 
       32.71        36.59        34.13         3.65        11.77         3.48 
TCGA-92-8064 TCGA-94-8490 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL 
        5.26         5.03        16.11        13.18        11.84         2.89 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52S 
       14.73        83.57        12.72 

$subtype3
TCGA-22-5471 TCGA-43-7657 TCGA-43-7658 TCGA-51-6867 TCGA-56-8305 TCGA-94-7943 
       60.66         7.76        78.18        61.02         3.45        18.38 
TCGA-94-A5I4 TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-5592 TCGA-21-5783 
       16.14         0.07        40.90        16.80        49.94        88.11 
TCGA-21-5786 TCGA-22-4601 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-33-4582 
       33.93        34.75        14.63        71.34        79.20       103.53 
TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASL TCGA-34-5928 TCGA-34-7107 
        0.30         6.94       110.99        27.16        39.32         1.12 
TCGA-46-6025 TCGA-56-5898 TCGA-56-7223 TCGA-56-8307 TCGA-56-8626 TCGA-56-8629 
       10.65        18.25        14.53        26.89         9.93        15.81 
TCGA-56-A4BW TCGA-58-8388 TCGA-58-A46K TCGA-58-A46L TCGA-63-A5MB TCGA-63-A5ML 
       19.23        13.55        34.36        56.65       102.67        45.57 
TCGA-68-A59J TCGA-77-7142 TCGA-77-8133 TCGA-85-7696 TCGA-85-7844 TCGA-85-8052 
       14.73        73.22        53.92        36.53        29.95        24.13 
TCGA-85-8277 TCGA-85-8350 TCGA-85-A4CL TCGA-85-A512 TCGA-90-7767 TCGA-94-8491 
       10.09        22.45        30.28        15.29         2.93        26.63 
TCGA-94-A5I6 TCGA-98-8021 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-NC-A5HK 
       17.69        30.81        18.15        18.58        20.71         4.21 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-O2-A52N TCGA-O2-A5IB 
       43.92        25.32        33.07        11.18 

$subtype4
TCGA-21-A5DI TCGA-33-4589 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-56-8201 
       32.19         1.55        19.76        17.88        18.38        13.05 
TCGA-56-A4ZJ TCGA-77-A5GB TCGA-94-7557 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE 
       21.04        30.81         0.16         5.69        21.21        76.80 
TCGA-NK-A5CT TCGA-NK-A7XE TCGA-21-5784 TCGA-21-5787 TCGA-22-4605 TCGA-22-4609 
       65.65         0.43        41.69        10.82        32.02         9.57 
TCGA-22-5489 TCGA-33-4566 TCGA-33-6738 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       62.86       173.82        63.35        81.24        74.66         9.07 
TCGA-34-5241 TCGA-34-8454 TCGA-34-A5IX TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 
       16.93        38.79        33.90         3.39       133.25        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5040 
       55.20        82.52         1.71         1.94        36.39        17.06 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-A56U TCGA-52-7811 
       24.89         5.46         3.81        19.59        14.20         8.75 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7731 TCGA-56-8309 TCGA-56-8503 
       27.45        12.43        21.90         0.10        14.07         1.35 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A5DS 
       22.75        13.81        10.36        20.25        20.94         0.26 
TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       13.25        34.78        85.12        12.23        96.82        37.94 
TCGA-60-2709 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MM 
       49.48        52.67        70.42        68.15        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-68-7756 TCGA-68-7757 
       11.34        89.29        78.28        36.16         6.64         6.94 
TCGA-68-A59I TCGA-70-6722 TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
       16.18        12.07        11.18         6.51        86.76        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8146 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       39.09        17.72       104.84        36.36       126.18       132.36 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-8048 TCGA-85-8049 
       38.86         9.67        41.39        34.95        25.15        19.04 
TCGA-85-8287 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
        0.76         3.09         2.01         7.76        38.14        12.59 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       22.59        30.97        19.86        24.36        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED 
       15.85        14.96        29.92        12.39        24.92        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-96-8169 TCGA-96-8170 
       22.62        10.59         4.01         2.30        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       27.68        21.44        21.34        27.02        20.32        12.89 
TCGA-LA-A7SW TCGA-NC-A5HJ TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       13.41        13.74         3.72        43.89         0.20 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.16     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  156.66   154.32   110.99   173.82 
subtype1 subtype2 subtype3 subtype4 
  19.990   28.500   24.725   20.220 
[1] "0.0 - 156.7 (20.0)" "0.2 - 154.3 (28.5)" "0.1 - 111.0 (24.7)"
[4] "0.1 - 173.8 (20.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       16       24        0        16        17         0
  subtype2       0       17       29        1        16        17         1
  subtype3       2       13       14        1        10        10         1
  subtype4       0       25       31        1        18        28         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         11          2        3
  subtype2         11          2        0
  subtype3          6          0        1
  subtype4         19          2        0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        0        2        0
  STAGE IA         16       17       13       25
  STAGE IB         24       29       14       31
  STAGE II          0        1        1        1
  STAGE IIA        16       16       10       18
  STAGE IIB        17       17       10       28
  STAGE III         0        1        1        1
  STAGE IIIA       11       11        6       19
  STAGE IIIB        2        2        0        2
  STAGE IV          3        0        1        0
[1] 10  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 19 56 10  5
  subtype2 24 55 14  3
  subtype3 17 30 10  1
  subtype4 30 66 26  4
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       19       24       17       30
  T2       56       55       30       66
  T3       10       14       10       26
  T4        5        3        1        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"
          vv
clus       N0 N1 N2
  subtype1 59 24  6
  subtype2 59 27  9
  subtype3 38 17  2
  subtype4 80 31 12
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       59       59       38       80
  N1       24       27       17       31
  N2        6        9        2       12
[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"
D4V6, binary
          cls
clus        0  1
  subtype1 70  3
  subtype2 77  0
  subtype3 43  1
  subtype4 97  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    3
  subtype2   77    0
  subtype3   43    1
  subtype4   97    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       70       77       43       97
  1        3        0        1        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"
D4V7, binary
          cls
clus        0  1
  subtype1 18 72
  subtype2 24 72
  subtype3 16 42
  subtype4 38 88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   72
  subtype2   24   72
  subtype3   16   42
  subtype4   38   88
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18       24       16       38
  MALE         72       72       42       88
[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, binary
          cls
clus         0   1
  subtype1  74   7
  subtype2  73  17
  subtype3  49   4
  subtype4 106  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74    7
  subtype2   73   17
  subtype3   49    4
  subtype4  106   13
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        74       73       49      106
  YES        7       17        4       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"
D4V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     4
  subtype2                                     3
  subtype3                                     5
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      1
  subtype3                                      0
  subtype4                                      3
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          84
  subtype2                                                          92
  subtype3                                                          53
  subtype4                                                         123
D4V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       84       92
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              5        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       53      123
[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"
D4V11, continuous
D4V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 65  2  1  4
  subtype2 75  6  0  5
  subtype3 46  0  1  2
  subtype4 93  1  0  7
D4V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       65       75       46       93
  R1        2        6        0        1
  R2        1        0        1        0
  RX        4        5        2        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         7    64
  subtype2     1                         4    71
  subtype3     0                         4    50
  subtype4     6                         9    89
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        6
  BLACK OR AFRICAN AMERICAN        7        4        4        9
  WHITE                           64       71       50       89
[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"
D4V15, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  2 53
  subtype3  0 42
  subtype4  3 88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    2   53
  subtype3    0   42
  subtype4    3   88
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        3
  NOT HISPANIC OR LATINO       56       53       42       88
[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 42
  subtype2 62 44
  subtype3 52 34
  subtype4 12 14
subtype1 subtype2 subtype3 subtype4 
     105      106       86       26 
subtype1 subtype2 subtype3 subtype4 
      42       44       34       14 
$subtype1
TCGA-22-1000 TCGA-22-5471 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-5668 
       14.93        60.66        31.50        28.96        31.27        18.38 
TCGA-43-7658 TCGA-43-8118 TCGA-60-2696 TCGA-60-2712 TCGA-94-7557 TCGA-94-7943 
       78.18         2.93         3.58         9.01         0.16        18.38 
TCGA-96-A4JK TCGA-18-4721 TCGA-21-1076 TCGA-21-1078 TCGA-21-1082 TCGA-21-5782 
       19.36       154.32        60.89        15.58       119.80        31.63 
TCGA-22-1011 TCGA-22-5474 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5489 
        1.74        14.63         0.79        71.34        11.74        62.86 
TCGA-22-5491 TCGA-33-6738 TCGA-33-AASI TCGA-34-2596 TCGA-34-2608 TCGA-34-5239 
       56.32        63.35        44.19         2.63        32.88        60.30 
TCGA-34-5927 TCGA-37-4129 TCGA-37-4141 TCGA-39-5022 TCGA-39-5030 TCGA-39-5034 
       44.75         7.96         0.39        55.20         1.94        36.39 
TCGA-43-2581 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 TCGA-56-5897 TCGA-56-7730 
       38.66        19.59        13.38         9.73        12.43         6.51 
TCGA-56-8083 TCGA-56-8309 TCGA-58-8392 TCGA-58-8393 TCGA-60-2695 TCGA-60-2706 
        4.93        14.07        16.47        34.78        21.11        92.71 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2720 TCGA-60-2725 
       49.48        66.54        56.91        50.33         3.19        26.83 
TCGA-63-6202 TCGA-63-7022 TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV 
       52.67        68.15        11.34        25.28        78.28        36.16 
TCGA-66-2737 TCGA-66-2785 TCGA-66-2790 TCGA-66-2800 TCGA-68-A59I TCGA-77-7142 
        2.01         1.97        22.98        49.05        16.18        73.22 
TCGA-77-7335 TCGA-77-8143 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-6175 
       70.13        26.40        54.41       150.25        38.86         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 TCGA-85-8287 
       41.39        36.53        25.15        19.04        30.64         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL 
       13.22        22.45         3.09         2.01        36.59        30.28 
TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
       34.13        24.36        30.48        15.85        15.29        29.92 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-94-A4VJ TCGA-96-7544 
        3.65        24.92        11.77        20.22        14.14        71.01 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HK 
       27.68        21.44         2.01        27.02        20.32         4.21 
TCGA-NC-A5HP TCGA-O2-A52Q TCGA-O2-A52V 
       25.32         3.72        43.89 

$subtype2
TCGA-18-5595 TCGA-22-5472 TCGA-33-4589 TCGA-33-6737 TCGA-43-A474 TCGA-43-A56V 
       27.19        64.93         1.55        19.76        11.61        12.03 
TCGA-60-2721 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
       32.32         5.69         0.07        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A7XE TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 
       65.65         0.43        49.94       119.54        46.88         9.34 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-4607 TCGA-22-5477 
       41.69        33.93        10.82        21.99        19.30        44.25 
TCGA-22-5479 TCGA-22-5492 TCGA-33-4547 TCGA-33-AASB TCGA-34-5232 TCGA-34-5234 
       86.30        16.64        79.53         6.94        81.24        74.66 
TCGA-34-5236 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 
        9.07        39.32        38.79         4.04        33.90         0.43 
TCGA-37-3792 TCGA-37-A5EM TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 
        0.39        28.50       133.25       111.35        68.58        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 TCGA-39-5037 TCGA-43-5670 
      102.18         1.71        24.33        68.38        55.56        27.91 
TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-52-7811 TCGA-52-7812 TCGA-56-6545 
       21.47         5.46        10.65         8.75        27.45        21.90 
TCGA-56-7222 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2724 TCGA-60-2726 
       18.48        12.23        10.22        96.82        23.57        11.77 
TCGA-63-7021 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MT TCGA-63-A5MY 
       70.42        70.62        58.65        14.99        16.37        34.59 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 
        2.01         7.07        19.00         3.98        12.00        22.98 
TCGA-66-2791 TCGA-68-7757 TCGA-70-6722 TCGA-77-6845 TCGA-77-7337 TCGA-77-7338 
        5.03         6.94        12.07        23.28       106.95         0.16 
TCGA-77-7463 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6561 TCGA-85-6798 
       46.78        60.53       126.18       132.36        40.24         6.41 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8351 TCGA-85-8479 TCGA-85-8664 
        1.38         1.15        29.95        16.77        15.39        18.08 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L 
       22.59        30.97        19.86        16.21        14.96        12.39 
TCGA-90-A59Q TCGA-92-7340 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 TCGA-98-A538 
       10.59         2.70         4.01        26.63        17.69        27.16 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HO TCGA-NC-A5HQ 
       12.89        13.41        43.92        14.73 

$subtype3
TCGA-33-4532 TCGA-43-2578 TCGA-56-7221 TCGA-60-2711 TCGA-21-1072 TCGA-21-1075 
      129.01        22.49        19.99        41.42        99.16        70.16 
TCGA-21-1080 TCGA-21-1083 TCGA-22-5473 TCGA-22-5483 TCGA-33-4566 TCGA-33-4582 
      122.43        43.23        63.55        18.84       173.82       103.53 
TCGA-33-4586 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASJ TCGA-34-5231 TCGA-34-5929 
       14.07         4.70       110.99       118.36        65.23         4.96 
TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL 
        1.12        26.43         7.82         6.81         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5040 TCGA-43-3394 TCGA-43-6143 TCGA-46-6026 
       21.70       126.58        17.06        39.12        22.98        13.91 
TCGA-52-7810 TCGA-56-A4BX TCGA-58-8388 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K 
       30.35        13.32        13.55        71.24        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2704 TCGA-60-2708 TCGA-60-2716 
       56.65        35.24        29.92        37.94        80.45        48.49 
TCGA-60-2719 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2727 
       42.64        55.30       102.67        59.97        45.57        16.96 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
       21.01         1.02         2.01        23.01         3.02         2.01 
TCGA-66-2783 TCGA-66-2794 TCGA-66-2795 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
       24.95        54.08         4.01        12.33        29.56        73.12 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7465 TCGA-77-8153 TCGA-77-A5G6 TCGA-77-A5GF 
      140.09         0.49        32.55        65.49        22.29        27.62 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 TCGA-85-8276 TCGA-85-8352 
       34.95        31.30        32.91        18.94        34.52         5.29 
TCGA-85-A4QR TCGA-90-7767 TCGA-90-A4EE TCGA-94-8490 TCGA-98-A53A TCGA-L3-A524 
       19.73         2.93        22.62         5.03        18.15        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT 
       13.18        11.84        13.74         2.89        49.28        26.43 
TCGA-NK-A5CR TCGA-O2-A52N 
       83.57        33.07 

$subtype4
TCGA-21-A5DI TCGA-22-A5C4 TCGA-51-6867 TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 
       32.19        22.06        61.02         9.50        21.04        16.14 
TCGA-21-1079 TCGA-22-4591 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 TCGA-22-5485 
       31.73        20.48         0.56        32.02         9.57        30.12 
TCGA-33-A5GW TCGA-34-5241 TCGA-39-5031 TCGA-56-5898 TCGA-56-A5DS TCGA-58-8386 
        0.30        16.93        60.53        18.25         0.26         0.03 
TCGA-63-7020 TCGA-68-7756 TCGA-68-A59J TCGA-77-6844 TCGA-98-A53J TCGA-NC-A5HF 
       70.13         6.64        14.73        75.09        20.71         4.54 
TCGA-NC-A5HI TCGA-O2-A5IB 
       57.30        11.18 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.07     0.49     0.03 
subtype1 subtype2 subtype3 subtype4 
  154.32   133.25   173.82    75.09 
subtype1 subtype2 subtype3 subtype4 
  25.150   21.685   28.590   19.365 
[1] "0.2 - 154.3 (25.1)" "0.1 - 133.2 (21.7)" "0.5 - 173.8 (28.6)"
[4] "0.0 - 75.1 (19.4)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       27       33        1        12        19         1
  subtype2       0       11       30        1        17        26         0
  subtype3       1        7       29        1        13        17         0
  subtype4       1        7        9        0         3         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          8          3        1
  subtype2         18          5        1
  subtype3         12          5        0
  subtype4          4          1        1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        1        1
  STAGE IA         27       11        7        7
  STAGE IB         33       30       29        9
  STAGE II          1        1        1        0
  STAGE IIA        12       17       13        3
  STAGE IIB        19       26       17        0
  STAGE III         1        0        0        1
  STAGE IIIA        8       18       12        4
  STAGE IIIB        3        5        5        1
  STAGE IV          1        1        0        1
[1] 10  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 33 56 12  4
  subtype2 15 68 22  5
  subtype3 12 59 10  5
  subtype4 10 10  5  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       33       15       12       10
  T2       56       68       59       10
  T3       12       22       10        5
  T4        4        5        5        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 72 27  4  0
  subtype2 63 33 11  2
  subtype3 50 24 10  2
  subtype4 20  5  1  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       72       63       50       20
  N1       27       33       24        5
  N2        4       11       10        1
  N3        0        2        2        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"
D5V6, binary
          cls
clus        0  1
  subtype1 89  1
  subtype2 99  1
  subtype3 76  0
  subtype4 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89    1
  subtype2   99    1
  subtype3   76    0
  subtype4   17    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       89       99       76       17
  1        1        1        0        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 39 66
  subtype2 20 90
  subtype3 11 75
  subtype4 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   66
  subtype2   20   90
  subtype3   11   75
  subtype4   10   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       39       20       11       10
  MALE         66       90       75       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 89 10
  subtype2 89 11
  subtype3 58 13
  subtype4 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89   10
  subtype2   89   11
  subtype3   58   13
  subtype4   23    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        89       89       58       23
  YES       10       11       13        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     1
  subtype3                                     6
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      2
  subtype3                                      2
  subtype4                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         104
  subtype2                                                         107
  subtype3                                                          78
  subtype4                                                          27
D5V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        2
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      104      107
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              6        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       78       27
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 82  3  1  2
  subtype2 82  4  1  6
  subtype3 70  0  2  3
  subtype4 23  0  0  1
D5V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       82       82       70       23
  R1        3        4        0        0
  R2        1        1        2        0
  RX        2        6        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         7    80
  subtype2     2                         8    78
  subtype3     1                         4    62
  subtype4     0                         0    22
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        2        1        0
  BLACK OR AFRICAN AMERICAN        7        8        4        0
  WHITE                           80       78       62       22
[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"
D5V15, binary
          cls
clus        0  1
  subtype1  0 77
  subtype2  4 65
  subtype3  0 56
  subtype4  0 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   77
  subtype2    4   65
  subtype3    0   56
  subtype4    0   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        4        0        0
  NOT HISPANIC OR LATINO       77       65       56       15
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 45 34
  subtype2 37 31
  subtype3 39 22
  subtype4 35 23
  subtype5 16 13
  subtype6 17 11
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      79       68       61       58       29       28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      34       31       22       23       13       11 
$subtype1
TCGA-18-5595 TCGA-22-1000 TCGA-33-4589 TCGA-43-7658 TCGA-60-2711 TCGA-96-A4JK 
       27.19        14.93         1.55        78.18        41.42        19.36 
TCGA-18-4721 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5787 
      154.32        60.89       122.43       119.80        43.23        10.82 
TCGA-22-5480 TCGA-22-5483 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ 
       71.34        18.84         4.70         6.94        44.19       118.36 
TCGA-34-2608 TCGA-34-5239 TCGA-34-5927 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 
       32.88        60.30        44.75         1.12         0.39         7.96 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 
        6.81         0.39         3.39       133.25       126.58        82.52 
TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-43-2581 TCGA-43-6771 TCGA-43-7656 
       24.33        36.39        68.38        38.66         5.46        19.59 
TCGA-52-7812 TCGA-58-A46M TCGA-60-2695 TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 
       27.45        35.24        21.11        49.48        50.33        48.49 
TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MJ TCGA-66-2727 TCGA-66-2794 TCGA-68-7756 
       52.67        55.30        59.97        16.96        54.08         6.64 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7465 
       12.07        29.56        73.12       140.09         0.49        32.55 
TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-7698 TCGA-85-7699 
       54.41       150.25        27.62        38.86        31.30        32.91 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8287 TCGA-85-8352 TCGA-85-A4CL 
       18.94        25.15        19.04         0.76         5.29        30.28 
TCGA-85-A511 TCGA-90-7767 TCGA-90-A4EE TCGA-94-8491 TCGA-96-7544 TCGA-96-A4JL 
       14.96         2.93        22.62        26.63        71.01        27.68 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HJ TCGA-O2-A52Q 
       27.16        18.15        20.32        16.11        13.74         3.72 
TCGA-O2-A52V 
       43.89 

$subtype2
TCGA-21-A5DI TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2605 TCGA-43-5668 TCGA-51-6867 
       32.19        22.06        19.76        28.96        18.38        61.02 
TCGA-94-7557 TCGA-18-5592 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-22-4605 
        0.16        49.94        99.16        15.58        31.73        32.02 
TCGA-22-5474 TCGA-22-5489 TCGA-22-5491 TCGA-33-4566 TCGA-33-AASD TCGA-34-5231 
       14.63        62.86        56.32       173.82       110.99        65.23 
TCGA-34-8456 TCGA-37-4133 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5022 TCGA-39-5040 
       26.43         7.82        37.58        21.70        55.20        17.06 
TCGA-43-3394 TCGA-43-6143 TCGA-43-8115 TCGA-56-7730 TCGA-56-8083 TCGA-56-8309 
       39.12        22.98        13.38         6.51         4.93        14.07 
TCGA-56-A4BX TCGA-58-8386 TCGA-58-8388 TCGA-58-A46K TCGA-58-A46L TCGA-60-2710 
       13.32         0.03        13.55        34.36        56.65        66.54 
TCGA-60-2719 TCGA-63-A5MB TCGA-66-2767 TCGA-66-2777 TCGA-66-2785 TCGA-66-2790 
       42.64       102.67         2.01         2.01         1.97        22.98 
TCGA-77-6844 TCGA-77-7142 TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 
       75.09        73.22         9.67        41.39        36.53         1.38 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8355 TCGA-85-A4CN 
       34.52        13.22        22.45        16.77         2.01        34.13 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A513 TCGA-90-A4ED TCGA-94-8490 TCGA-LA-A446 
       30.48        19.73        29.92        20.22         5.03        13.18 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR 
       11.84         4.54         4.21        49.28        25.32        83.57 
TCGA-O2-A52N TCGA-O2-A5IB 
       33.07        11.18 

$subtype3
TCGA-43-A474 TCGA-43-A56V TCGA-60-2721 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM 
       11.61        12.03        32.32         5.69         0.07        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 
       40.90        65.65         0.43       119.54        46.88         9.34 
TCGA-21-5786 TCGA-22-0940 TCGA-22-4607 TCGA-22-5479 TCGA-22-5492 TCGA-34-5232 
       33.93        21.99        19.30        86.30        16.64        81.24 
TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-39-5021 
       39.32        38.79         4.04        33.90         0.43        68.58 
TCGA-43-5670 TCGA-43-6770 TCGA-46-6025 TCGA-56-6545 TCGA-56-7222 TCGA-60-2698 
       27.91        21.47        10.65        21.90        18.48        10.22 
TCGA-60-2703 TCGA-60-2720 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 
       96.82         3.19        23.57        11.77        70.13        70.42 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MT TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 
       70.62        58.65        16.37         2.01         7.07        19.00 
TCGA-66-2788 TCGA-66-2791 TCGA-77-7337 TCGA-77-7463 TCGA-77-8154 TCGA-77-A5FZ 
       22.98         5.03       106.95        46.78        60.53       126.18 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 TCGA-85-8479 TCGA-85-8666 TCGA-85-A4JB 
       40.24         6.41         1.15        15.39        22.59        30.97 
TCGA-85-A4JC TCGA-85-A53L TCGA-94-8035 TCGA-94-A5I6 TCGA-L3-A4E7 TCGA-LA-A7SW 
       19.86        12.39         4.01        17.69        12.89        13.41 
TCGA-NC-A5HO 
       43.92 

$subtype4
TCGA-33-4532 TCGA-43-2578 TCGA-56-7221 TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 
      129.01        22.49        19.99         9.50        21.04        16.14 
TCGA-21-1075 TCGA-21-5782 TCGA-22-4591 TCGA-22-4609 TCGA-22-5473 TCGA-22-5482 
       70.16        31.63        20.48         9.57        63.55        11.74 
TCGA-22-5485 TCGA-33-4582 TCGA-33-4586 TCGA-33-A5GW TCGA-34-5929 TCGA-39-5027 
       30.12       103.53        14.07         0.30         4.96       102.18 
TCGA-39-5031 TCGA-39-5037 TCGA-46-6026 TCGA-52-7810 TCGA-56-5898 TCGA-56-A5DS 
       60.53        55.56        13.91        30.35        18.25         0.26 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46N TCGA-60-2704 TCGA-60-2708 
       71.24        16.47        85.12        29.92        37.94        80.45 
TCGA-60-2713 TCGA-63-7022 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV 
       56.91        68.15        45.57        25.28        78.28        36.16 
TCGA-63-A5MY TCGA-66-2758 TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 TCGA-66-2783 
       34.59        21.01         1.02        23.01         3.02        24.95 
TCGA-66-2795 TCGA-66-2800 TCGA-68-A59J TCGA-70-6723 TCGA-77-7335 TCGA-77-8153 
        4.01        49.05        14.73        12.33        70.13        65.49 
TCGA-77-A5G6 TCGA-85-7697 TCGA-85-8353 TCGA-85-8664 TCGA-98-A53B TCGA-98-A53J 
       22.29        34.95         3.09        18.08         2.01        20.71 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NC-A5HT 
       57.30         2.89        14.73        26.43 

$subtype5
TCGA-22-5471 TCGA-22-5472 TCGA-94-7943 TCGA-NC-A5HE TCGA-21-5784 TCGA-22-4596 
       60.66        64.93        18.38        76.80        41.69         0.56 
TCGA-22-5477 TCGA-33-4547 TCGA-33-6738 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
       44.25        79.53        63.35        74.66         9.07        16.93 
TCGA-37-A5EM TCGA-39-5019 TCGA-39-5028 TCGA-52-7811 TCGA-56-5897 TCGA-60-2697 
       28.50       111.35         1.71         8.75        12.43        12.23 
TCGA-63-A5MM TCGA-66-2781 TCGA-66-2782 TCGA-68-7757 TCGA-77-6845 TCGA-77-7338 
       14.99         3.98        12.00         6.94        23.28         0.16 
TCGA-77-A5G1 TCGA-85-7844 TCGA-85-A50Z TCGA-90-A59Q TCGA-92-7340 
      132.36        29.95        16.21        10.59         2.70 

$subtype6
TCGA-34-2604 TCGA-34-2609 TCGA-43-8118 TCGA-60-2696 TCGA-60-2712 TCGA-22-1011 
       31.50        31.27         2.93         3.58         9.01         1.74 
TCGA-22-5478 TCGA-34-2596 TCGA-39-5030 TCGA-43-A475 TCGA-58-8393 TCGA-60-2706 
        0.79         2.63         1.94         9.73        34.78        92.71 
TCGA-60-2725 TCGA-63-A5MN TCGA-66-2737 TCGA-68-A59I TCGA-77-8143 TCGA-85-8072 
       26.83        11.34         2.01        16.18        26.40        30.64 
TCGA-85-8580 TCGA-85-A4PA TCGA-85-A510 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 
       36.59        24.36        15.85        15.29         3.65        24.92 
TCGA-90-7769 TCGA-94-A4VJ TCGA-98-7454 TCGA-98-A53C 
       11.77        14.14        21.44        27.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.39     0.03     0.07     0.26     0.16     0.79 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  154.32   173.82   126.18   129.01   132.36    92.71 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   27.68    22.98    21.90    23.98    16.93    15.57 
[1] "0.4 - 154.3 (27.7)" "0.0 - 173.8 (23.0)" "0.1 - 126.2 (21.9)"
[4] "0.3 - 129.0 (24.0)" "0.2 - 132.4 (16.9)" "0.8 - 92.7 (15.6)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       15       21        2        11        16         1
  subtype2       2       12       21        0        12         7         1
  subtype3       0        5       18        0         9        15         0
  subtype4       0        9       22        0         6        10         0
  subtype5       0        5       11        1         5         5         0
  subtype6       0        6        8        0         2         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         11          1        0
  subtype2          7          4        2
  subtype3          9          5        1
  subtype4          8          4        0
  subtype5          4          0        0
  subtype6          3          0        0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        2        0        0        0        0
  STAGE IA         15       12        5        9        5        6
  STAGE IB         21       21       18       22       11        8
  STAGE II          2        0        0        0        1        0
  STAGE IIA        11       12        9        6        5        2
  STAGE IIB        16        7       15       10        5        9
  STAGE III         1        1        0        0        0        0
  STAGE IIIA       11        7        9        8        4        3
  STAGE IIIB        1        4        5        4        0        0
  STAGE IV          0        2        1        0        0        0
[1] 10  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 19 46 10  4
  subtype2 19 36  9  4
  subtype3  7 38 13  4
  subtype4 11 38  8  3
  subtype5  7 18  5  1
  subtype6  7 17  4  0
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       19       19        7       11        7        7
  T2       46       36       38       38       18       17
  T3       10        9       13        8        5        4
  T4        4        4        4        3        1        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 45 28  6  0
  subtype2 46 14  5  1
  subtype3 37 18  4  2
  subtype4 38 14  7  1
  subtype5 21  7  2  0
  subtype6 18  8  2  0
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       45       46       37       38       21       18
  N1       28       14       18       14        7        8
  N2        6        5        4        7        2        2
  N3        0        1        2        1        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 66  0
  subtype2 54  2
  subtype3 57  1
  subtype4 54  0
  subtype5 24  0
  subtype6 26  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    0
  subtype2   54    2
  subtype3   57    1
  subtype4   54    0
  subtype5   24    0
  subtype6   26    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       66       54       57       54       24       26
  1        0        2        1        0        0        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"
D6V7, binary
          cls
clus        0  1
  subtype1 22 57
  subtype2 13 55
  subtype3 11 51
  subtype4 15 45
  subtype5  6 25
  subtype6 13 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   57
  subtype2   13   55
  subtype3   11   51
  subtype4   15   45
  subtype5    6   25
  subtype6   13   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       22       13       11       15        6       13
  MALE         57       55       51       45       25       15
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 60  9
  subtype2 53  8
  subtype3 50  4
  subtype4 46  9
  subtype5 27  3
  subtype6 23  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    9
  subtype2   53    8
  subtype3   50    4
  subtype4   46    9
  subtype5   27    3
  subtype6   23    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        60       53       50       46       27       23
  YES        9        8        4        9        3        4
[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"
D6V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     4
  subtype3                                     1
  subtype4                                     1
  subtype5                                     0
  subtype6                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      0
  subtype3                                      2
  subtype4                                      1
  subtype5                                      0
  subtype6                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          76
  subtype2                                                          64
  subtype3                                                          59
  subtype4                                                          58
  subtype5                                                          31
  subtype6                                                          28
D6V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       76       64
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       59       58
                                                             clus
vv                                                            subtype5 subtype6
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       31       28
[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"
D6V11, continuous
D6V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 63  0  0  4
  subtype2 53  1  0  1
  subtype3 47  2  1  3
  subtype4 53  0  2  2
  subtype5 20  2  1  1
  subtype6 21  2  0  1
D6V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       63       53       47       53       20       21
  R1        0        1        2        0        2        2
  R2        0        0        1        2        1        0
  RX        4        1        3        2        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         7    59
  subtype2     1                         3    55
  subtype3     1                         6    41
  subtype4     1                         0    41
  subtype5     0                         0    26
  subtype6     1                         3    20
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        1        1        0
  BLACK OR AFRICAN AMERICAN        7        3        6        0        0
  WHITE                           59       55       41       41       26
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           20
[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"
D6V15, binary
          cls
clus        0  1
  subtype1  3 54
  subtype2  0 49
  subtype3  0 38
  subtype4  0 32
  subtype5  1 17
  subtype6  0 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   54
  subtype2    0   49
  subtype3    0   38
  subtype4    0   32
  subtype5    1   17
  subtype6    0   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        0        0        0        1        0
  NOT HISPANIC OR LATINO       54       49       38       32       17       23
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 62 42
  subtype2 88 60
  subtype3 90 68
  subtype4 42 42
subtype1 subtype2 subtype3 subtype4 
     104      148      158       84 
subtype1 subtype2 subtype3 subtype4 
      42       60       68       42 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-21-A5DI TCGA-22-5471 TCGA-33-4589 TCGA-43-8118 
       12.20         4.47        32.19        60.66         1.55         2.93 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2721 
       12.03        19.99         3.45        16.77         0.13        32.32 
TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 TCGA-98-8020 TCGA-NK-A5CT TCGA-O2-A52W 
       30.81         9.50        21.04         2.76        65.65         8.58 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-21-1070 TCGA-21-1080 TCGA-21-1081 
       11.34        23.54        92.42       119.54       122.43         9.34 
TCGA-21-1082 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4607 TCGA-22-5491 
      119.80         7.33         1.74        14.10        19.30        56.32 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-39-5024 
       81.24         9.07        16.93         4.01         0.43        82.52 
TCGA-39-5028 TCGA-39-5029 TCGA-43-6771 TCGA-43-A56U TCGA-52-7811 TCGA-56-5897 
        1.71        24.33         5.46        14.20         8.75        12.43 
TCGA-56-7579 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 TCGA-56-8622 TCGA-56-A5DS 
       31.27        17.49        14.96         3.48         1.81         0.26 
TCGA-58-A46L TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 TCGA-60-2724 TCGA-63-7021 
       56.65        21.93        80.45        48.49        23.57        70.42 
TCGA-63-A5MG TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2734 TCGA-66-2759 TCGA-66-2763 
       70.62        89.29        34.59        43.10        25.05         0.99 
TCGA-66-2765 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2788 
        2.01        19.00        19.00        12.03        12.00        22.98 
TCGA-68-7757 TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 
        6.94        75.09        11.18       106.95        46.78        86.76 
TCGA-77-8130 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 
      156.66        11.54        26.40        27.39         6.97        60.53 
TCGA-77-A5G7 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8479 
        5.92        34.95         1.38         1.15        26.79        15.39 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-90-6837 
       38.14        22.59        19.86        30.48        16.21        24.92 
TCGA-92-7340 TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 
        2.70         2.30         4.01        14.14        71.01        17.46 
TCGA-98-A538 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HQ 
       27.16         4.54        64.54        57.30        43.92        14.73 
TCGA-NK-A5CX TCGA-O2-A52V 
        3.65        43.89 

$subtype2
TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-33-4532 TCGA-43-A474 TCGA-51-6867 
       31.99         6.18        27.19       129.01        11.61        61.02 
TCGA-56-8308 TCGA-56-A4BY TCGA-60-2711 TCGA-77-7140 TCGA-77-A5GA TCGA-94-A5I4 
       17.00        17.85        41.42        20.78        42.08        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HR TCGA-18-3408 TCGA-18-3411 
       57.07        19.36        19.10        40.90        75.75       117.57 
TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       92.15         2.79       154.32        49.94        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       70.16        60.89        34.78        38.17        34.75        13.12 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 
       11.77        63.55        14.63        44.25        86.30        11.74 
TCGA-22-5485 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW 
       30.12        97.94       151.27        14.07         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-5240 
       36.62       110.99       118.36        27.16         2.63        50.66 
TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        1.12        26.43         7.82        21.70       126.58       111.35 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 
       68.58       102.18        71.18        55.56        39.12        21.47 
TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
        9.73        13.32         9.83        10.65         0.39         0.39 
TCGA-51-4081 TCGA-56-5898 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-A4BX 
       29.95        18.25        19.76         6.51        33.24        13.32 
TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N 
       18.74        71.24        16.47        34.36        35.24        29.92 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MJ 
       49.48        66.54        29.85        35.90       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2766 
       45.57        25.28        16.96         2.01        21.01         1.02 
TCGA-66-2770 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       23.01        40.01         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 
       49.05         2.73        14.73        12.33        73.12        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 
      140.09         0.49        73.22        70.13         0.16        55.73 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       37.81        53.92        66.51        54.41        65.49        36.36 
TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
      150.25        61.94        27.62        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
       31.30        29.95        24.13        31.56        34.52        10.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR 
       32.71         2.01        36.59        30.28        34.13        19.73 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 
       15.29         3.65        11.77         3.48         5.26         5.03 
TCGA-94-A5I6 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       17.69        18.58        20.71        16.11        13.18        11.84 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NK-A5CR TCGA-O2-A52S 
        2.89        49.28        83.57        12.72 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-22-A5C4 TCGA-33-4533 TCGA-43-5668 TCGA-43-7657 
      123.19         4.80        22.06       133.74        18.38         7.76 
TCGA-43-7658 TCGA-56-8201 TCGA-60-2712 TCGA-63-A5MH TCGA-94-7557 TCGA-NC-A5HD 
       78.18        13.05         9.01        66.61         0.16         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3417 TCGA-21-1078 
       76.80        39.85        16.80         0.43        36.07        15.58 
TCGA-21-1079 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-22-0940 
       31.73        43.23        31.63        88.11        33.93        21.99 
TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       27.02        35.08        24.13         0.79        71.34        79.20 
TCGA-22-5483 TCGA-22-5489 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-AASB 
       18.84        62.86       173.82       103.53        54.44         6.94 
TCGA-33-AASI TCGA-34-2600 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 
       44.19        61.61        65.23        60.30        44.75        39.32 
TCGA-34-5929 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.96        33.90         0.39         7.96         8.12         7.46 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EM TCGA-39-5030 
        6.81         0.39         3.39        37.58        28.50         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       60.53        36.39        68.38        17.06        40.21        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-8115 
       33.11        27.91        22.98        24.89        19.59        13.38 
TCGA-43-8116 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 
       11.77        13.02         4.44        13.91         5.46        30.35 
TCGA-56-6545 TCGA-56-7223 TCGA-56-7580 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
       21.90        14.53        30.41         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
        1.35        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 
       14.47        13.25        13.55        29.95        21.11        96.82 
TCGA-60-2713 TCGA-60-2720 TCGA-60-2726 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 
       56.91         3.19        11.77        52.67        68.15        55.30 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       58.65        14.99        78.28        16.37        36.16        53.88 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 
        0.99         2.01         0.92         0.99        43.99         2.01 
TCGA-66-2769 TCGA-66-2781 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        7.07         3.98         1.97         4.04        22.98        10.06 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 
       13.35        16.18        29.56        32.55         6.51        39.09 
TCGA-77-8139 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 
      104.09       132.36        22.29        38.86        41.39        32.91 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
       18.94        25.15         0.76        13.22        22.45         5.29 
TCGA-85-8481 TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A510 TCGA-85-A511 
        7.76        18.08        30.97        24.36        15.85        14.96 
TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
       12.39         2.93        20.22        22.62        10.59         4.01 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       27.68        30.81        30.67        21.34        18.15         2.01 
TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HT TCGA-O2-A52N 
       13.41         1.22         4.21        25.32        26.43        33.07 
TCGA-O2-A52Q TCGA-O2-A5IB 
        3.72        11.18 

$subtype4
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 
       14.93        48.82        64.93        19.76        17.88        22.49 
TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2715 TCGA-68-8250 TCGA-90-7964 TCGA-94-7943 
       21.04         3.58        35.34         8.02        14.07        18.38 
TCGA-98-A539 TCGA-98-A53D TCGA-18-3421 TCGA-21-5784 TCGA-21-5787 TCGA-22-1002 
        5.69        21.21        86.96        41.69        10.82         4.31 
TCGA-22-1005 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 
       64.21        20.48        48.33         0.56        32.02         9.57 
TCGA-22-5492 TCGA-33-4547 TCGA-33-6738 TCGA-34-2608 TCGA-34-5234 TCGA-34-8454 
       16.64        79.53        63.35        32.88        74.66        38.79 
TCGA-34-8455 TCGA-39-5011 TCGA-39-5022 TCGA-43-6773 TCGA-46-3766 TCGA-52-7622 
        4.04       133.25        55.20         3.81        12.16        28.34 
TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7731 TCGA-56-8623 TCGA-56-8624 
       27.45        28.96        18.48         0.10        22.75        13.81 
TCGA-56-A49D TCGA-58-8386 TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2698 
       20.94         0.03        34.78        85.12        12.23        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2714 TCGA-60-2719 TCGA-60-2725 TCGA-63-7020 
       37.94        92.71        50.33        42.64        26.83        70.13 
TCGA-63-A5MN TCGA-66-2742 TCGA-66-2753 TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 
       11.34        21.07         1.02         2.01         3.02         2.01 
TCGA-66-2783 TCGA-66-2786 TCGA-68-7756 TCGA-70-6722 TCGA-77-8131 TCGA-77-8138 
       24.95        25.97         6.64        12.07        12.59        17.72 
TCGA-77-8146 TCGA-77-A5FZ TCGA-85-6175 TCGA-85-8049 TCGA-85-8072 TCGA-85-8351 
      104.84       126.18         9.67        19.04        30.64        16.77 
TCGA-85-8353 TCGA-85-8584 TCGA-85-A50M TCGA-85-A513 TCGA-94-8491 TCGA-96-8169 
        3.09        12.59        27.16        29.92        26.63        18.31 
TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ TCGA-XC-AA0X 
       21.44        27.02        20.32        12.89        13.74         0.20 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.16     0.07     0.03 
subtype1 subtype2 subtype3 subtype4 
  156.66   154.32   173.82   133.25 
subtype1 subtype2 subtype3 subtype4 
  19.000   29.985   20.680   20.710 
[1] "0.1 - 156.7 (19.0)" "0.2 - 154.3 (30.0)" "0.1 - 173.8 (20.7)"
[4] "0.0 - 133.2 (20.7)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       19       36        1         9        20         0
  subtype2       1       18       52        1        24        30         1
  subtype3       1       30       38        1        25        33         2
  subtype4       0       23       25        0         7        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         16          3        1
  subtype2         15          7        0
  subtype3         21          5        3
  subtype4         11          3        3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        1        0
  STAGE IA         19       18       30       23
  STAGE IB         36       52       38       25
  STAGE II          1        1        1        0
  STAGE IIA         9       24       25        7
  STAGE IIB        20       30       33       11
  STAGE III         0        1        2        0
  STAGE IIIA       16       15       21       11
  STAGE IIIB        3        7        5        3
  STAGE IV          1        0        3        3
[1] 10  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 23 64 15  4
  subtype2 28 97 17  9
  subtype3 37 89 27  7
  subtype4 26 43 12  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       23       28       37       26
  T2       64       97       89       43
  T3       15       17       27       12
  T4        4        9        7        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1  69  25  10   1
  subtype2  91  47  11   1
  subtype3 103  46  10   1
  subtype4  56  13   9   2
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       69       91      103       56
  N1       25       47       46       13
  N2       10       11       10        9
  N3        1        1        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1  84   1
  subtype2 127   0
  subtype3 129   3
  subtype4  71   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84    1
  subtype2  127    0
  subtype3  129    3
  subtype4   71    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       84      127      129       71
  1        1        0        3        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  26  80
  subtype2  35 116
  subtype3  44 116
  subtype4  25  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   80
  subtype2   35  116
  subtype3   44  116
  subtype4   25   59
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       26       35       44       25
  MALE         80      116      116       59
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1  79  11
  subtype2 119  17
  subtype3 118  17
  subtype4  68   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79   11
  subtype2  119   17
  subtype3  118   17
  subtype4   68    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        79      119      118       68
  YES       11       17       17        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     6
  subtype3                                     7
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      1
  subtype3                                      1
  subtype4                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         102
  subtype2                                                         144
  subtype3                                                         151
  subtype4                                                          82
D7V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      102      144
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      151       82
[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"
D7V11, continuous
D7V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  82   2   2   3
  subtype2 126   6   0   8
  subtype3 123   3   1   7
  subtype4  67   1   1   5
D7V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       82      126      123       67
  R1        2        6        3        1
  R2        2        0        1        1
  RX        3        8        7        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         7    69
  subtype2     1                         9   105
  subtype3     3                        10   115
  subtype4     3                         4    60
D7V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        3        3
  BLACK OR AFRICAN AMERICAN        7        9       10        4
  WHITE                           69      105      115       60
[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"
D7V15, binary
          cls
clus         0   1
  subtype1   4  62
  subtype2   1  92
  subtype3   1 109
  subtype4   2  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   62
  subtype2    1   92
  subtype3    1  109
  subtype4    2   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        1        1        2
  NOT HISPANIC OR LATINO       62       92      109       53
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 107  71
  subtype2 111  76
  subtype3  64  65
subtype1 subtype2 subtype3 
     178      187      129 
subtype1 subtype2 subtype3 
      71       76       65 
$subtype1
TCGA-18-3406 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       12.20        32.19        14.93        64.93        22.06       129.01 
TCGA-33-4589 TCGA-39-5039 TCGA-43-A56V TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
        1.55        17.88        12.03        21.04         0.13         3.58 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       35.34        32.32         8.02        30.81         9.50        14.07 
TCGA-94-7033 TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM TCGA-O2-A52W 
       21.04         2.76         5.69         0.07        39.85         8.58 
TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 
       23.54        92.42        86.96       119.54        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-22-1011 
      122.43         9.34       119.80        31.63        41.69         1.74 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5478 
       20.48        24.13        32.02        19.30        11.77         0.79 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4582 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 
       16.64        79.53       103.53        61.61        32.88        81.24 
TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       74.66        16.93        44.75         4.96        38.79         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       33.90         4.01         0.43        82.52         1.71        24.33 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-8115 TCGA-43-A56U 
       33.11        27.91        24.89         5.46        13.38        14.20 
TCGA-46-3766 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
       12.16        30.35         8.75        28.96        12.43        21.90 
TCGA-56-7222 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 
       18.48        30.41         0.10        17.49        14.96         3.48 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW 
        1.35         1.81        13.81        10.36        20.94        19.23 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-60-2698 
        0.26         0.03        13.25        34.78        85.12        10.22 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 
       21.93        80.45        48.49        42.64         3.19        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       26.83        11.77        70.13        68.15        70.62        58.65 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 
       89.29        16.37        36.16        34.59        43.10        21.07 
TCGA-66-2753 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
        1.02         0.99         2.01         2.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 
        2.01        19.00        12.03         3.98        12.00        25.97 
TCGA-66-2788 TCGA-66-2793 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 
       22.98        10.06         6.64         6.94        16.18        12.07 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 
       75.09        11.18        73.22       106.95        46.78        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
      156.66        12.59        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5G1 
       26.40        27.39         6.97       104.84        60.53       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6175 TCGA-85-8276 TCGA-85-8351 TCGA-85-8479 
       22.29         5.92         9.67        34.52        16.77        15.39 
TCGA-85-8481 TCGA-85-8582 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
        7.76        38.14        19.86        30.48        19.73        16.21 
TCGA-90-6837 TCGA-92-7340 TCGA-92-8065 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 
       24.92         2.70         2.30        26.63        14.14        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-A538 TCGA-98-A53H 
       18.31        17.46        27.68        30.81        27.16        20.32 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO 
       12.89        13.41         4.54        64.54        57.30        43.92 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52V 
       14.73        26.43         3.65        43.89 

$subtype2
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-5471 TCGA-43-8118 
        4.47        31.99         6.18        27.19        60.66         2.93 
TCGA-43-A474 TCGA-51-6867 TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        61.02        19.99         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-60-2711 TCGA-77-7140 TCGA-77-A5GA TCGA-94-A5I4 TCGA-96-7545 
       17.85        41.42        20.78        42.08        16.14        57.07 
TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 
       19.36        19.10        76.80        40.90         0.43        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
      117.57        11.34        92.15         2.79       154.32        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-22-0944 
       46.88        99.16        70.16        60.89        34.78         7.33 
TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4609 TCGA-22-5473 
       14.10        38.17        34.75        13.12         9.57        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 
       14.63        44.25        86.30        11.74        30.12        56.32 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       97.94       151.27        14.07        63.35         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-5231 
       36.62       110.99       118.36        27.16         2.63        65.23 
TCGA-34-5236 TCGA-34-5240 TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-A5EL 
        9.07        50.66         1.12        26.43         7.82        37.58 
TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
       28.50        21.70       126.58       111.35        68.58        55.20 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 
      102.18        60.53        71.18        55.56        39.12        21.47 
TCGA-43-6773 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        3.81         9.73        13.32         9.83        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-56-5898 TCGA-56-7579 
        0.39         0.39        29.95        28.34        18.25        31.27 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4ZK 
       19.76         6.51        33.24        15.81        13.32        18.74 
TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       14.47        71.24        16.47        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 
       29.92        49.48        66.54        56.91        29.85        35.90 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       70.42        55.30       102.67        59.97        45.57        25.28 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 
       16.96         2.01        21.01        25.05         1.02         2.01 
TCGA-66-2770 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
       23.01        24.95        40.01         5.03        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-70-6723 TCGA-77-6843 
        4.01        49.05         2.73        14.73        12.33        73.12 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 
       23.28       140.09         0.49        70.13         0.16        55.73 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       37.81        53.92        66.51        54.41        65.49        36.36 
TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
      150.25        61.94        27.62        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 
       34.95        31.30         1.15        29.95        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8355 
       31.56        26.79        30.64        10.09        32.71         2.01 
TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A511 TCGA-85-A512 
       36.59        22.59        30.28        34.13        14.96        15.29 
TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 
        3.65        11.77         3.48         4.01         5.26         4.01 
TCGA-94-8490 TCGA-94-A5I6 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
        5.03        17.69        18.15        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NK-A5CR TCGA-O2-A52S 
       13.18        11.84         2.89        49.28        83.57        12.72 
TCGA-XC-AA0X 
        0.20 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-22-1017 TCGA-33-4533 TCGA-33-6737 TCGA-43-2578 
      123.19         4.80        48.82       133.74        19.76        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-56-8201 TCGA-60-2712 TCGA-63-A5MH 
       18.38         7.76        78.18        13.05         9.01        66.61 
TCGA-94-7557 TCGA-94-7943 TCGA-98-A53D TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3417 
        0.16        18.38        21.21        65.65        16.80        36.07 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 
       43.23        88.11        33.93        10.82        21.99         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-5480 
       64.21        27.02        35.08        48.33         0.56        71.34 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-33-4566 TCGA-33-4587 TCGA-33-AASB 
       79.20        18.84        62.86       173.82        54.44         6.94 
TCGA-33-AASI TCGA-34-5239 TCGA-34-5928 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       44.19        60.30        39.32         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5030 
        7.46         6.81         0.39         3.39       133.25         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 
       36.39        68.38        17.06        40.21        38.66        22.98 
TCGA-43-7656 TCGA-43-8116 TCGA-46-3767 TCGA-46-3769 TCGA-52-7809 TCGA-52-7812 
       19.59        11.77        13.02         4.44         5.46        27.45 
TCGA-56-7223 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8626 
       14.53         4.93        26.89        14.07        22.75         9.93 
TCGA-56-8628 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 
       20.25        13.55        29.95        21.11        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2714 TCGA-63-6202 TCGA-63-A5MM TCGA-63-A5MN 
       37.94        92.71        50.33        52.67        14.99        11.34 
TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       78.28        53.88         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 
       43.99         7.07         1.97         4.04        22.98        13.35 
TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6560 
       29.56        32.55         6.51       126.18        38.86        41.39 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 
       32.91         1.38        18.94        25.15         0.76        13.22 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4JB 
       22.45         5.29         3.09        12.59        18.08        30.97 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 
       24.36        27.16        15.85        29.92        12.39         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
       20.22        22.62        10.59        21.44        30.67        21.34 
TCGA-98-A53B TCGA-98-A53C TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP 
        2.01        27.02         1.22        13.74         4.21        25.32 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       33.07         3.72        11.18 

subtype1 subtype2 subtype3 
    0.03     0.16     0.16 
subtype1 subtype2 subtype3 
  156.66   154.32   173.82 
subtype1 subtype2 subtype3 
   20.09    27.19    20.25 
[1] "0.0 - 156.7 (20.1)" "0.2 - 154.3 (27.2)" "0.2 - 173.8 (20.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       30       60        1        20        31         0
  subtype2       1       26       62        2        28        39         1
  subtype3       1       34       29        0        17        24         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         28          4        4
  subtype2         20         10        0
  subtype3         15          4        3
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         30       26       34
  STAGE IB         60       62       29
  STAGE II          1        2        0
  STAGE IIA        20       28       17
  STAGE IIB        31       39       24
  STAGE III         0        1        2
  STAGE IIIA       28       20       15
  STAGE IIIB        4       10        4
  STAGE IV          4        0        3
[1] 10  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  35 105  32   7
  subtype2  38 121  22  10
  subtype3  41  67  17   6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       35       38       41
  T2      105      121       67
  T3       32       22       17
  T4        7       10        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 118  43  14   1
  subtype2 116  55  16   3
  subtype3  85  33  10   1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      118      116       85
  N1       43       55       33
  N2       14       16       10
  N3        1        3        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1 145   4
  subtype2 160   0
  subtype3 106   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  145    4
  subtype2  160    0
  subtype3  106    3
   clus
vv  subtype1 subtype2 subtype3
  0      145      160      106
  1        4        0        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  56 123
  subtype2  38 153
  subtype3  36  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  123
  subtype2   38  153
  subtype3   36   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       38       36
  MALE        123      153       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"
D8V8, binary
          cls
clus         0   1
  subtype1 141  17
  subtype2 143  27
  subtype3 100   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  141   17
  subtype2  143   27
  subtype3  100    9
     clus
vv    subtype1 subtype2 subtype3
  NO       141      143      100
  YES       17       27        9
[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"
D8V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     7
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      3
  subtype2                                      1
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         175
  subtype2                                                         183
  subtype3                                                         121
D8V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      175      183
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      121
[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"
D8V11, continuous
D8V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 142   2   1   9
  subtype2 153   7   3   9
  subtype3 103   3   0   5
D8V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142      153      103
  R1        2        7        3
  R2        1        3        0
  RX        9        9        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        11   116
  subtype2     2                        13   133
  subtype3     4                         6   100
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        4
  BLACK OR AFRICAN AMERICAN       11       13        6
  WHITE                          116      133      100
[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"
D8V15, binary
          cls
clus         0   1
  subtype1   4 104
  subtype2   2 119
  subtype3   2  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  104
  subtype2    2  119
  subtype3    2   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO      104      119       93
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 104  78
  subtype2  50  36
  subtype3  68  56
  subtype4  50  29
subtype1 subtype2 subtype3 subtype4 
     182       86      124       79 
subtype1 subtype2 subtype3 subtype4 
      78       36       56       29 
$subtype1
TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-5471 TCGA-33-4532 TCGA-33-4533 
        4.80        31.99        27.19        60.66       129.01       133.74 
TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       19.76        28.96        22.49        18.38         7.76        78.18 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       13.05         3.45        16.77        41.42         9.01        32.32 
TCGA-94-A5I4 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 
       16.14         0.07        76.80        39.85        40.90        16.80 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 
       86.96        49.94        99.16        70.16        15.58        31.73 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
      122.43        43.23        31.63        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4601 
        7.33        14.10        20.48        48.33        24.13        34.75 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 
       13.12        19.30        11.77        14.63        71.34        79.20 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       62.86        56.32        97.94        79.53       173.82       103.53 
TCGA-33-4586 TCGA-33-4587 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-5929 
       14.07        54.44         6.94        44.19       118.36         4.96 
TCGA-34-7107 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 
        1.12        33.90         4.01         0.43         0.39         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EM TCGA-39-5011 
        6.81         0.39         3.39        37.58        28.50       133.25 
TCGA-39-5021 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       68.58        24.33        60.53        36.39        68.38        71.18 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-7656 TCGA-46-3765 TCGA-46-3768 
       40.21        39.12        33.11        19.59        13.32         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4081 TCGA-52-7809 TCGA-56-1622 TCGA-56-7223 
        4.44        10.65        29.95         5.46        28.96        14.53 
TCGA-56-7580 TCGA-56-7823 TCGA-56-8307 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK 
       30.41        33.24        26.89        15.81        19.23        18.74 
TCGA-58-8387 TCGA-58-A46N TCGA-60-2695 TCGA-60-2708 TCGA-60-2713 TCGA-60-2714 
       13.25        29.92        21.11        80.45        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-63-7021 TCGA-63-A5MJ 
       48.49        42.64        35.90        23.57        70.42        59.97 
TCGA-63-A5ML TCGA-63-A5MR TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       45.57        89.29        43.10        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        2.01         0.92        25.05         0.99         2.01         1.02 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        2.01        19.00         2.01        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
       24.95         1.97        22.98         4.04         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-68-8251 TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 
       10.06         4.01        13.35        12.33        23.28        11.18 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7465 TCGA-77-8128 TCGA-77-8143 TCGA-77-8144 
      140.09        70.13        32.55        37.81        26.40        27.39 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-7699 TCGA-85-7710 
       60.53       150.25        22.29        61.94        32.91         1.38 
TCGA-85-7843 TCGA-85-8276 TCGA-85-8288 TCGA-85-8479 TCGA-85-A4CN TCGA-85-A50Z 
        1.15        34.52        13.22        15.39        34.13        16.21 
TCGA-85-A53L TCGA-90-7767 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 
       12.39         2.93        10.59         3.48         5.26         5.03 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53J TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG 
       27.16        18.15        20.71        16.11        11.84        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-O2-A52Q 
        1.22        57.30         4.21         2.89        43.92         3.72 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

$subtype2
TCGA-34-2604 TCGA-43-8118 TCGA-43-A56V TCGA-51-6867 TCGA-56-8308 TCGA-56-A4BY 
       31.50         2.93        12.03        61.02        17.00        17.85 
TCGA-56-A5DR TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-94-7557 
        0.13        66.61         8.02        20.78         9.50         0.16 
TCGA-96-A4JK TCGA-O2-A52W TCGA-21-5783 TCGA-22-5478 TCGA-33-A4WN TCGA-33-A5GW 
       19.36         8.58        88.11         0.79         4.70         0.30 
TCGA-33-AASD TCGA-34-2600 TCGA-34-5231 TCGA-34-5927 TCGA-34-5928 TCGA-34-8456 
      110.99        61.61        65.23        44.75        39.32        26.43 
TCGA-37-A5EN TCGA-39-5027 TCGA-43-5670 TCGA-43-6143 TCGA-43-8115 TCGA-43-8116 
       21.70       102.18        27.91        22.98        13.38        11.77 
TCGA-43-A56U TCGA-46-6026 TCGA-56-7579 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
       14.20        13.91        31.27        14.96         4.93         3.48 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8390 TCGA-58-8392 
       10.36        20.94        13.32        14.47        29.95        16.47 
TCGA-60-2703 TCGA-60-2704 TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY 
       96.82        37.94        58.65        78.28        53.88        34.59 
TCGA-77-6842 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
       29.56        39.09       104.09        11.54         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-8070 
       54.41        65.49        36.36       132.36         5.92        31.56 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB 
        0.76        16.77        32.71        18.08        22.59        30.97 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-92-8063 TCGA-92-8065 
       19.73        15.85        14.96         3.65         4.01         2.30 
TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-98-8022 TCGA-98-A53B 
        4.01        14.14        17.69        18.31        30.67         2.01 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR 
       13.41         4.54        49.28        25.32        26.43        83.57 
TCGA-O2-A52N TCGA-O2-A52V 
       33.07        43.89 

$subtype3
TCGA-21-A5DI TCGA-22-5472 TCGA-22-A5C4 TCGA-34-2609 TCGA-39-5039 TCGA-56-A4ZJ 
       32.19        64.93        22.06        31.27        17.88        21.04 
TCGA-60-2696 TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
        3.58        30.81        14.07        21.04        18.38        57.07 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NK-A7XE TCGA-21-5784 TCGA-22-1011 
        2.76         5.69        21.21         0.43        41.69         1.74 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4609 TCGA-22-5479 TCGA-22-5483 TCGA-22-5492 
       35.08         0.56         9.57        86.30        18.84        16.64 
TCGA-33-6738 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       63.35        32.88        81.24        74.66         9.07        60.30 
TCGA-34-5241 TCGA-34-8454 TCGA-34-8455 TCGA-37-4130 TCGA-39-5019 TCGA-39-5022 
       16.93        38.79         4.04         8.12       111.35        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5040 TCGA-43-2581 TCGA-43-6647 
       82.52         1.71         1.94        17.06        38.66        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-46-3766 TCGA-46-3767 TCGA-52-7810 TCGA-52-7811 
        5.46         3.81        12.16        13.02        30.35         8.75 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
       27.45        12.43        21.90         0.10        17.49         1.35 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-58-8386 TCGA-58-8388 
       22.75        13.81         9.93        20.25         0.03        13.55 
TCGA-58-A46J TCGA-60-2697 TCGA-60-2698 TCGA-60-2720 TCGA-60-2725 TCGA-63-6202 
       85.12        12.23        10.22         3.19        26.83        52.67 
TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MT TCGA-63-A5MV 
       70.13        68.15        70.62        14.99        16.37        36.16 
TCGA-66-2767 TCGA-66-2786 TCGA-66-2790 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
        2.01        25.97        22.98         6.64         6.94        16.18 
TCGA-70-6722 TCGA-77-6844 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
       12.07        75.09       106.95        46.78         6.51        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8146 TCGA-77-A5FZ 
      156.66        12.59        53.92        17.72       104.84       126.18 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-8048 
        9.67        41.39        40.24        34.95        31.30        25.15 
TCGA-85-8049 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       19.04        22.45         3.09         2.01         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       38.14        12.59        19.86        24.36        30.48        27.16 
TCGA-85-A513 TCGA-90-6837 TCGA-92-7340 TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 
       29.92        24.92         2.70        26.63        71.01        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       27.68        21.44        21.34        27.02        20.32        12.89 
TCGA-NC-A5HJ TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-XC-AA0X 
       13.74        14.73         3.65         0.20 

$subtype4
TCGA-18-3406 TCGA-18-3407 TCGA-33-4589 TCGA-43-A474 TCGA-56-7221 TCGA-77-A5GA 
       12.20         4.47         1.55        11.61        19.99        42.08 
TCGA-J1-A4AH TCGA-NK-A5CT TCGA-18-3408 TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 
       19.10        65.65        75.75         2.79       154.32        60.89 
TCGA-21-1077 TCGA-22-4605 TCGA-22-5473 TCGA-22-5477 TCGA-22-5482 TCGA-22-5485 
       34.78        32.02        63.55        44.25        11.74        30.12 
TCGA-33-4583 TCGA-33-AAS8 TCGA-33-AASL TCGA-34-2596 TCGA-34-5240 TCGA-39-5037 
      151.27        36.62        27.16         2.63        50.66        55.56 
TCGA-43-6770 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-56-5898 
       21.47         9.73         0.39         0.39        28.34        18.25 
TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-8309 TCGA-56-8622 TCGA-58-8391 
       18.48        19.76         6.51        14.07         1.81        71.24 
TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2706 TCGA-60-2709 
       34.78        34.36        56.65        35.24        92.71        49.48 
TCGA-60-2710 TCGA-60-2722 TCGA-63-A5MB TCGA-63-A5MN TCGA-63-A5MP TCGA-66-2727 
       66.54        29.85       102.67        11.34        25.28        16.96 
TCGA-66-2737 TCGA-66-2758 TCGA-66-2770 TCGA-66-2787 TCGA-66-2794 TCGA-66-2800 
        2.01        21.01        23.01        40.01        54.08        49.05 
TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
        2.73        14.73        73.12         0.49        73.22         0.16 
TCGA-77-8009 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 
       55.73        27.62        38.86         6.41        36.53        29.95 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 TCGA-85-A4CL 
       18.94        24.13        26.79        30.64         5.29        30.28 
TCGA-85-A512 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-98-8021 TCGA-98-A53I 
       15.29        11.77        20.22        22.62        30.81        18.58 
TCGA-LA-A446 
       13.18 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.13     0.03     0.16 
subtype1 subtype2 subtype3 subtype4 
  173.82   132.36   156.66   154.32 
subtype1 subtype2 subtype3 subtype4 
  23.130   20.255   21.040   26.790 
[1] "0.1 - 173.8 (23.1)" "0.1 - 132.4 (20.3)" "0.0 - 156.7 (21.0)"
[4] "0.2 - 154.3 (26.8)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       20       65        2        19        37         3
  subtype2       3       19       20        1        11        18         0
  subtype3       0       26       32        0        20        24         0
  subtype4       0       18       27        0        12        14         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         27          7        3
  subtype2         12          3        1
  subtype3         17          3        2
  subtype4          5          3        0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        3        0        0
  STAGE IA         20       19       26       18
  STAGE IB         65       20       32       27
  STAGE II          2        1        0        0
  STAGE IIA        19       11       20       12
  STAGE IIB        37       18       24       14
  STAGE III         3        0        0        0
  STAGE IIIA       27       12       17        5
  STAGE IIIB        7        3        3        3
  STAGE IV          3        1        2        0
[1] 10  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  28 120  27  10
  subtype2  21  49  15   3
  subtype3  33  65  21   6
  subtype4  24  47   6   3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       28       21       33       24
  T2      120       49       65       47
  T3       27       15       21        6
  T4       10        3        6        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 114  47  21   3
  subtype2  56  27   5   0
  subtype3  78  30  10   1
  subtype4  53  23   4   0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      114       56       78       53
  N1       47       27       30       23
  N2       21        5       10        4
  N3        3        0        1        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"
D9V6, binary
          cls
clus         0   1
  subtype1 160   3
  subtype2  61   1
  subtype3 102   2
  subtype4  67   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  160    3
  subtype2   61    1
  subtype3  102    2
  subtype4   67    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      160       61      102       67
  1        3        1        2        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"
D9V7, binary
          cls
clus         0   1
  subtype1  48 137
  subtype2  22  66
  subtype3  32  93
  subtype4  22  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48  137
  subtype2   22   66
  subtype3   32   93
  subtype4   22   58
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       48       22       32       22
  MALE        137       66       93       58
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1 123  22
  subtype2  76   9
  subtype3 106   9
  subtype4  66   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  123   22
  subtype2   76    9
  subtype3  106    9
  subtype4   66    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       123       76      106       66
  YES       22        9        9        8
[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"
D9V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     7
  subtype2                                     1
  subtype3                                     1
  subtype4                                     4
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      3
  subtype2                                      0
  subtype3                                      3
  subtype4                                      0
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         174
  subtype2                                                          87
  subtype3                                                         121
  subtype4                                                          76
D9V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7        1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      174       87
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      121       76
[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"
D9V11, continuous
D9V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 154   3   2   6
  subtype2  62   3   1   6
  subtype3  99   1   0   6
  subtype4  64   4   0   3
D9V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      154       62       99       64
  R1        3        3        1        4
  R2        2        1        0        0
  RX        6        6        6        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         8   125
  subtype2     0                         8    61
  subtype3     5                         8    91
  subtype4     1                         6    56
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        5        1
  BLACK OR AFRICAN AMERICAN        8        8        8        6
  WHITE                          125       61       91       56
[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"
D9V15, binary
          cls
clus         0   1
  subtype1   3 105
  subtype2   0  61
  subtype3   2  83
  subtype4   2  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  105
  subtype2    0   61
  subtype3    2   83
  subtype4    2   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        2        2
  NOT HISPANIC OR LATINO      105       61       83       53
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  54  33
  subtype2  65  52
  subtype3 115  84
  subtype4  38  30
subtype1 subtype2 subtype3 subtype4 
      87      117      199       68 
subtype1 subtype2 subtype3 subtype4 
      33       52       84       30 
$subtype1
TCGA-18-3406 TCGA-22-5471 TCGA-33-4589 TCGA-34-2605 TCGA-43-A474 TCGA-J1-A4AH 
       12.20        60.66         1.55        28.96        11.61        19.10 
TCGA-18-3408 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1076 
       75.75         2.79       154.32        49.94        99.16        60.89 
TCGA-21-1077 TCGA-22-1012 TCGA-22-4609 TCGA-22-5473 TCGA-22-5477 TCGA-22-5482 
       34.78        14.10         9.57        63.55        44.25        11.74 
TCGA-33-4583 TCGA-33-4586 TCGA-33-AAS8 TCGA-33-AASL TCGA-34-2596 TCGA-34-5240 
      151.27        14.07        36.62        27.16         2.63        50.66 
TCGA-39-5022 TCGA-43-6770 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       55.20        21.47         9.73         0.39         0.39        29.95 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8309 TCGA-56-8622 TCGA-58-8391 TCGA-58-A46K 
       19.76         6.51        14.07         1.81        71.24        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 
       35.24        29.92        49.48        66.54        56.91        29.85 
TCGA-60-2723 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       35.90        68.15       102.67        59.97        45.57        25.28 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2770 TCGA-66-2787 TCGA-66-2791 
       16.96         2.01        21.01        23.01        40.01         5.03 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 
       54.08         4.01        49.05         2.73        14.73        73.12 
TCGA-77-7141 TCGA-77-7338 TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF 
        0.49         0.16        55.73       150.25        22.29        27.62 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8071 
        6.41        36.53        29.95        18.94        24.13        26.79 
TCGA-85-8072 TCGA-85-8352 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A512 TCGA-90-7769 
       30.64         5.29        30.28        34.13        15.29        11.77 
TCGA-90-A4EE TCGA-94-8491 TCGA-94-A5I6 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53I 
       22.62        26.63        17.69        21.34        18.15        18.58 
TCGA-98-A53J TCGA-LA-A446 TCGA-O2-A52S 
       20.71        13.18        12.72 

$subtype2
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-39-5039 TCGA-43-7657 
        4.47         4.80        31.99        27.19        17.88         7.76 
TCGA-43-7658 TCGA-56-8201 TCGA-56-8504 TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 
       78.18        13.05        16.77         3.58         9.01        32.32 
TCGA-94-7033 TCGA-94-A5I4 TCGA-NC-A5HE TCGA-NC-A5HR TCGA-18-3412 TCGA-18-3415 
       21.04        16.14        76.80        40.90        11.34        92.15 
TCGA-18-3417 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-22-0940 
       36.07        15.58       122.43        43.23        33.93        21.99 
TCGA-22-0944 TCGA-22-1011 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
        7.33         1.74        48.33        34.75        13.12        19.30 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-22-5491 
       14.63        86.30        71.34        79.20        62.86        56.32 
TCGA-33-4547 TCGA-33-4566 TCGA-33-AASJ TCGA-34-5929 TCGA-34-7107 TCGA-34-A5IX 
       79.53       173.82       118.36         4.96         1.12        33.90 
TCGA-37-3783 TCGA-37-3792 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5021 TCGA-39-5036 
        4.01         0.39        37.58       133.25        68.58        71.18 
TCGA-43-2576 TCGA-43-2581 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 
       40.21        38.66         5.46        13.32        12.16         9.83 
TCGA-46-3769 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-6545 TCGA-56-7579 
        4.44         5.46        30.35        12.43        21.90        31.27 
TCGA-56-7580 TCGA-56-7823 TCGA-56-8307 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-8388 
       30.41        33.24        26.89        19.23        18.74        13.55 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2716 TCGA-63-7021 TCGA-63-A5MR TCGA-66-2734 
       56.65        21.11        48.49        70.42        89.29        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 
       21.07         0.99         1.02         0.92        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2780 
        2.01         1.02         2.01         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-68-8251 TCGA-70-6723 TCGA-77-6845 
        3.98        12.00        25.97        13.35        12.33        23.28 
TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 
       11.18        70.13       106.95        32.55        37.81        53.92 
TCGA-77-A5G8 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-8048 TCGA-85-8276 
       61.94        34.95        31.30         1.38        25.15        34.52 
TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 TCGA-85-A53L TCGA-90-7767 TCGA-90-A59Q 
       13.22         2.01        15.39        12.39         2.93        10.59 
TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-96-7544 TCGA-L3-A524 TCGA-NC-A5HG 
        3.48         5.26         5.03        71.01        16.11        64.54 
TCGA-NC-A5HL TCGA-NK-A5CX TCGA-O2-A52Q 
        2.89         3.65         3.72 

$subtype3
TCGA-21-A5DI TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-34-2604 TCGA-34-2609 
       32.19        22.06       129.01       133.74        31.50        31.27 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A56V TCGA-51-6867 TCGA-56-7221 
       22.49        18.38         2.93        12.03        61.02        19.99 
TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2711 TCGA-63-A5MH 
        3.45        17.00        17.85         0.13        41.42        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-94-7557 TCGA-96-A4JK TCGA-98-8020 
        8.02        20.78         9.50         0.16        19.36         2.76 
TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        5.69         0.07        39.85        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1075 
        8.58       117.57        23.54        92.42        86.96        70.16 
TCGA-21-1079 TCGA-21-5782 TCGA-21-5783 TCGA-21-5787 TCGA-22-4591 TCGA-22-4593 
       31.73        31.63        88.11        10.82        20.48        35.08 
TCGA-22-4595 TCGA-22-4605 TCGA-22-4613 TCGA-22-5478 TCGA-22-5483 TCGA-22-5485 
       24.13        32.02        11.77         0.79        18.84        30.12 
TCGA-22-5492 TCGA-33-4582 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB 
       16.64       103.53        54.44         4.70         0.30         6.94 
TCGA-33-AASD TCGA-34-2600 TCGA-34-5231 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
      110.99        61.61        65.23        16.93        44.75        39.32 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
       38.79        26.43         0.43         8.12         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5024 TCGA-39-5027 
        0.39         3.39        28.50        21.70        82.52       102.18 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 
       24.33         1.94        60.53        36.39        55.56        17.06 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 
       39.12        33.11        27.91        22.98        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3767 TCGA-46-6026 TCGA-52-7622 TCGA-52-7811 
       11.77        14.20        13.02        13.91        28.34         8.75 
TCGA-56-1622 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7731 TCGA-56-7822 
       28.96        18.25        18.48        14.53         0.10        17.49 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 
       14.96         4.93         3.48         1.35        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8387 
       20.25        15.81        20.94        13.32        14.47        13.25 
TCGA-58-8390 TCGA-58-8392 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       29.95        16.47        96.82        37.94        92.71        80.45 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-A5MI 
       50.33        42.64        23.57        26.83        70.13        58.65 
TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       11.34        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2754 TCGA-66-2777 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        2.01         2.01         1.97        22.98         4.04        22.98 
TCGA-66-2792 TCGA-66-2793 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
       30.02        10.06         6.94        16.18        29.56        75.09 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7463 TCGA-77-8008 TCGA-77-8136 TCGA-77-8138 
      140.09        73.22        46.78        86.76        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GH 
       54.41        65.49        36.36       132.36         5.92        38.86 
TCGA-85-6560 TCGA-85-7699 TCGA-85-7843 TCGA-85-8049 TCGA-85-8070 TCGA-85-8287 
       41.39        32.91         1.15        19.04        31.56         0.76 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
       16.77        32.71         7.76        36.59        38.14        18.08 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       22.59        30.97        19.73        15.85        14.96         3.65 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 
       20.22         4.01         2.30         4.01        14.14        18.31 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-LA-A7SW TCGA-MF-A522 
       30.81        30.67        27.16         2.01        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        4.54         1.22        57.30         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52V 
       25.32        14.73        26.43        83.57        33.07        43.89 
TCGA-O2-A5IB 
       11.18 

$subtype4
TCGA-22-5472 TCGA-33-6737 TCGA-56-A4ZJ TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 
       64.93        19.76        21.04        42.08        30.81        14.07 
TCGA-94-7943 TCGA-96-7545 TCGA-98-A53D TCGA-21-5784 TCGA-22-4596 TCGA-33-4538 
       18.38        57.07        21.21        41.69         0.56        97.94 
TCGA-33-6738 TCGA-33-AASI TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       63.35        44.19        32.88        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-8455 TCGA-39-5019 TCGA-39-5028 TCGA-39-5035 TCGA-43-6647 
       60.30         4.04       111.35         1.71        68.38        24.89 
TCGA-43-6773 TCGA-46-6025 TCGA-52-7812 TCGA-56-8623 TCGA-56-8624 TCGA-58-8386 
        3.81        10.65        27.45        22.75        13.81         0.03 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2698 TCGA-60-2720 TCGA-63-6202 
       34.78        85.12        12.23        10.22         3.19        52.67 
TCGA-63-A5MG TCGA-63-A5MM TCGA-66-2783 TCGA-68-7756 TCGA-70-6722 TCGA-77-8007 
       70.62        14.99        24.95         6.64        12.07         6.51 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5FZ TCGA-85-6175 
      156.66        12.59       104.84        60.53       126.18         9.67 
TCGA-85-6561 TCGA-85-8350 TCGA-85-8353 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4PA 
       40.24        22.45         3.09        12.59        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 TCGA-92-7340 
       30.48        27.16        16.21        29.92        24.92         2.70 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       17.46        27.68        21.44        27.02        20.32        12.89 
TCGA-NC-A5HJ TCGA-XC-AA0X 
       13.74         0.20 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.39     0.07     0.03 
subtype1 subtype2 subtype3 subtype4 
  154.32   173.82   140.09   156.66 
subtype1 subtype2 subtype3 subtype4 
   25.28    19.30    21.70    22.60 
[1] "0.2 - 154.3 (25.3)" "0.4 - 173.8 (19.3)" "0.1 - 140.1 (21.7)"
[4] "0.0 - 156.7 (22.6)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       14       29        0        12        19         1
  subtype2       0       17       40        1        17        24         1
  subtype3       3       40       56        2        22        35         1
  subtype4       0       12       19        0        11        15         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          7          6        0
  subtype2         12          2        2
  subtype3         34          6        2
  subtype4          8          2        2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        3        0
  STAGE IA         14       17       40       12
  STAGE IB         29       40       56       19
  STAGE II          0        1        2        0
  STAGE IIA        12       17       22       11
  STAGE IIB        19       24       35       15
  STAGE III         1        1        1        0
  STAGE IIIA        7       12       34        8
  STAGE IIIB        6        2        6        2
  STAGE IV          0        2        2        2
[1] 10  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  19  56   8   6
  subtype2  22  74  19   3
  subtype3  49 111  33   8
  subtype4  16  40   9   5
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       19       22       49       16
  T2       56       74      111       40
  T3        8       19       33        9
  T4        6        3        8        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1  52  30   6   1
  subtype2  79  29   9   1
  subtype3 130  50  20   1
  subtype4  40  18   5   1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       52       79      130       40
  N1       30       29       50       18
  N2        6        9       20        5
  N3        1        1        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1  76   0
  subtype2 101   2
  subtype3 159   2
  subtype4  54   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76    0
  subtype2  101    2
  subtype3  159    2
  subtype4   54    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       76      101      159       54
  1        0        2        2        2
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  20  69
  subtype2  30  88
  subtype3  54 147
  subtype4  20  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   69
  subtype2   30   88
  subtype3   54  147
  subtype4   20   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       30       54       20
  MALE         69       88      147       50
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1  69  11
  subtype2  83  11
  subtype3 159  20
  subtype4  60   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   11
  subtype2   83   11
  subtype3  159   20
  subtype4   60    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        69       83      159       60
  YES       11       11       20        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     4
  subtype2                                     6
  subtype3                                     3
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      3
  subtype3                                      1
  subtype4                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          85
  subtype2                                                         109
  subtype3                                                         196
  subtype4                                                          68
D10V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       85      109
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      196       68
[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"
D10V11, continuous
D10V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  72   4   1   4
  subtype2  97   2   0   5
  subtype3 159   4   1   5
  subtype4  51   1   1   7
D10V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       72       97      159       51
  R1        4        2        4        1
  R2        1        0        1        1
  RX        4        5        5        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         7    60
  subtype2     3                         2    83
  subtype3     2                        17   141
  subtype4     4                         4    49
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        3        2        4
  BLACK OR AFRICAN AMERICAN        7        2       17        4
  WHITE                           60       83      141       49
[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"
D10V15, binary
          cls
clus         0   1
  subtype1   1  58
  subtype2   1  67
  subtype3   3 129
  subtype4   2  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    1   67
  subtype3    3  129
  subtype4    2   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        3        2
  NOT HISPANIC OR LATINO       58       67      129       48
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 35 26
  subtype2 61 54
  subtype3 42 24
  subtype4 61 30
subtype1 subtype2 subtype3 subtype4 
      61      115       66       91 
subtype1 subtype2 subtype3 subtype4 
      26       54       24       30 
$subtype1
TCGA-21-A5DI TCGA-22-A5C4 TCGA-43-7657 TCGA-56-8201 TCGA-77-A5GB TCGA-98-8020 
       32.19        22.06         7.76        13.05        30.81         2.76 
TCGA-NK-A7XE TCGA-21-5782 TCGA-21-5786 TCGA-22-5478 TCGA-33-AASI TCGA-34-5236 
        0.43        31.63        33.93         0.79        44.19         9.07 
TCGA-34-5927 TCGA-34-5928 TCGA-43-6771 TCGA-43-8115 TCGA-52-7811 TCGA-56-7731 
       44.75        39.32         5.46        13.38         8.75         0.10 
TCGA-56-8083 TCGA-56-8503 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-63-7022 
        4.93         1.35        10.36        20.25        20.94        68.15 
TCGA-63-A5MM TCGA-63-A5MV TCGA-63-A5MW TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       14.99        36.16        53.88         6.64         6.94        13.35 
TCGA-68-A59I TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
       16.18        70.13       106.95        86.76        37.81       156.66 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-85-7696 
       39.09        17.72       104.09        27.39         6.97        36.53 
TCGA-85-7698 TCGA-85-7950 TCGA-85-8276 TCGA-85-8288 TCGA-85-8481 TCGA-85-8582 
       31.30        18.94        34.52        13.22         7.76        38.14 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M TCGA-92-7340 TCGA-94-A4VJ TCGA-96-7544 
       34.13        30.97        27.16         2.70        14.14        71.01 
TCGA-98-8023 TCGA-LA-A7SW TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX 
       21.34        13.41         4.21        25.32        26.43         3.65 
TCGA-O2-A52V 
       43.89 

$subtype2
TCGA-33-6737 TCGA-43-5668 TCGA-43-7658 TCGA-51-6867 TCGA-56-7221 TCGA-56-8305 
       19.76        18.38        78.18        61.02        19.99         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-94-7033 
       17.00        16.77         8.02        20.78         9.50        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-21-5783 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        0.16        18.38        88.11        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-33-4587 
       86.30        79.20        11.74        18.84        30.12        54.44 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-34-5231 TCGA-34-5929 
       36.62         6.94       110.99       118.36        65.23         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-5819 TCGA-39-5027 
        1.12         4.04        26.43         4.01         3.39       102.18 
TCGA-39-5040 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-46-6025 
       17.06        27.91        22.98        21.47        19.59        10.65 
TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-7222 TCGA-56-7223 
       13.91         5.46        30.35        27.45        18.48        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 
       31.27        30.41        19.76         6.51        17.49        33.24 
TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8629 TCGA-56-A4BX TCGA-58-8387 
       14.96         3.48        26.89        15.81        13.32        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-60-2703 
       13.55        29.95        71.24        16.47        34.78        96.82 
TCGA-63-7020 TCGA-68-7755 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       70.13         2.73        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28        11.18       140.09         0.49        73.22         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8143 TCGA-77-8148 
       46.78        32.55         6.51        55.73        26.40        66.51 
TCGA-77-8153 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       65.49        41.39         6.41        34.95        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8287 
        1.15        29.95        24.13        31.56        26.79         0.76 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
       16.77         5.29        32.71        15.39        36.59        18.08 
TCGA-85-8666 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       22.59         2.93        11.77         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-96-8169 TCGA-98-8021 TCGA-98-A53A 
        2.30         4.01         5.03        18.31        30.81        18.15 
TCGA-O2-A52S 
       12.72 

$subtype3
TCGA-43-8118 TCGA-56-A4ZJ TCGA-90-7964 TCGA-96-7545 TCGA-98-A53D TCGA-21-5784 
        2.93        21.04        14.07        57.07        21.21        41.69 
TCGA-22-4605 TCGA-22-4609 TCGA-22-5489 TCGA-33-6738 TCGA-34-5232 TCGA-34-5234 
       32.02         9.57        62.86        63.35        81.24        74.66 
TCGA-34-5239 TCGA-34-8454 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-43-6647 
       60.30        38.79       111.35        55.20        82.52        24.89 
TCGA-43-6773 TCGA-43-8116 TCGA-43-A56U TCGA-52-7622 TCGA-56-5897 TCGA-56-6545 
        3.81        11.77        14.20        28.34        12.43        21.90 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-58-8386 
       14.07         1.81        22.75        13.81         9.93         0.03 
TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 TCGA-63-6202 TCGA-63-7021 TCGA-63-A5MN 
       12.23        37.94        49.48        52.67        70.42        11.34 
TCGA-63-A5MS TCGA-70-6722 TCGA-77-8131 TCGA-77-8133 TCGA-77-8146 TCGA-77-8156 
       78.28        12.07        12.59        53.92       104.84        36.36 
TCGA-77-A5FZ TCGA-85-6175 TCGA-85-6561 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 
      126.18         9.67        40.24        25.15        19.04        30.64 
TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A513 
       22.45         3.09         2.01        12.59        24.36        29.92 
TCGA-90-6837 TCGA-90-A4ED TCGA-94-8491 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       24.92        20.22        26.63        17.46        27.68        21.44 
TCGA-98-8022 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HJ TCGA-XC-AA0X 
       30.67         2.01        27.02        20.32        13.74         0.20 

$subtype4
TCGA-22-5471 TCGA-22-5472 TCGA-43-A474 TCGA-43-A56V TCGA-56-A4BY TCGA-56-A5DR 
       60.66        64.93        11.61        12.03        17.85         0.13 
TCGA-63-A5MH TCGA-77-A5GA TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH 
       66.61        42.08        16.14        19.36         5.69        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        0.07        76.80        39.85        40.90        65.65        16.80 
TCGA-O2-A52W TCGA-22-5480 TCGA-22-5491 TCGA-22-5492 TCGA-33-A4WN TCGA-33-A5GW 
        8.58        71.34        56.32        16.64         4.70         0.30 
TCGA-33-AASL TCGA-34-A5IX TCGA-37-A5EL TCGA-37-A5EM TCGA-37-A5EN TCGA-43-A475 
       27.16        33.90        37.58        28.50        21.70         9.73 
TCGA-56-5898 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-A46J TCGA-58-A46K 
       18.25        19.23        18.74        14.47        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       56.65        35.24        29.92       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MY 
       59.97        45.57        25.28        89.29        16.37        34.59 
TCGA-68-A59J TCGA-77-8140 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 
       14.73        11.54        54.41        60.53       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-A4CL 
       22.29         5.92        61.94        27.62        38.86        30.28 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       19.86        30.48        19.73        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4EE TCGA-90-A59Q TCGA-94-A5I6 
       15.29        12.39         3.65        22.62        10.59        17.69 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       27.16        18.58        20.71        12.89        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL 
       11.84         4.54        64.54         1.22        57.30         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       49.28        43.92        14.73        83.57        33.07         3.72 
TCGA-O2-A5IB 
       11.18 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.03     0.07 
subtype1 subtype2 subtype3 subtype4 
  156.66   140.09   126.18   150.25 
subtype1 subtype2 subtype3 subtype4 
  21.340   19.590   23.555   21.700 
[1] "0.1 - 156.7 (21.3)" "0.2 - 140.1 (19.6)" "0.0 - 126.2 (23.6)"
[4] "0.1 - 150.2 (21.7)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       10       14        1         8        15         0
  subtype2       1       17       37        1        19        22         1
  subtype3       0       23       18        0         9         9         0
  subtype4       2       14       21        1        19        21         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          3        1
  subtype2         14          0        1
  subtype3          6          1        1
  subtype4         11          2        0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        1        0        2
  STAGE IA         10       17       23       14
  STAGE IB         14       37       18       21
  STAGE II          1        1        0        1
  STAGE IIA         8       19        9       19
  STAGE IIB        15       22        9       21
  STAGE III         0        1        0        2
  STAGE IIIA        9       14        6       11
  STAGE IIIB        3        0        1        2
  STAGE IV          1        1        1        0
[1] 10  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 12 32 13  4
  subtype2 25 70 18  3
  subtype3 27 28 10  2
  subtype4 16 59 16  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       12       25       27       16
  T2       32       70       28       59
  T3       13       18       10       16
  T4        4        3        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 36 19  5
  subtype2 76 30  9
  subtype3 48 12  3
  subtype4 56 28  9
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       36       76       48       56
  N1       19       30       12       28
  N2        5        9        3        9
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 43  1
  subtype2 88  1
  subtype3 51  1
  subtype4 74  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    1
  subtype2   88    1
  subtype3   51    1
  subtype4   74    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       43       88       51       74
  1        1        1        1        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"
D11V7, binary
          cls
clus        0  1
  subtype1 20 41
  subtype2 28 88
  subtype3 20 47
  subtype4 17 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   41
  subtype2   28   88
  subtype3   20   47
  subtype4   17   76
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       20       28       20       17
  MALE         41       88       47       76
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1 52  7
  subtype2 90 14
  subtype3 60  4
  subtype4 76 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    7
  subtype2   90   14
  subtype3   60    4
  subtype4   76   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        52       90       60       76
  YES        7       14        4       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     0
  subtype4                                     7
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
  subtype4                                      0
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          60
  subtype2                                                         110
  subtype3                                                          65
  subtype4                                                          86
D11V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       60      110
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       65       86
[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"
D11V11, continuous
D11V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 41  2  0  4
  subtype2 88  3  1  7
  subtype3 51  1  0  3
  subtype4 70  3  1  4
D11V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       41       88       51       70
  R1        2        3        1        3
  R2        0        1        0        1
  RX        4        7        3        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    40
  subtype2     1                        10    98
  subtype3     3                         3    50
  subtype4     1                         4    63
D11V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        3        1
  BLACK OR AFRICAN AMERICAN        6       10        3        4
  WHITE                           40       98       50       63
[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"
D11V15, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  1 86
  subtype3  1 47
  subtype4  0 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   37
  subtype2    1   86
  subtype3    1   47
  subtype4    0   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        1        0
  NOT HISPANIC OR LATINO       37       86       47       54
[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  23  14
  subtype2 111  77
  subtype3  65  43
subtype1 subtype2 subtype3 
      37      188      108 
subtype1 subtype2 subtype3 
      14       77       43 
$subtype1
TCGA-22-A5C4 TCGA-43-A56V TCGA-98-8020 TCGA-NC-A5HD TCGA-NK-A5D1 TCGA-NK-A7XE 
       22.06        12.03         2.76         0.07        16.80         0.43 
TCGA-21-5782 TCGA-22-5478 TCGA-34-5927 TCGA-56-7223 TCGA-56-8083 TCGA-56-8503 
       31.63         0.79        44.75        14.53         4.93         1.35 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-63-7022 TCGA-63-A5MS TCGA-63-A5MT 
       10.36        20.25        20.94        68.15        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-68-7757 TCGA-68-A59I TCGA-77-8008 TCGA-77-8136 
       36.16        53.88         6.94        16.18        86.76        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5G6 TCGA-85-8481 
       17.72       104.09        27.39         6.97        22.29         7.76 
TCGA-85-8582 TCGA-85-A4JB TCGA-94-A4VJ TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HT 
       38.14        30.97        14.14        13.41         1.22        26.43 
TCGA-O2-A52V 
       43.89 

$subtype2
TCGA-22-5471 TCGA-22-5472 TCGA-33-6737 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 
       60.66        64.93        19.76        18.38        78.18         2.93 
TCGA-43-A474 TCGA-51-6867 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A5DR 
       11.61        61.02         3.45        17.00        17.85         0.13 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-94-7943 
       66.61         8.02        20.78        30.81         9.50        18.38 
TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM 
       16.14        19.36         5.69        19.10        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-21-5783 TCGA-21-5786 TCGA-22-5473 
       40.90        65.65         8.58        88.11        33.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
       14.63        44.25        71.34        79.20        11.74        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       62.86        56.32        16.64        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASL TCGA-34-5231 TCGA-34-5928 
        0.30        36.62       110.99        27.16        65.23        39.32 
TCGA-34-5929 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-5819 TCGA-37-A5EL 
        4.96        26.43        33.90         4.01         3.39        37.58 
TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5027 TCGA-39-5040 TCGA-43-5670 TCGA-43-6143 
       28.50        21.70       102.18        17.06        27.91        22.98 
TCGA-43-6770 TCGA-43-6771 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 
       21.47         5.46        11.77         9.73        14.20        10.65 
TCGA-46-6026 TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
       13.91         5.46        18.25        18.48        31.27        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 
        6.51         0.10        33.24        14.96         3.48        26.89 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T 
        9.93        15.81        19.23        13.32        18.74        14.47 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L 
       13.25        13.55        71.24        16.47        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MG 
       35.24        29.92        96.82        70.13       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       58.65        59.97        45.57        11.34        25.28        89.29 
TCGA-63-A5MY TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       34.59        14.73        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28        11.18       140.09         0.49        73.22         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 
       46.78        32.55        55.73        11.54        26.40        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 
       54.41        65.49        36.36       132.36       150.25         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7710 
       61.94        27.62        38.86        41.39        32.91         1.38 
TCGA-85-7843 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8351 
        1.15        24.13        31.56        26.79        30.64        16.77 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
        5.29        32.71         2.01        15.39        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       22.59        30.28        19.86        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       14.96        15.29        12.39         3.65         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
       20.22        22.62        10.59         4.01         2.30         4.01 
TCGA-94-8490 TCGA-94-A5I6 TCGA-96-8169 TCGA-96-A4JL TCGA-98-8022 TCGA-98-A538 
        5.03        17.69        18.31        27.68        30.67        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 
       18.15         2.01        18.58        20.71        13.18        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        4.54        64.54        57.30         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S 
       43.92        25.32        14.73        83.57        33.07        12.72 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$subtype3
TCGA-21-A5DI TCGA-43-7657 TCGA-56-7221 TCGA-56-8201 TCGA-56-8504 TCGA-56-A4ZJ 
       32.19         7.76        19.99        13.05        16.77        21.04 
TCGA-77-A5GA TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-96-7545 TCGA-98-A53D 
       42.08        14.07        21.04         0.16        57.07        21.21 
TCGA-21-5784 TCGA-22-4605 TCGA-22-4609 TCGA-22-5479 TCGA-22-5483 TCGA-33-AASB 
       41.69        32.02         9.57        86.30        18.84         6.94 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       44.19       118.36        81.24        74.66         9.07        60.30 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
        1.12        38.79         4.04       111.35        55.20        82.52 
TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-52-7622 TCGA-52-7810 
       24.89         3.81        19.59        13.38        28.34        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7580 TCGA-56-7822 
        8.75        27.45        12.43        21.90        30.41        17.49 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-58-8386 TCGA-58-8390 
       14.07         1.81        22.75        13.81         0.03        29.95 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 TCGA-63-6202 
       34.78        85.12        12.23        37.94        49.48        52.67 
TCGA-63-7021 TCGA-63-A5MM TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-70-6722 
       70.42        14.99         2.73         6.64        13.35        12.07 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       70.13       106.95         6.51        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5FZ TCGA-85-6175 TCGA-85-6561 
       53.92       104.84        60.53       126.18         9.67        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7844 TCGA-85-7950 
        6.41        36.53        34.95        31.30        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       25.15        19.04        34.52         0.76        13.22        22.45 
TCGA-85-8353 TCGA-85-8584 TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
        3.09        12.59        34.13        24.36        30.48        27.16 
TCGA-85-A513 TCGA-90-6837 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8491 
       29.92        24.92         2.70         3.48         5.26        26.63 
TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53C 
       71.01        17.46        21.44        30.81        21.34        27.02 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HJ TCGA-NK-A5CX TCGA-O2-A52Q 
       20.32        12.89        16.11        13.74         3.65         3.72 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  104.09   150.25   156.66 
subtype1 subtype2 subtype3 
  17.720   20.745   22.175 
[1] "0.1 - 104.1 (17.7)" "0.1 - 150.2 (20.7)" "0.0 - 156.7 (22.2)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        7        8        1         3         7         0
  subtype2       3       35       50        1        35        38         2
  subtype3       0       22       32        1        17        22         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          2        0
  subtype2         22          2        1
  subtype3          9          2        2
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        3        0
  STAGE IA          7       35       22
  STAGE IB          8       50       32
  STAGE II          1        1        1
  STAGE IIA         3       35       17
  STAGE IIB         7       38       22
  STAGE III         0        2        1
  STAGE IIIA        9       22        9
  STAGE IIIB        2        2        2
  STAGE IV          0        1        2
[1] 10  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   7  16  12   2
  subtype2  44 114  28   4
  subtype3  29  59  17   5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7       44       29
  T2       16      114       59
  T3       12       28       17
  T4        2        4        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2
  subtype1  24   8   5
  subtype2 121  51  16
  subtype3  71  30   5
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       24      121       71
  N1        8       51       30
  N2        5       16        5
[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"
D12V6, binary
          cls
clus         0   1
  subtype1  29   0
  subtype2 147   1
  subtype3  80   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    0
  subtype2  147    1
  subtype3   80    2
   clus
vv  subtype1 subtype2 subtype3
  0       29      147       80
  1        0        1        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus         0   1
  subtype1  10  27
  subtype2  46 144
  subtype3  29  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   27
  subtype2   46  144
  subtype3   29   81
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       46       29
  MALE         27      144       81
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus         0   1
  subtype1  30   4
  subtype2 152  24
  subtype3  96   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    4
  subtype2  152   24
  subtype3   96    8
     clus
vv    subtype1 subtype2 subtype3
  NO        30      152       96
  YES        4       24        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     8
  subtype3                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          34
  subtype2                                                         179
  subtype3                                                         108
D12V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       34      179
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      108
[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"
D12V11, continuous
D12V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  27   1   0   1
  subtype2 141   7   2  10
  subtype3  82   1   0   7
D12V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       27      141       82
  R1        1        7        1
  R2        0        2        0
  RX        1       10        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         6    18
  subtype2     3                         9   148
  subtype3     3                         8    85
D12V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        3        3
  BLACK OR AFRICAN AMERICAN        6        9        8
  WHITE                           18      148       85
[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"
D12V15, binary
          cls
clus         0   1
  subtype1   0  19
  subtype2   0 124
  subtype3   4  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   19
  subtype2    0  124
  subtype3    4   81
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        4
  NOT HISPANIC OR LATINO       19      124       81
[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"
