[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/19775388/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/20140646/LUSC-TP.mergedcluster.txt"

nPatients in clinical file=502, in cluster file=504, common to both=502
[1]  12 502
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
42 52 32 28 
 1  2  3  4 
42 52 32 28 
[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 
182 164 153 
  1   2   3 
182 164 153 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
153 123  92 
  1   2   3 
153 123  92 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
105 110  85  27 
  1   2   3   4 
105 110  85  27 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
79 67 62 60 31 28 
 1  2  3  4  5  6 
79 67 62 60 31 28 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
113 152 154  80 
  1   2   3   4 
113 152 154  80 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
179 189 131 
  1   2   3 
179 189 131 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
121 135 122  61  37 
  1   2   3   4   5 
121 135 122  61  37 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 88 117 201  70 
  1   2   3   4 
 88 117 201  70 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 89 131 115 
  1   2   3 
 89 131 115 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 39 151 145 
  1   2   3 
 39 151 145 
[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 502 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=201,	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=332,	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=78,	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 502 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 
114 294  70  24 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
114 294  70  24 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
114 294  70  24 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
114 294  70  24 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
319 132  40   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
319 132  40   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
319 132  40   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
319 132  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 27 24
  subtype3 15 17
  subtype4 15 13
subtype1 subtype2 subtype3 subtype4 
      41       51       32       28 
subtype1 subtype2 subtype3 subtype4 
      17       24       17       13 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1079 
       12.20        23.54        92.42        86.96       119.54        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-22-0944 TCGA-22-1011 TCGA-22-4595 
      122.43         9.34       119.80         7.33         1.74        24.13 
TCGA-22-4607 TCGA-33-4547 TCGA-33-4589 TCGA-34-2600 TCGA-34-2609 TCGA-34-5241 
       19.30        79.53         1.55        61.61        31.27        16.93 
TCGA-37-3783 TCGA-37-3789 TCGA-39-5029 TCGA-43-3920 TCGA-56-1622 TCGA-60-2707 
        4.01         0.43        24.33        33.11        28.96        21.73 
TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-66-2734 
       80.45        42.64         3.19        32.32        23.57        43.10 
TCGA-66-2742 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 
       21.07         0.99         2.01         2.01        19.00        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 
       12.03         3.98        12.00        22.98         4.04 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
        4.47        75.75       117.57        11.34        92.15        31.99 
TCGA-18-4086 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        2.79        46.88        99.16        70.16        60.89        34.78 
TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-33-4532 TCGA-33-4538 
       14.10        38.17        34.75        13.12       129.01        97.94 
TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 
        2.63        28.96        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        13.02         9.99         0.39         0.39 
TCGA-51-4081 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 
       29.95        66.54        41.42        56.91        29.85        35.90 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 
       16.96         2.01        21.01        25.05         1.02        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
        3.02         2.01        24.95        40.01         5.03        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       54.08         4.01        49.05 

$subtype3
TCGA-18-3409 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
      123.19        21.99        14.93         4.31        64.21        27.02 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-33-4566 TCGA-34-2604 TCGA-34-2608 
       48.82        48.33         0.56       173.82        31.50        32.88 
TCGA-37-3792 TCGA-39-5030 TCGA-43-2576 TCGA-43-2581 TCGA-46-3766 TCGA-46-3767 
        0.39         1.94        40.21        38.66        12.00        13.02 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 
        3.58        10.22        92.71         9.01        50.33        35.34 
TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2767 TCGA-66-2769 
       26.83         0.99         1.02         0.92         2.01         7.07 
TCGA-66-2785 TCGA-66-2786 
        1.97        25.97 

$subtype4
TCGA-18-3410 TCGA-18-3417 TCGA-18-4083 TCGA-21-1078 TCGA-21-1083 TCGA-22-4591 
        4.80        36.07         6.18        15.58        43.23        20.48 
TCGA-22-4613 TCGA-33-4533 TCGA-33-4582 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       11.77       133.74       103.53         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5034 TCGA-39-5035 
        7.82         6.81         0.39       133.25        36.39        68.38 
TCGA-43-2578 TCGA-46-3769 TCGA-60-2695 TCGA-60-2716 TCGA-60-2726 TCGA-66-2754 
       22.49         3.98        21.11        48.49        11.77         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2790 TCGA-66-2793 
        0.99        43.99        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 
  21.730   31.990   18.460   13.675 
[1] "0.4 - 122.4 (21.7)" "0.4 - 129.0 (32.0)" "0.4 - 173.8 (18.5)"
[4] "0.4 - 133.7 (13.7)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  subtype1        2       21         0         9          6          2        2
  subtype2        2       24         4         9          6          7        0
  subtype3        9       11         2         4          4          2        0
  subtype4       10        4         1         6          3          2        2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          2        2        9       10
  STAGE IB         21       24       11        4
  STAGE IIA         0        4        2        1
  STAGE IIB         9        9        4        6
  STAGE IIIA        6        6        4        3
  STAGE IIIB        2        7        2        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  5 30  6  1
  subtype2  4 41  1  6
  subtype3 11 18  2  1
  subtype4 10 11  3  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5        4       11       10
  T2       30       41       18       11
  T3        6        1        2        3
  T4        1        6        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 N3
  subtype1 26 11  3  2
  subtype2 28 17  5  2
  subtype3 22  6  3  1
  subtype4 20  6  2  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       26       28       22       20
  N1       11       17        6        6
  N2        3        5        3        2
  N3        2        2        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"
D1V6, binary
          cls
clus        0  1
  subtype1 38  2
  subtype2 50  0
  subtype3 32  0
  subtype4 26  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    2
  subtype2   50    0
  subtype3   32    0
  subtype4   26    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       38       50       32       26
  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 33
  subtype2 13 39
  subtype3 11 21
  subtype4 11 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   33
  subtype2   13   39
  subtype3   11   21
  subtype4   11   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       13       11       11
  MALE         33       39       21       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 28  3
  subtype2 34  4
  subtype3 18  2
  subtype4 18  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    3
  subtype2   34    4
  subtype3   18    2
  subtype4   18    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        28       34       18       18
  YES        3        4        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"
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                                                          42
  subtype2                                                          49
  subtype3                                                          31
  subtype4                                                          26
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)       42       49
                                                             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)       31       26
[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 38  0  1  1
  subtype2 47  1  1  1
  subtype3 27  1  0  3
  subtype4 27  1  0  0
D1V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       38       47       27       27
  R1        0        1        1        1
  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    28
  subtype3     1                         1    22
  subtype4     0                         1    19
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        0
  BLACK OR AFRICAN AMERICAN        2        3        1        1
  WHITE                           24       28       22       19
[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 26
  subtype3  0 21
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   23
  subtype2    1   26
  subtype3    0   21
  subtype4    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        0        0
  NOT HISPANIC OR LATINO       23       26       21       19
[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 24 22
  subtype2 29 26
  subtype3 28 23
subtype1 subtype2 subtype3 
      46       55       51 
subtype1 subtype2 subtype3 
      22       26       23 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 
       12.20        23.54        36.07        92.42        86.96       119.54 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-22-1011 
       15.58        31.73       122.43         9.34       119.80         1.74 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4607 TCGA-22-4613 TCGA-33-4547 TCGA-33-4582 
       20.48        24.13        19.30        11.77        79.53       103.53 
TCGA-33-4589 TCGA-34-2600 TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-39-5029 
        1.55        61.61        16.93         4.01         0.43        24.33 
TCGA-43-3920 TCGA-56-1622 TCGA-60-2696 TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 
       33.11        28.96         3.58        21.73        80.45        48.49 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-66-2734 TCGA-66-2742 
       42.64        32.32        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-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
        4.47        75.75       117.57        11.34        92.15        31.99 
TCGA-18-4083 TCGA-18-4086 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
        6.18         2.79        46.88        99.16        70.16        60.89 
TCGA-21-1077 TCGA-22-0944 TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       34.78         7.33        14.10        38.17        34.75        13.12 
TCGA-33-4532 TCGA-33-4538 TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-37-4133 
      129.01        97.94         2.63        28.96        50.66         7.82 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-46-3765 
      126.58        68.58        71.18        55.56        39.12        13.02 
TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-60-2710 TCGA-60-2711 
        9.99         0.39         0.39        29.95        66.54        41.42 
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-21-1083 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
      123.19         4.80        43.23        21.99        14.93         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-33-4533 
       64.21        27.02        48.82        48.33         0.56       133.74 
TCGA-33-4566 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-37-3792 TCGA-37-4129 
      173.82        31.50        32.88        31.27         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5030 
        8.12         7.46         6.81         0.39       133.25         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-46-3766 
       36.39        68.38        40.21        22.49        38.66        12.00 
TCGA-46-3767 TCGA-46-3769 TCGA-60-2695 TCGA-60-2698 TCGA-60-2706 TCGA-60-2712 
       13.02         3.98        21.11        10.22        92.71         9.01 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2720 TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 
       50.33        35.34         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 
   21.40    29.95    21.11 
[1] "0.4 - 122.4 (21.4)" "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         9          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        9
  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 35  4
  subtype3 29  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    4
  subtype2   35    4
  subtype3   29    3
     clus
vv    subtype1 subtype2 subtype3
  NO        34       35       29
  YES        4        4        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"
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 93 85
  subtype2 91 68
  subtype3 91 59
subtype1 subtype2 subtype3 
     178      159      150 
subtype1 subtype2 subtype3 
      85       68       59 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       12.20         4.47       123.19         2.79       154.32        27.19 
TCGA-21-1076 TCGA-21-1078 TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
       60.89        15.58        41.69        21.99        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
       64.21         1.74        27.02        48.82        48.33         0.56 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5479 TCGA-22-5480 
       32.02        19.30         9.57        64.93        86.30        71.34 
TCGA-22-5481 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.20       173.82       151.27        54.44         1.55        19.76 
TCGA-33-A4WN TCGA-33-AASB TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
        4.70         6.94        31.50        32.88        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
        9.07        60.30        16.93        38.79        33.90         4.01 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        0.39         7.96         7.46       133.25        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
       82.52         1.71         1.94        36.39        68.38        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 
       17.06        40.21        38.66        18.38        24.89         5.46 
TCGA-43-6773 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 
        3.81        13.38         2.93         9.73        14.20        12.00 
TCGA-46-3767 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 
       13.02        28.34         8.75        27.45         0.10         0.62 
TCGA-56-7221 TCGA-56-7731 TCGA-56-8201 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.99         0.10        13.05         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35        16.77        22.75         1.18        10.36         9.93 
TCGA-56-A4ZJ TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J 
       21.04         0.26        14.47        13.25        34.78        85.12 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2712 
        3.58        12.23        37.94        21.73        49.48         9.01 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2725 TCGA-63-A5MG 
       50.33        35.34        48.49         3.19        26.83        70.62 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       14.99        11.34        25.28        89.29        78.28        16.37 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2755 TCGA-66-2765 TCGA-66-2771 TCGA-66-2773 
       43.10         2.01         0.92         2.01        19.00         3.02 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-68-7756 TCGA-68-7757 
       19.00        12.00        24.95        22.98         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-7138 TCGA-77-7335 TCGA-77-8007 TCGA-77-8008 
       13.35        14.07        11.18        70.13         6.51        86.76 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
       12.59        39.09        17.72       104.09        27.39         6.97 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
      126.18       132.36         5.92        30.81        38.86         9.67 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       12.99        34.95        29.95        18.94        25.15        19.04 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09         2.01         7.76        36.59        38.14        12.59 
TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       22.59        19.86        24.36        27.16        16.21        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 
       29.92        24.92        20.22        10.59         2.70         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        2.30         4.01        18.31        17.46        27.68        21.44 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HE 
       21.34        27.02        21.21        20.32        12.89        76.80 
TCGA-NC-A5HJ TCGA-NK-A5CX TCGA-O2-A52V TCGA-XC-AA0X 
       13.74         3.65        43.89         0.20 

$subtype2
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       75.75       117.57        11.34        92.15        31.99        36.07 
TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        6.18        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1083 TCGA-22-0944 TCGA-22-1012 TCGA-22-4595 TCGA-22-4599 
       34.78        43.23         7.33        14.10        24.13        38.17 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       13.12        11.77        60.66        63.55        14.63        44.25 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       18.84        30.12        62.86       129.01       133.74        97.94 
TCGA-33-4582 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL 
      103.53        14.07         0.30        36.62       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 TCGA-34-5240 TCGA-34-5927 
        2.63        61.61        28.96        65.23        50.66        44.75 
TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5016 
        1.12        26.43         7.82         3.39        21.70       126.58 
TCGA-39-5019 TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 
      111.35       102.18        71.18        55.56        39.12        12.36 
TCGA-43-6770 TCGA-43-7657 TCGA-43-7658 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       21.47         7.76        78.18         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-56-7223 TCGA-56-7582 
        0.39         0.39        29.95         5.46         0.99         0.85 
TCGA-56-7730 TCGA-56-7823 TCGA-56-8308 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
        6.51        33.24        17.00        13.32        17.85        18.74 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       71.24        16.47        34.36        56.65        35.24        29.92 
TCGA-60-2698 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-63-A5MB 
       10.22        66.54        41.42        56.91        29.85       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2742 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 
       59.97        45.57        21.07        21.01         1.02         2.01 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
       23.01         2.01         3.98        40.01         5.03        30.02 
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        13.45        73.12 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28       140.09        20.78         0.49        73.22         0.16 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 
       15.75        55.73        37.81        53.92        66.51        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
       65.49        36.36       150.25        61.94        42.08        27.62 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
        6.41        36.53        31.30        24.13        31.56        30.64 
TCGA-85-8277 TCGA-85-8354 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A53L 
       10.09        32.71        18.08        30.28        34.13        12.39 
TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8063 TCGA-94-7943 
        3.65        11.77        22.62         3.48         4.01        18.38 
TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53I 
        5.03        16.14        17.69        57.07        19.36        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        19.10        16.11        13.18        13.41        11.84 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        49.28        43.92        25.32        14.73        40.90 
TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A5IB 
        0.43        12.72        11.18 

$subtype3
TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1079 TCGA-21-1080 
        4.80        23.54        92.42        86.96        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 
        9.34       119.80        31.63        88.11        33.93        10.82 
TCGA-21-A5DI TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-5478 TCGA-22-5482 
       32.19        20.48        35.08        34.75         0.79        11.74 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-6738 TCGA-33-AASD 
       56.32        16.64        22.06        79.53        63.35       110.99 
TCGA-33-AASI TCGA-34-2609 TCGA-34-5928 TCGA-34-5929 TCGA-34-8455 TCGA-37-3789 
       44.19        31.27        39.32         4.96         4.04         0.43 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5029 TCGA-39-5031 TCGA-43-2578 
        8.12         6.81         0.39        24.33        60.53        22.49 
TCGA-43-3920 TCGA-43-5670 TCGA-43-7656 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V 
       33.11        27.91        19.59        11.77        11.61        12.03 
TCGA-46-3765 TCGA-46-3769 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
       13.02         3.98        30.35        28.96        18.25         2.04 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 
        0.43        31.27         1.32        17.49        14.96         4.93 
TCGA-56-8305 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
        3.45         1.81        20.25        15.81        20.94        19.23 
TCGA-56-A5DR TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 
        0.13         0.03        13.55        29.95        21.11        96.82 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       92.71        80.45        42.64        32.32        35.90        23.57 
TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.77        66.61        58.65        25.41        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
       34.59        16.96         0.99         1.02         2.01         0.99 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2768 TCGA-66-2769 TCGA-66-2780 
       43.99        25.05         0.99         2.01         7.07        12.03 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-8250 
        1.97        25.97         4.04        22.98        10.06         8.02 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7337 TCGA-77-7463 TCGA-77-8130 TCGA-77-8140 
       29.56        75.09       106.95        46.78        82.92        11.54 
TCGA-77-8143 TCGA-77-8154 TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7699 TCGA-85-7710 
       26.40        60.53        22.29        11.97        32.91         1.38 
TCGA-85-7843 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
        1.15        26.79        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR 
       16.77         5.29        15.39        30.97        30.48        19.73 
TCGA-85-A510 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       15.85         9.50         2.93        14.07        21.04         0.16 
TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       26.63        14.14        71.01         2.76        30.81        30.67 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-NC-A5HD TCGA-NC-A5HF 
       27.16         5.69        18.15         2.01         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HT 
       64.54         1.22        57.30         4.21        39.85        26.43 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52W 
       83.57        65.49        16.80        33.07         3.72         8.58 

subtype1 subtype2 subtype3 
    0.10     0.16     0.03 
subtype1 subtype2 subtype3 
  173.82   150.25   122.43 
subtype1 subtype2 subtype3 
   18.97    27.16    20.71 
[1] "0.1 - 173.8 (19.0)" "0.2 - 150.2 (27.2)" "0.0 - 122.4 (20.7)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       36       62        1        21        37         0
  subtype2       0       22       48        1        27        29         2
  subtype3       2       31       42        0        18        28         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         18          5        1
  subtype2         23          9        3
  subtype3         22          5        3
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        2
  STAGE IA         36       22       31
  STAGE IB         62       48       42
  STAGE II          1        1        0
  STAGE IIA        21       27       18
  STAGE IIB        37       29       28
  STAGE III         0        2        1
  STAGE IIIA       18       23       22
  STAGE IIIB        5        9        5
  STAGE IV          1        3        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  41 104  31   6
  subtype2  32 100  23   9
  subtype3  39  89  16   9
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       41       32       39
  T2      104      100       89
  T3       31       23       16
  T4        6        9        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 129  37  10   2
  subtype2  88  57  16   2
  subtype3  99  38  14   1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      129       88       99
  N1       37       57       38
  N2       10       16       14
  N3        2        2        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"
D3V6, binary
          cls
clus         0   1
  subtype1 147   1
  subtype2 134   3
  subtype3 126   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  147    1
  subtype2  134    3
  subtype3  126    3
   clus
vv  subtype1 subtype2 subtype3
  0      147      134      126
  1        1        3        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"
D3V7, binary
          cls
clus         0   1
  subtype1  63 119
  subtype2  34 130
  subtype3  32 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  119
  subtype2   34  130
  subtype3   32  121
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       63       34       32
  MALE        119      130      121
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1 137  18
  subtype2 123  20
  subtype3 110  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  137   18
  subtype2  123   20
  subtype3  110   11
     clus
vv    subtype1 subtype2 subtype3
  NO       137      123      110
  YES       18       20       11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     9
  subtype3                                     5
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      4
  subtype2                                      1
  subtype3                                      1
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         176
  subtype2                                                         154
  subtype3                                                         147
D3V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             4        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      176      154
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      147
[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"
D3V11, continuous
D3V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 141   5   2  11
  subtype2 130   5   2   9
  subtype3 127   2   0   2
D3V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      141      130      127
  R1        5        5        2
  R2        2        2        0
  RX       11        9        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         8   128
  subtype2     2                        11   116
  subtype3     1                        12   104
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        2        1
  BLACK OR AFRICAN AMERICAN        8       11       12
  WHITE                          128      116      104
[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"
D3V15, binary
          cls
clus         0   1
  subtype1   6 122
  subtype2   1  98
  subtype3   1  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  122
  subtype2    1   98
  subtype3    1   96
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        1        1
  NOT HISPANIC OR LATINO      122       98       96
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 80 69
  subtype2 68 51
  subtype3 54 34
subtype1 subtype2 subtype3 
     149      119       88 
subtype1 subtype2 subtype3 
      69       51       34 
$subtype1
TCGA-18-3417 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-4605 TCGA-22-4609 
       36.07        41.69        10.82        32.19        32.02         9.57 
TCGA-22-5481 TCGA-22-5489 TCGA-33-4566 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
       79.20        62.86       173.82         1.55        19.76        63.35 
TCGA-33-AASB TCGA-33-AASI TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
        6.94        44.19        81.24        74.66         9.07        16.93 
TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-39-5011 TCGA-39-5022 
       39.32        38.79         4.04        33.90       133.25        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 
       82.52         1.71         1.94        36.39        17.88        17.06 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 
       18.38        24.89         5.46         3.81        19.59        78.18 
TCGA-43-A56U TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 
       14.20         8.75        27.45         0.10         2.04         0.62 
TCGA-56-7580 TCGA-56-7731 TCGA-56-8201 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.32         0.10        13.05        26.89        14.07         1.35 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
       22.75         1.18        10.36         9.93        20.25        20.94 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       21.04         0.13         0.26         0.03        13.25        13.55 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 
       34.78        85.12        12.23        96.82        37.94        49.48 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       70.62        14.99        11.34        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       36.16         6.64         6.94        13.35        14.07        29.56 
TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       11.18         6.51        86.76        12.59        39.09        17.72 
TCGA-77-8145 TCGA-77-8146 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB 
        6.97       104.84        36.36       126.18       132.36        30.81 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7950 TCGA-85-8048 
       38.86         9.67        11.97        34.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8287 TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
       19.04         0.76        22.45         2.01         7.76        38.14 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
       12.59        22.59        30.97        19.86        24.36        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       16.21        15.85        14.96        29.92        12.39        24.92 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
        2.93        20.22        22.62        10.59         2.70         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8491 
        2.30        21.04         0.16        18.38         4.01        26.63 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        27.68        21.44        30.67        21.34 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 
        5.69         2.01        27.02        21.21        20.32        12.89 
TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NK-A5CT TCGA-NK-A5CX 
       13.41        76.80        13.74         4.21        65.49         3.65 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        0.43        33.07         3.72        43.89         0.20 

$subtype2
TCGA-18-4721 TCGA-18-5592 TCGA-21-5783 TCGA-21-5786 TCGA-22-4599 TCGA-22-4601 
      154.32        49.94        88.11        33.93        38.17        34.75 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       11.77        60.66        63.55        14.63        44.25        86.30 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 
       11.74        18.84        30.12        56.32       103.53       151.27 
TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
       14.07         4.70         0.30        36.62       110.99       118.36 
TCGA-33-AASL TCGA-34-5240 TCGA-34-7107 TCGA-34-8456 TCGA-37-A5EM TCGA-37-A5EN 
       27.16        50.66         1.12        26.43        28.50        21.70 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 
      126.58       111.35        68.58       102.18        60.53        71.18 
TCGA-39-5037 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 
       55.56        21.47         7.76        13.38         2.93         9.73 
TCGA-46-6025 TCGA-51-6867 TCGA-52-7622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 
       10.65        61.02        28.34        18.25         0.99        31.27 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8305 TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZK 
        0.85         6.51         3.45        15.81        17.85        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-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-68-7755 
       29.92       102.67        59.97        45.57        25.28         2.73 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       13.45        73.12        23.28         0.49        73.22        70.13 
TCGA-77-7338 TCGA-77-8009 TCGA-77-8133 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 
        0.16        55.73        53.92        54.41        65.49       150.25 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       61.94        42.08        27.62        12.99         6.41        36.53 
TCGA-85-7698 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
       31.30        29.95        24.13        31.56        30.64        34.52 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN 
       10.09         3.09        32.71        36.59        30.28        34.13 
TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I4 
        3.65        11.77         3.48         5.26         5.03        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J 
       17.69        57.07        19.36        18.15        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HL 
       19.10        16.11        13.18        11.84         0.07         2.89 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52S 
       43.92        25.32        40.90        16.80        12.72 

$subtype3
TCGA-18-5595 TCGA-21-5782 TCGA-22-4593 TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 
       27.19        31.63        35.08        64.93         0.79        71.34 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4587 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 
       16.64        22.06        54.44        65.23        60.30        44.75 
TCGA-34-5929 TCGA-37-5819 TCGA-39-5029 TCGA-39-5035 TCGA-43-5670 TCGA-43-6143 
        4.96         3.39        24.33        68.38        27.91        12.36 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 
       11.77        11.61        12.03        13.91         5.46        30.35 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        0.99         0.43        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX 
        3.48        17.00        16.77         1.81        19.23        13.32 
TCGA-58-8390 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY 
       29.95        66.61        58.65        25.41        53.88        34.59 
TCGA-68-8250 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7337 TCGA-77-7463 
        8.02        75.09       140.09        20.78       106.95        46.78 
TCGA-77-7465 TCGA-77-8128 TCGA-77-8130 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       15.75        37.81        82.92       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-7699 
       27.39        66.51        60.53        22.29         5.92        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
        1.38         1.15        26.79        13.22        16.77         5.29 
TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR TCGA-90-7766 TCGA-90-7964 
       15.39        18.08        30.48        19.73         9.50        14.07 
TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8020 TCGA-98-8021 TCGA-98-A538 TCGA-NC-A5HF 
       14.14        71.01         2.76        30.81        27.16         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HQ 
       64.54         1.22        57.30        39.85        49.28        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52W TCGA-O2-A5IB 
       26.43        83.57         8.58        11.18 

subtype1 subtype2 subtype3 
    0.03     0.07     0.43 
subtype1 subtype2 subtype3 
  173.82   154.32   140.09 
subtype1 subtype2 subtype3 
  18.380   28.340   22.175 
[1] "0.0 - 173.8 (18.4)" "0.1 - 154.3 (28.3)" "0.4 - 140.1 (22.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       31       37        1        22        37         1
  subtype2       1       22       40        2        23        18         1
  subtype3       1       18       21        0        16        15         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         17          3        3
  subtype2         13          2        1
  subtype3         17          1        0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         31       22       18
  STAGE IB         37       40       21
  STAGE II          1        2        0
  STAGE IIA        22       23       16
  STAGE IIB        37       18       15
  STAGE III         1        1        1
  STAGE IIIA       17       13       17
  STAGE IIIB        3        2        1
  STAGE IV          3        1        0
[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 36 81 30  6
  subtype2 31 69 19  4
  subtype3 23 56 10  3
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       36       31       23
  T2       81       69       56
  T3       30       19       10
  T4        6        4        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
  subtype1 98 39 11
  subtype2 81 34  7
  subtype3 56 25 11
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       98       81       56
  N1       39       34       25
  N2       11        7       11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1 110   3
  subtype2  99   1
  subtype3  74   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110    3
  subtype2   99    1
  subtype3   74    0
   clus
vv  subtype1 subtype2 subtype3
  0      110       99       74
  1        3        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1  45 108
  subtype2  29  94
  subtype3  21  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45  108
  subtype2   29   94
  subtype3   21   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       29       21
  MALE        108       94       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus         0   1
  subtype1 126  14
  subtype2  96  16
  subtype3  69   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  126   14
  subtype2   96   16
  subtype3   69    9
     clus
vv    subtype1 subtype2 subtype3
  NO       126       96       69
  YES       14       16        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"
D4V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     4
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      3
  subtype2                                      1
  subtype3                                      1
          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                                                         149
  subtype2                                                         115
  subtype3                                                          86
D4V10, 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)      149      115
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       86
[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"
D4V11, continuous
D4V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 110   3   0   9
  subtype2  98   5   1   6
  subtype3  70   1   1   2
D4V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      110       98       70
  R1        3        5        1
  R2        0        1        1
  RX        9        6        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     6                        11   110
  subtype2     1                         7    99
  subtype3     0                         6    64
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        1        0
  BLACK OR AFRICAN AMERICAN       11        7        6
  WHITE                          110       99       64
[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"
D4V15, binary
          cls
clus         0   1
  subtype1   4 105
  subtype2   1  81
  subtype3   1  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  105
  subtype2    1   81
  subtype3    1   52
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        1
  NOT HISPANIC OR LATINO      105       81       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 60 42
  subtype2 61 45
  subtype3 50 33
  subtype4 11 14
subtype1 subtype2 subtype3 subtype4 
     102      106       83       25 
subtype1 subtype2 subtype3 subtype4 
      42       45       33       14 
$subtype1
TCGA-18-4721 TCGA-21-1076 TCGA-21-1078 TCGA-21-1082 TCGA-21-5782 TCGA-22-1000 
      154.32        60.89        15.58       119.80        31.63        14.93 
TCGA-22-1011 TCGA-22-5471 TCGA-22-5474 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
        1.74        60.66        14.63         0.79        71.34        11.74 
TCGA-22-5489 TCGA-22-5491 TCGA-33-6738 TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 
       62.86        56.32        63.35        44.19         2.63        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5239 TCGA-34-5927 TCGA-37-4129 
       28.96        32.88        31.27        60.30        44.75         7.96 
TCGA-37-4141 TCGA-39-5022 TCGA-39-5030 TCGA-39-5034 TCGA-43-2581 TCGA-43-5668 
        0.39        55.20         1.94        36.39        38.66        18.38 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-56-5897 
       19.59        78.18        13.38         2.93         9.73         0.10 
TCGA-56-7730 TCGA-56-8083 TCGA-56-8309 TCGA-58-8392 TCGA-58-8393 TCGA-60-2695 
        6.51         4.93        14.07        16.47        34.78        21.11 
TCGA-60-2696 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
        3.58        92.71        49.48        66.54         9.01        56.91 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2725 TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       50.33         3.19        26.83        11.34        25.28        78.28 
TCGA-63-A5MV TCGA-66-2737 TCGA-66-2785 TCGA-66-2790 TCGA-66-2800 TCGA-68-A59I 
       36.16         2.01         1.97        22.98        49.05        14.07 
TCGA-77-7142 TCGA-77-7335 TCGA-77-8143 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GH 
       73.22        70.13        26.40        54.41       150.25        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 
        9.67        11.97        36.53        25.15        19.04        30.64 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 
        0.76        13.22        22.45         3.09         2.01        36.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A513 
       30.28        34.13        24.36        30.48        15.85        29.92 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-94-7557 TCGA-94-7943 
        3.65        24.92        11.77        20.22         0.16        18.38 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53B 
       14.14        71.01        19.36        27.68        21.44         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HK TCGA-NC-A5HP TCGA-O2-A52Q TCGA-O2-A52V 
       27.02        20.32         4.21        25.32         3.72        43.89 

$subtype2
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 TCGA-21-5784 
       49.94        27.19       119.54        46.88         9.34        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-4607 TCGA-22-5472 TCGA-22-5477 
       33.93        10.82        21.99        19.30        64.93        44.25 
TCGA-22-5479 TCGA-22-5492 TCGA-33-4547 TCGA-33-4589 TCGA-33-6737 TCGA-33-AASB 
       86.30        16.64        79.53         1.55        19.76         6.94 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 
       81.24        74.66         9.07        39.32        38.79         4.04 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-A5EM TCGA-39-5011 TCGA-39-5019 
       33.90         0.43         0.39        28.50       133.25       111.35 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 
       68.58        82.52       102.18         1.71        24.33        68.38 
TCGA-39-5037 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-A474 TCGA-43-A56V 
       55.56        27.91        21.47         5.46        11.61        12.03 
TCGA-46-6025 TCGA-52-7811 TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
       10.65         8.75        27.45         2.04         0.62         0.43 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 
       12.23        10.22        96.82        32.32        23.57        11.77 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MY 
       70.62        58.65        14.99        16.37        25.41        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-77-6845 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        5.03         6.94        23.28       106.95         0.16        46.78 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6561 TCGA-85-6798 TCGA-85-7710 
       60.53       126.18       132.36        12.99         6.41         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8351 TCGA-85-8479 TCGA-85-8664 TCGA-85-8666 
        1.15        29.95        16.77        15.39        18.08        22.59 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-90-A59Q 
       30.97        19.86        16.21        14.96        12.39        10.59 
TCGA-92-7340 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 TCGA-98-A538 TCGA-98-A539 
        2.70         4.01        26.63        17.69        27.16         5.69 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HO 
       12.89        13.41         0.07        76.80        39.85        43.92 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE 
       14.73        40.90        65.49         0.43 

$subtype3
TCGA-21-1072 TCGA-21-1075 TCGA-21-1080 TCGA-21-1083 TCGA-22-5473 TCGA-22-5483 
       99.16        70.16       122.43        43.23        63.55        18.84 
TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-A4WN TCGA-33-AASD 
      129.01       173.82       103.53        14.07         4.70       110.99 
TCGA-33-AASJ TCGA-34-5231 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 
      118.36        65.23         4.96         1.12        26.43         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5040 TCGA-43-2578 
        6.81         3.39        21.70       126.58        17.06        22.49 
TCGA-43-3394 TCGA-43-6143 TCGA-46-6026 TCGA-52-7810 TCGA-56-7221 TCGA-56-A4BX 
       39.12        12.36        13.91        30.35         0.99        13.32 
TCGA-58-8388 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       13.55        71.24        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2704 TCGA-60-2708 TCGA-60-2711 TCGA-60-2716 TCGA-60-2719 
       29.92        37.94        80.45        41.42        48.49        42.64 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2727 TCGA-66-2758 TCGA-66-2766 
      102.67        59.97        45.57        16.96        21.01         1.02 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2794 
        2.01        23.01         3.02         2.01        24.95        54.08 
TCGA-66-2795 TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7465 
        4.01        29.56        73.12       140.09         0.49        15.75 
TCGA-77-8153 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       65.49        22.29        27.62        34.95        31.30        32.91 
TCGA-85-7950 TCGA-85-8276 TCGA-85-8352 TCGA-85-A4QR TCGA-90-7767 TCGA-90-A4EE 
       18.94        34.52         5.29        19.73         2.93        22.62 
TCGA-94-8490 TCGA-98-A53A TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HJ 
        5.03        18.15        16.11        13.18        11.84        13.74 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N 
        2.89        49.28        26.43        83.57        33.07 

$subtype4
TCGA-21-1079 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 
       31.73        32.19        20.48         0.56        32.02         9.57 
TCGA-22-5485 TCGA-22-A5C4 TCGA-33-A5GW TCGA-34-5241 TCGA-39-5031 TCGA-51-6867 
       30.12        22.06         0.30        16.93        60.53        61.02 
TCGA-56-5898 TCGA-56-A5DS TCGA-58-8386 TCGA-68-7756 TCGA-68-A59J TCGA-77-6844 
       18.25         0.26         0.03         6.64        13.45        75.09 
TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 TCGA-98-A53J TCGA-NC-A5HF TCGA-NC-A5HI 
        9.50        21.04        16.14        20.71         4.54        57.30 
TCGA-O2-A5IB 
       11.18 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.49     0.03 
subtype1 subtype2 subtype3 subtype4 
  154.32   133.25   173.82    75.09 
subtype1 subtype2 subtype3 subtype4 
   24.64    19.81    26.43    18.25 
[1] "0.1 - 154.3 (24.6)" "0.1 - 133.2 (19.8)" "0.5 - 173.8 (26.4)"
[4] "0.0 - 75.1 (18.2)" 
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       29        1        18        26         0
  subtype3       1        7       29        1        13        16         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       29       29        9
  STAGE II          1        1        1        0
  STAGE IIA        12       18       13        3
  STAGE IIB        19       26       16        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  9  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        9        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 49 24 10  2
  subtype4 20  5  1  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       72       63       49       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 98  1
  subtype3 74  0
  subtype4 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89    1
  subtype2   98    1
  subtype3   74    0
  subtype4   17    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       89       98       74       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 74
  subtype4 10 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   66
  subtype2   20   90
  subtype3   11   74
  subtype4   10   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       39       20       11       10
  MALE         66       90       74       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 87 10
  subtype2 86 10
  subtype3 57 11
  subtype4 23  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   87   10
  subtype2   86   10
  subtype3   57   11
  subtype4   23    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        87       86       57       23
  YES       10       10       11        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                                                          77
  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)       77       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 69  0  2  3
  subtype4 23  0  0  1
D5V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       82       82       69       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    61
  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       61       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 55
  subtype4  0 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   77
  subtype2    4   65
  subtype3    0   55
  subtype4    0   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        4        0        0
  NOT HISPANIC OR LATINO       77       65       55       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 42 34
  subtype2 37 30
  subtype3 38 21
  subtype4 33 24
  subtype5 16 14
  subtype6 16 11
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      76       67       59       57       30       27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      34       30       21       24       14       11 
$subtype1
TCGA-18-4721 TCGA-18-5595 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
      154.32        27.19        60.89       122.43       119.80        43.23 
TCGA-21-5787 TCGA-22-1000 TCGA-22-5480 TCGA-22-5483 TCGA-33-4589 TCGA-33-A4WN 
       10.82        14.93        71.34        18.84         1.55         4.70 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2608 TCGA-34-5239 TCGA-34-5927 
        6.94        44.19       118.36        32.88        60.30        44.75 
TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        1.12         0.39         7.96         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 
      133.25       126.58        82.52        24.33        36.39        68.38 
TCGA-43-2581 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-52-7812 TCGA-58-A46M 
       38.66         5.46        19.59        78.18        27.45        35.24 
TCGA-60-2695 TCGA-60-2709 TCGA-60-2711 TCGA-60-2714 TCGA-60-2716 TCGA-63-A5MJ 
       21.11        49.48        41.42        50.33        48.49        59.97 
TCGA-66-2727 TCGA-66-2794 TCGA-68-7756 TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 
       16.96        54.08         6.64        29.56        73.12       140.09 
TCGA-77-7141 TCGA-77-7465 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GF TCGA-77-A5GH 
        0.49        15.75        54.41       150.25        27.62        38.86 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8287 
       31.30        32.91        18.94        25.15        19.04         0.76 
TCGA-85-8352 TCGA-85-A4CL TCGA-85-A511 TCGA-90-7767 TCGA-90-A4EE TCGA-94-8491 
        5.29        30.28        14.96         2.93        22.62        26.63 
TCGA-96-7544 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-A538 TCGA-98-A53A TCGA-98-A53H 
       71.01        19.36        27.68        27.16        18.15        20.32 
TCGA-L3-A524 TCGA-NC-A5HJ TCGA-O2-A52Q TCGA-O2-A52V 
       16.11        13.74         3.72        43.89 

$subtype2
TCGA-18-5592 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-21-A5DI TCGA-22-4605 
       49.94        99.16        15.58        31.73        32.19        32.02 
TCGA-22-5474 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-6737 
       14.63        62.86        56.32        22.06       173.82        19.76 
TCGA-33-AASD TCGA-34-2605 TCGA-34-5231 TCGA-34-8456 TCGA-37-4133 TCGA-37-A5EN 
      110.99        28.96        65.23        26.43         7.82        21.70 
TCGA-39-5022 TCGA-39-5040 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-8115 
       55.20        17.06        39.12        18.38        12.36        13.38 
TCGA-51-6867 TCGA-56-7730 TCGA-56-8083 TCGA-56-8309 TCGA-56-A4BX TCGA-58-8386 
       61.02         6.51         4.93        14.07        13.32         0.03 
TCGA-58-8388 TCGA-58-A46K TCGA-58-A46L TCGA-60-2710 TCGA-60-2719 TCGA-63-A5MB 
       13.55        34.36        56.65        66.54        42.64       102.67 
TCGA-66-2767 TCGA-66-2777 TCGA-66-2785 TCGA-66-2790 TCGA-77-6844 TCGA-77-7142 
        2.01         2.01         1.97        22.98        75.09        73.22 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-8276 TCGA-85-8288 
        9.67        11.97        36.53         1.38        34.52        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8355 TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR 
       22.45        16.77         2.01        34.13        30.48        19.73 
TCGA-85-A513 TCGA-90-A4ED TCGA-94-7557 TCGA-94-8490 TCGA-LA-A446 TCGA-MF-A522 
       29.92        20.22         0.16         5.03        13.18        11.84 
TCGA-NC-A5HF TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52N 
        4.54         4.21        49.28        25.32        83.57        33.07 
TCGA-O2-A5IB 
       11.18 

$subtype3
TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 TCGA-21-5786 TCGA-22-0940 TCGA-22-4607 
      119.54        46.88         9.34        33.93        21.99        19.30 
TCGA-22-5479 TCGA-22-5492 TCGA-34-5232 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 
       86.30        16.64        81.24        39.32        38.79         4.04 
TCGA-34-A5IX TCGA-37-3789 TCGA-39-5021 TCGA-43-5670 TCGA-43-6770 TCGA-43-A474 
       33.90         0.43        68.58        27.91        21.47        11.61 
TCGA-43-A56V TCGA-46-6025 TCGA-56-6545 TCGA-56-7222 TCGA-60-2698 TCGA-60-2703 
       12.03        10.65         2.04         0.43        10.22        96.82 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MI 
        3.19        32.32        23.57        11.77        70.62        58.65 
TCGA-63-A5MT TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2788 TCGA-66-2791 
       16.37         2.01         7.07        19.00        22.98         5.03 
TCGA-77-7337 TCGA-77-7463 TCGA-77-8154 TCGA-77-A5FZ TCGA-85-6561 TCGA-85-6798 
      106.95        46.78        60.53       126.18        12.99         6.41 
TCGA-85-7843 TCGA-85-8479 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A53L 
        1.15        15.39        22.59        30.97        19.86        12.39 
TCGA-94-8035 TCGA-94-A5I6 TCGA-98-A539 TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HD 
        4.01        17.69         5.69        12.89        13.41         0.07 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE 
       39.85        43.92        40.90        65.49         0.43 

$subtype4
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-33-4532 TCGA-33-4582 TCGA-33-4586 TCGA-33-A5GW TCGA-34-5929 
       30.12       129.01       103.53        14.07         0.30         4.96 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-43-2578 TCGA-46-6026 TCGA-52-7810 
      102.18        60.53        55.56        22.49        13.91        30.35 
TCGA-56-5898 TCGA-56-7221 TCGA-56-A5DS TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
       18.25         0.99         0.26        71.24        16.47        85.12 
TCGA-58-A46N TCGA-60-2704 TCGA-60-2708 TCGA-60-2713 TCGA-63-A5ML TCGA-63-A5MP 
       29.92        37.94        80.45        56.91        45.57        25.28 
TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2758 TCGA-66-2766 
       78.28        25.41        36.16        34.59        21.01         1.02 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2783 TCGA-66-2795 TCGA-66-2800 TCGA-68-A59J 
       23.01         3.02        24.95         4.01        49.05        13.45 
TCGA-77-7335 TCGA-77-8153 TCGA-77-A5G6 TCGA-85-7697 TCGA-85-8353 TCGA-85-8664 
       70.13        65.49        22.29        34.95         3.09        18.08 
TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 TCGA-98-A53B TCGA-98-A53J TCGA-NC-A5HI 
        9.50        21.04        16.14         2.01        20.71        57.30 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NC-A5HT 
        2.89        14.73        26.43 

$subtype5
TCGA-21-5784 TCGA-22-4596 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-33-4547 
       41.69         0.56        60.66        64.93        44.25        79.53 
TCGA-33-6738 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-37-A5EM TCGA-39-5019 
       63.35        74.66         9.07        16.93        28.50       111.35 
TCGA-39-5028 TCGA-52-7811 TCGA-56-5897 TCGA-56-6546 TCGA-60-2697 TCGA-63-A5MM 
        1.71         8.75         0.10         0.62        12.23        14.99 
TCGA-66-2781 TCGA-66-2782 TCGA-68-7757 TCGA-77-6845 TCGA-77-7338 TCGA-77-A5G1 
        3.98        12.00         6.94        23.28         0.16       132.36 
TCGA-85-7844 TCGA-85-A50Z TCGA-90-A59Q TCGA-92-7340 TCGA-94-7943 TCGA-NC-A5HE 
       29.95        16.21        10.59         2.70        18.38        76.80 

$subtype6
TCGA-22-1011 TCGA-22-5478 TCGA-34-2596 TCGA-34-2604 TCGA-34-2609 TCGA-39-5030 
        1.74         0.79         2.63        31.50        31.27         1.94 
TCGA-43-8118 TCGA-43-A475 TCGA-58-8393 TCGA-60-2696 TCGA-60-2706 TCGA-60-2712 
        2.93         9.73        34.78         3.58        92.71         9.01 
TCGA-60-2725 TCGA-63-A5MN TCGA-66-2737 TCGA-68-A59I TCGA-77-8143 TCGA-85-8072 
       26.83        11.34         2.01        14.07        26.40        30.64 
TCGA-85-8580 TCGA-85-A4PA TCGA-85-A510 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 
       36.59        24.36        15.85         3.65        24.92        11.77 
TCGA-94-A4VJ TCGA-98-7454 TCGA-98-A53C 
       14.14        21.44        27.02 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.39     0.03     0.07     0.26     0.10     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 
  27.535   22.060   19.300   24.950   16.570   14.140 
[1] "0.4 - 154.3 (27.5)" "0.0 - 173.8 (22.1)" "0.1 - 126.2 (19.3)"
[4] "0.3 - 129.0 (24.9)" "0.1 - 132.4 (16.6)" "0.8 - 92.7 (14.1)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       15       21        2        12        16         1
  subtype2       2       12       21        0        12         6         1
  subtype3       0        5       17        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       17       22       11        8
  STAGE II          2        0        0        0        1        0
  STAGE IIA        12       12        9        6        5        2
  STAGE IIB        16        6       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  8  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        8       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 45 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       45       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 53  2
  subtype3 56  1
  subtype4 53  0
  subtype5 24  0
  subtype6 26  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    0
  subtype2   53    2
  subtype3   56    1
  subtype4   53    0
  subtype5   24    0
  subtype6   26    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       66       53       56       53       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 54
  subtype3 11 51
  subtype4 15 45
  subtype5  6 25
  subtype6 13 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   57
  subtype2   13   54
  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       54       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  8
  subtype2 53  7
  subtype3 48  4
  subtype4 45  8
  subtype5 25  3
  subtype6 22  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    8
  subtype2   53    7
  subtype3   48    4
  subtype4   45    8
  subtype5   25    3
  subtype6   22    4
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        60       53       48       45       25       22
  YES        8        7        4        8        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                                                          63
  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       63
                                                             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 52  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       52       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    54
  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       54       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 48
  subtype3  0 38
  subtype4  0 32
  subtype5  1 17
  subtype6  0 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   54
  subtype2    0   48
  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       48       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 67 44
  subtype2 87 61
  subtype3 84 66
  subtype4 39 39
subtype1 subtype2 subtype3 subtype4 
     111      148      150       78 
subtype1 subtype2 subtype3 subtype4 
      44       61       66       39 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-21-1070 
       12.20         4.47        11.34        23.54        92.42       119.54 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 
      122.43         9.34       119.80        32.19         7.33         1.74 
TCGA-22-1012 TCGA-22-4607 TCGA-22-5471 TCGA-22-5491 TCGA-33-4547 TCGA-33-4589 
       14.10        19.30        60.66        56.32        79.53         1.55 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       81.24         9.07        16.93        33.90         4.01         0.43 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-43-6771 TCGA-43-8118 
       82.52         1.71        24.33        60.53         5.46         2.93 
TCGA-43-A56U TCGA-43-A56V TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 TCGA-56-7221 
       14.20        12.03        30.35         8.75         0.10         0.99 
TCGA-56-7579 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 TCGA-56-8305 TCGA-56-8504 
       31.27        17.49        14.96         3.48         3.45        16.77 
TCGA-56-8622 TCGA-56-A4BW TCGA-56-A5DR TCGA-56-A5DS TCGA-58-A46L TCGA-60-2707 
        1.81        19.23         0.13         0.26        56.65        21.73 
TCGA-60-2708 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MR 
       80.45        48.49        32.32        23.57        70.62        89.29 
TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2734 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
       25.41        34.59        43.10        25.05         0.99         2.01 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 
       19.00        19.00        12.03         3.98        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-77-8131 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       82.92        12.59        11.54        26.40        27.39         6.97 
TCGA-77-8154 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 
       60.53         5.92        30.81        34.95         1.38         1.15 
TCGA-85-8071 TCGA-85-8479 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4QQ 
       26.79        15.39        38.14        22.59        19.86        30.48 
TCGA-85-A50Z TCGA-90-6837 TCGA-90-7766 TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 
       16.21        24.92         9.50         2.70         2.30        21.04 
TCGA-94-8035 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-98-8020 TCGA-98-A538 
        4.01        14.14        71.01        17.46         2.76        27.16 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CT 
        4.54        64.54        57.30        43.92        14.73        65.49 
TCGA-NK-A5CX TCGA-O2-A52V TCGA-O2-A52W 
        3.65        43.89         8.58 

$subtype2
TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 TCGA-18-4086 
       75.75       117.57        92.15        31.99         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94        27.19        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4613 
       60.89        34.78        38.17        34.75        13.12        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
       63.55        14.63        44.25        86.30        11.74        30.12 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW 
      129.01        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-39-5022 TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 
       68.58        55.20       102.18        71.18        55.56        39.12 
TCGA-43-6770 TCGA-43-A474 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 
       21.47        11.61         9.73        13.02         9.99        10.65 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-51-6867 TCGA-56-5898 TCGA-56-7582 
        0.39         0.39        29.95        61.02        18.25         0.85 
TCGA-56-7730 TCGA-56-7823 TCGA-56-8308 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
        6.51        33.24        17.00        13.32        17.85        18.74 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 
       71.24        16.47        34.36        35.24        29.92        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MJ 
       66.54        41.42        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-77-6843 TCGA-77-6845 TCGA-77-7139 
       49.05         2.73        13.45        73.12        23.28       140.09 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 
       20.78         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-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
      150.25        61.94        42.08        27.62        12.99         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       36.53        31.30        29.95        24.13        31.56        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL 
       34.52        10.09        32.71         2.01        36.59        30.28 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 
       34.13        19.73         3.65        11.77         3.48         5.26 
TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53I 
        5.03        16.14        17.69        57.07        19.36        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL 
       20.71        19.10        16.11        13.18        11.84         2.89 
TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NK-A5CR TCGA-O2-A52S 
       49.28        40.90        83.57        12.72 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-18-3417 TCGA-21-1078 TCGA-21-1079 TCGA-21-1083 
      123.19         4.80        36.07        15.58        31.73        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-22-0940 TCGA-22-1016 TCGA-22-4593 
       31.63        88.11        33.93        21.99        27.02        35.08 
TCGA-22-4595 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 
       24.13         0.79        71.34        79.20        18.84        62.86 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-AASB 
       22.06       133.74       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-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        4.96         0.39         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EM TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        0.39         3.39        28.50         1.94        36.39        68.38 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       17.06        40.21        38.66        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       12.36        24.89        19.59         7.76        78.18        13.38 
TCGA-43-8116 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 
       11.77        13.02         3.98        13.91         5.46         2.04 
TCGA-56-6546 TCGA-56-7223 TCGA-56-7580 TCGA-56-8083 TCGA-56-8201 TCGA-56-8307 
        0.62         0.99         1.32         4.93        13.05        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       14.07         1.35        10.36         9.93        20.25        15.81 
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-60-2712 TCGA-60-2713 TCGA-60-2720 TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MI 
        9.01        56.91         3.19        11.77        66.61        58.65 
TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2744 
       14.99        78.28        16.37        36.16        53.88         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 TCGA-66-2769 
        2.01         0.92         0.99        43.99         2.01         7.07 
TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-8251 TCGA-68-A59I 
        1.97         4.04        22.98        10.06        13.35        14.07 
TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 TCGA-77-8139 TCGA-77-A5G1 
       29.56        15.75         6.51        39.09       104.09       132.36 
TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7950 TCGA-85-8048 
       22.29        38.86        11.97        32.91        18.94        25.15 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8481 TCGA-85-8664 
        0.76        13.22        22.45         5.29         7.76        18.08 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 
       30.97        24.36        15.85        14.96        12.39         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-94-7557 TCGA-96-A4JL 
       20.22        22.62        10.59         4.01         0.16        27.68 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-LA-A7SW 
       30.81        30.67        21.34        18.15         2.01        13.41 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HP 
        0.07        76.80         1.22         4.21        39.85        25.32 
TCGA-NC-A5HT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       26.43        16.80         0.43        33.07         3.72        11.18 

$subtype4
TCGA-18-3421 TCGA-21-5784 TCGA-21-5787 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       86.96        41.69        10.82        14.93         4.31        64.21 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 
       48.82        20.48        48.33         0.56        32.02         9.57 
TCGA-22-5472 TCGA-22-5492 TCGA-33-6737 TCGA-33-6738 TCGA-34-2608 TCGA-34-5234 
       64.93        16.64        19.76        63.35        32.88        74.66 
TCGA-34-8454 TCGA-34-8455 TCGA-39-5011 TCGA-39-5039 TCGA-43-2578 TCGA-43-6773 
       38.79         4.04       133.25        17.88        22.49         3.81 
TCGA-46-3766 TCGA-52-7622 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7731 
       12.00        28.34        27.45        28.96         0.43         0.10 
TCGA-56-8623 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZJ TCGA-58-8386 TCGA-58-8393 
       22.75         1.18        20.94        21.04         0.03        34.78 
TCGA-58-A46J TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       85.12         3.58        12.23        10.22        37.94        92.71 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2725 TCGA-63-A5MN TCGA-66-2742 
       50.33        35.34        42.64        26.83        11.34        21.07 
TCGA-66-2753 TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2786 
        1.02         2.01         3.02         2.01        24.95        25.97 
TCGA-68-7756 TCGA-68-8250 TCGA-77-8138 TCGA-77-8146 TCGA-77-A5FZ TCGA-85-6175 
        6.64         8.02        17.72       104.84       126.18         9.67 
TCGA-85-8049 TCGA-85-8351 TCGA-85-8353 TCGA-85-8584 TCGA-85-A50M TCGA-85-A513 
       19.04        16.77         3.09        12.59        27.16        29.92 
TCGA-90-7964 TCGA-94-7943 TCGA-94-8491 TCGA-96-8169 TCGA-98-7454 TCGA-98-A539 
       14.07        18.38        26.63        18.31        21.44         5.69 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ TCGA-XC-AA0X 
       27.02        21.21        20.32        12.89        13.74         0.20 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.07     0.03 
subtype1 subtype2 subtype3 subtype4 
  122.43   154.32   173.82   133.25 
subtype1 subtype2 subtype3 subtype4 
   19.00    30.07    17.57    20.40 
[1] "0.1 - 122.4 (19.0)" "0.2 - 154.3 (30.1)" "0.1 - 173.8 (17.6)"
[4] "0.0 - 133.2 (20.4)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       20       38        1        10        22         0
  subtype2       1       19       55        1        24        29         1
  subtype3       1       29       37        1        24        31         2
  subtype4       0       22       21        0         8        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         20       19       29       22
  STAGE IB         38       55       37       21
  STAGE II          1        1        1        0
  STAGE IIA        10       24       24        8
  STAGE IIB        22       29       31       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 24 68 17  4
  subtype2 29 97 17  9
  subtype3 36 87 24  7
  subtype4 25 40 12  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       24       29       36       25
  T2       68       97       87       40
  T3       17       17       24       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 74 26 10  1
  subtype2 93 46 11  1
  subtype3 98 45 10  1
  subtype4 53 13  9  2
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       74       93       98       53
  N1       26       46       45       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  90   1
  subtype2 128   0
  subtype3 123   3
  subtype4  66   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90    1
  subtype2  128    0
  subtype3  123    3
  subtype4   66    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       90      128      123       66
  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  28  85
  subtype2  34 118
  subtype3  42 112
  subtype4  25  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   85
  subtype2   34  118
  subtype3   42  112
  subtype4   25   55
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28       34       42       25
  MALE         85      118      112       55
[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  80  12
  subtype2 118  15
  subtype3 111  15
  subtype4  61   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80   12
  subtype2  118   15
  subtype3  111   15
  subtype4   61    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        80      118      111       61
  YES       12       15       15        7
[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                                                         109
  subtype2                                                         145
  subtype3                                                         145
  subtype4                                                          78
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)      109      145
                                                             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)      145       78
[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  86   2   2   3
  subtype2 128   6   0   7
  subtype3 120   3   1   7
  subtype4  63   1   1   5
D7V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       86      128      120       63
  R1        2        6        3        1
  R2        2        0        1        1
  RX        3        7        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    73
  subtype2     1                         9   107
  subtype3     3                        10   111
  subtype4     3                         4    57
D7V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        3        3
  BLACK OR AFRICAN AMERICAN        7        9       10        4
  WHITE                           73      107      111       57
[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  66
  subtype2   1  94
  subtype3   1 105
  subtype4   2  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   66
  subtype2    1   94
  subtype3    1  105
  subtype4    2   50
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        1        1        2
  NOT HISPANIC OR LATINO       66       94      105       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"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 106  69
  subtype2 107  76
  subtype3  64  65
subtype1 subtype2 subtype3 
     175      183      129 
subtype1 subtype2 subtype3 
      69       76       65 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1078 
       12.20        23.54        92.42        86.96       119.54        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       31.73       122.43         9.34       119.80        31.63        41.69 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4605 
       32.19        14.93         1.74        20.48        24.13        32.02 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 TCGA-22-A5C4 
       19.30        11.77        64.93         0.79        16.64        22.06 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 TCGA-34-2600 TCGA-34-2608 
      129.01        79.53       103.53         1.55        61.61        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       81.24        74.66        16.93        44.75         4.96        38.79 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-39-5024 TCGA-39-5028 
        4.04        33.90         4.01         0.43        82.52         1.71 
TCGA-39-5029 TCGA-39-5039 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
       24.33        17.88        33.11        27.91        24.89         5.46 
TCGA-43-8115 TCGA-43-A56U TCGA-43-A56V TCGA-46-3766 TCGA-52-7810 TCGA-52-7811 
       13.38        14.20        12.03        12.00        30.35         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7731 
       28.96         0.10         2.04         0.43         1.32         0.10 
TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
       17.49        14.96         3.48         1.35         1.81         1.18 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       10.36        20.94        19.23        21.04         0.13         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2698 
        0.03        13.25        34.78        85.12         3.58        10.22 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       21.73        80.45        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MI 
       32.32        23.57        26.83        11.77        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-68-8250 TCGA-68-A59I 
       22.98        10.06         6.64         6.94         8.02        14.07 
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 
       82.92        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-77-A5GB TCGA-85-6175 TCGA-85-8276 TCGA-85-8351 
       22.29         5.92        30.81         9.67        34.52        16.77 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       15.39         7.76        38.14        19.86        30.48        19.73 
TCGA-85-A50Z TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-92-7340 TCGA-92-8065 
       16.21        24.92         9.50        14.07         2.70         2.30 
TCGA-94-7033 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       21.04        26.63        14.14        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53H 
       27.68         2.76        30.81        27.16         5.69        20.32 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       12.89        13.41         0.07         4.54        64.54        57.30 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52V 
       39.85        43.92        14.73        26.43         3.65        43.89 
TCGA-O2-A52W 
        8.58 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
        4.47        75.75       117.57        11.34        92.15        31.99 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
        6.18         2.79       154.32        49.94        27.19        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-22-4609 TCGA-22-5471 TCGA-22-5473 
       38.17        34.75        13.12         9.57        60.66        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-A5EM 
        9.07        50.66         1.12        26.43         7.82        28.50 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
       21.70       126.58       111.35        68.58        55.20       102.18 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-6773 
       60.53        71.18        55.56        39.12        21.47         3.81 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 
        2.93        11.61         9.73        13.02         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 
       13.91         0.39         0.39        29.95        61.02        28.34 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 
       18.25         0.99        31.27         0.85         6.51        33.24 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY 
        3.45        17.00        16.77        15.81        13.32        17.85 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L 
       18.74        14.47        71.24        16.47        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       35.24        29.92        49.48        66.54        41.42        56.91 
TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       29.85        35.90       102.67        59.97        45.57        25.28 
TCGA-63-A5MU TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
       25.41        16.96         2.01        21.01        25.05         1.02 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
        2.01        23.01        24.95        40.01         5.03        30.02 
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        13.45        73.12 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 
       23.28       140.09        20.78         0.49        70.13         0.16 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       55.73        37.81        53.92        66.51        54.41        65.49 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 
       36.36       150.25        61.94        42.08        27.62        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 
        6.41        36.53        34.95        31.30         1.15        29.95 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
       19.04        24.13        31.56        26.79        30.64        10.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       32.71         2.01        36.59        22.59        30.28        34.13 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       14.96         3.65        11.77         3.48         4.01         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK 
        4.01         5.03        16.14        17.69        57.07        19.36 
TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
       18.15        18.58        20.71        19.10        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NK-A5CR 
       11.84        76.80         2.89        49.28        40.90        83.57 
TCGA-NK-A7XE TCGA-O2-A52S TCGA-XC-AA0X 
        0.43        12.72         0.20 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-18-3417 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 
      123.19         4.80        36.07        43.23        88.11        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
       10.82        21.99         4.31        64.21        27.02        48.82 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       35.08        48.33         0.56        71.34        79.20        18.84 
TCGA-22-5489 TCGA-33-4533 TCGA-33-4566 TCGA-33-4587 TCGA-33-6737 TCGA-33-AASB 
       62.86       133.74       173.82        54.44        19.76         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-43-2578 TCGA-43-2581 
       36.39        68.38        17.06        40.21        22.49        38.66 
TCGA-43-5668 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
       18.38        12.36        19.59         7.76        78.18        11.77 
TCGA-46-3767 TCGA-46-3769 TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7223 
       13.02         3.98         5.46        27.45         0.62         0.99 
TCGA-56-8083 TCGA-56-8201 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8626 
        4.93        13.05        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-60-2712 TCGA-60-2714 TCGA-63-A5MH TCGA-63-A5MM 
       37.94        92.71         9.01        50.33        66.61        14.99 
TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
       11.34        78.28        53.88         0.99         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 
        0.99        43.99         7.07         1.97         4.04        22.98 
TCGA-68-8251 TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-A5FZ TCGA-77-A5GH 
       13.35        29.56        15.75         6.51       126.18        38.86 
TCGA-85-6560 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8287 
       11.97        32.91         1.38        18.94        25.15         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8584 TCGA-85-8664 
       13.22        22.45         5.29         3.09        12.59        18.08 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L 
       30.97        24.36        27.16        15.85        29.92        12.39 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7557 TCGA-94-7943 
        2.93        20.22        22.62        10.59         0.16        18.38 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       21.44        30.67        21.34         2.01        27.02        21.21 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NK-A5CT TCGA-NK-A5D1 
        1.22        13.74         4.21        25.32        65.49        16.80 
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 
  132.36   154.32   173.82 
subtype1 subtype2 subtype3 
   19.30    26.79    18.94 
[1] "0.0 - 132.4 (19.3)" "0.2 - 154.3 (26.8)" "0.2 - 173.8 (18.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       30       59        1        20        31         0
  subtype2       1       26       63        2        28        37         1
  subtype3       1       34       29        0        18        25         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         59       63       29
  STAGE II          1        2        0
  STAGE IIA        20       28       18
  STAGE IIB        31       37       25
  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  38 120  21  10
  subtype3  41  67  17   6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       35       38       41
  T2      105      120       67
  T3       32       21       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 115  54  16   3
  subtype3  85  33  10   1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      118      115       85
  N1       43       54       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 144   4
  subtype2 157   0
  subtype3 106   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144    4
  subtype2  157    0
  subtype3  106    3
   clus
vv  subtype1 subtype2 subtype3
  0      144      157      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  37 152
  subtype3  36  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  123
  subtype2   37  152
  subtype3   36   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       37       36
  MALE        123      152       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 134  16
  subtype2 139  24
  subtype3  97   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  134   16
  subtype2  139   24
  subtype3   97    9
     clus
vv    subtype1 subtype2 subtype3
  NO       134      139       97
  YES       16       24        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                                                         181
  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      181
                                                             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 152   7   3   8
  subtype3 103   3   0   5
D8V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142      152      103
  R1        2        7        3
  R2        1        3        0
  RX        9        8        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   132
  subtype3     4                         6   100
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        4
  BLACK OR AFRICAN AMERICAN       11       13        6
  WHITE                          116      132      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   2 118
  subtype3   2  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  104
  subtype2    2  118
  subtype3    2   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO      104      118       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 63 57
  subtype2 87 44
  subtype3 63 54
  subtype4 35 25
  subtype5 19 18
subtype1 subtype2 subtype3 subtype4 subtype5 
     120      131      117       60       37 
subtype1 subtype2 subtype3 subtype4 subtype5 
      57       44       54       25       18 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20         4.47        75.75         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07        92.42        86.96 
TCGA-18-5592 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 
       49.94        99.16        15.58        31.73       122.43        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 
       31.63        33.93        10.82        21.99         7.33         1.74 
TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
       14.10        48.33        24.13         0.56        34.75        13.12 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5480 
       19.30        11.77        60.66        63.55        14.63        71.34 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       62.86        16.64       129.01       133.74        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2605 TCGA-34-5241 
      173.82       103.53        14.07         1.55        28.96        16.93 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.43         0.39         8.12         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        3.39       133.25        68.58         1.71        24.33         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
       36.39        68.38        71.18        17.88        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       39.12        33.11        18.38        13.02        12.00        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-60-2695 
        9.99         3.98        29.95        28.96         0.10        21.11 
TCGA-60-2696 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        3.58        92.71        80.45         9.01        56.91        50.33 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-66-2734 TCGA-66-2737 
       48.49        32.32        35.90        23.57        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 
       21.07         0.99         1.02         2.01         0.92        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2771 TCGA-66-2777 
       25.05         0.99         2.01         2.01        19.00         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       40.01        22.98         4.04        22.98         5.03        30.02 
TCGA-66-2795 TCGA-77-8007 TCGA-77-8144 TCGA-85-7699 TCGA-90-A59Q TCGA-94-7033 
        4.01         6.51        27.39        32.91        10.59        21.04 

$subtype2
TCGA-18-5595 TCGA-21-1075 TCGA-21-5783 TCGA-22-5481 TCGA-22-5491 TCGA-33-4587 
       27.19        70.16        88.11        79.20        56.32        54.44 
TCGA-33-6737 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-34-5231 
       19.76         4.70         6.94       110.99       118.36        65.23 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       39.32         4.96         1.12        26.43        33.90         4.01 
TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5037 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 
       28.50        21.70        55.56        27.91        12.36         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-46-6025 TCGA-51-6867 TCGA-52-7809 
       78.18        13.38        11.61        10.65        61.02         5.46 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7823 
        0.43         0.99        31.27         1.32         0.85        33.24 
TCGA-56-8201 TCGA-56-8304 TCGA-56-8305 TCGA-56-8307 TCGA-56-8308 TCGA-56-8504 
       13.05         3.48         3.45        26.89        17.00        16.77 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
       15.81        19.23        13.32        17.85        18.74         0.13 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46N TCGA-60-2703 
       14.47        13.25        71.24        16.47        29.92        96.82 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
      102.67        66.61        58.65        59.97        45.57        89.29 
TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2766 TCGA-66-2768 TCGA-68-7755 TCGA-68-8251 
       25.41        34.59         1.02         2.01         2.73        13.35 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7465 
       23.28        11.18       140.09        20.78        70.13        15.75 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       37.81        53.92        26.40        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6561 
       60.53        36.36       150.25        22.29        61.94        12.99 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8070 TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 
        1.38         1.15        31.56        34.52        13.22         5.29 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QR 
       32.71        15.39        36.59        22.59        34.13        19.73 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 
       16.21        14.96        12.39         2.93        11.77         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-94-8490 TCGA-94-A5I4 
        4.01         5.26         2.30        18.38         5.03        16.14 
TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A53A TCGA-98-A53J TCGA-J1-A4AH 
       17.69        19.36        27.16        18.15        20.71        19.10 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        11.84         0.07        76.80        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR 
       57.30         2.89        39.85        49.28        43.92        40.90 
TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       83.57        16.80         3.72        12.72        11.18 

$subtype3
TCGA-21-5784 TCGA-21-A5DI TCGA-22-4593 TCGA-22-4605 TCGA-22-4609 TCGA-22-5472 
       41.69        32.19        35.08        32.02         9.57        64.93 
TCGA-22-5479 TCGA-22-5483 TCGA-22-A5C4 TCGA-33-6738 TCGA-33-AASI TCGA-34-2609 
       86.30        18.84        22.06        63.35        44.19        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-8454 TCGA-34-8455 
       81.24        74.66         9.07        60.30        38.79         4.04 
TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 TCGA-43-6647 TCGA-43-6771 
      111.35        82.52       102.18        17.06        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-6545 
        3.81        19.59        30.35         8.75        27.45         2.04 
TCGA-56-6546 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 
        0.62         0.10        17.49         1.35        22.75         1.18 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4ZJ TCGA-58-8386 TCGA-58-8388 TCGA-58-8393 
        9.93        20.25        21.04         0.03        13.55        34.78 
TCGA-58-A46J TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2720 TCGA-60-2725 
       85.12        12.23        10.22        37.94         3.19        26.83 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-68-7756 
       70.62        14.99        78.28        16.37        36.16         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6844 TCGA-77-7142 TCGA-77-7337 
        6.94         8.02        14.07        75.09        73.22       106.95 
TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8145 
       46.78        86.76        82.92        12.59        17.72         6.97 
TCGA-77-8146 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB TCGA-85-6175 TCGA-85-6560 
      104.84       126.18       132.36        30.81         9.67        11.97 
TCGA-85-7697 TCGA-85-7698 TCGA-85-8048 TCGA-85-8049 TCGA-85-8350 TCGA-85-8351 
       34.95        31.30        25.15        19.04        22.45        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JC 
        3.09         2.01         7.76        38.14        12.59        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
       24.36        30.48        27.16        29.92        24.92         9.50 
TCGA-90-7964 TCGA-92-7340 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
       14.07         2.70        26.63        14.14        71.01        57.07 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44         2.76        30.67        21.34 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 
        5.69         2.01        27.02        21.21        20.32        12.89 
TCGA-LA-A7SW TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-NK-A7XE 
       13.41        13.74         4.21        14.73         3.65         0.43 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

$subtype4
TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 TCGA-21-1077 TCGA-22-5477 TCGA-22-5482 
        2.79       154.32        60.89        34.78        44.25        11.74 
TCGA-22-5485 TCGA-33-4583 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASL TCGA-34-2596 
       30.12       151.27         0.30        36.62        27.16         2.63 
TCGA-34-2608 TCGA-34-5240 TCGA-39-5022 TCGA-43-6770 TCGA-43-8118 TCGA-43-A475 
       32.88        50.66        55.20        21.47         2.93         9.73 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7730 
        0.39         0.39        28.34        18.25         0.99         6.51 
TCGA-56-8309 TCGA-56-8622 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2709 
       14.07         1.81        34.36        56.65        35.24        49.48 
TCGA-60-2710 TCGA-60-2722 TCGA-63-A5MN TCGA-63-A5MP TCGA-66-2727 TCGA-66-2770 
       66.54        29.85        11.34        25.28        16.96        23.01 
TCGA-66-2794 TCGA-66-2800 TCGA-68-A59J TCGA-77-6843 TCGA-77-7141 TCGA-77-7338 
       54.08        49.05        13.45        73.12         0.49         0.16 
TCGA-77-8009 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 
       55.73        42.08        27.62        38.86         6.41        36.53 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-A4CL 
       29.95        18.94        24.13        26.79        30.64        30.28 
TCGA-90-A4ED TCGA-90-A4EE TCGA-98-8021 TCGA-98-A53I TCGA-LA-A446 TCGA-NK-A5CT 
       20.22        22.62        30.81        18.58        13.18        65.49 

$subtype5
TCGA-22-4591 TCGA-22-5478 TCGA-34-2600 TCGA-34-2604 TCGA-34-5927 TCGA-39-5031 
       20.48         0.79        61.61        31.50        44.75        60.53 
TCGA-43-2578 TCGA-43-8116 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-56-8082 
       22.49        11.77        14.20        12.03        13.91        14.96 
TCGA-56-8083 TCGA-56-8625 TCGA-56-A49D TCGA-58-8390 TCGA-60-2711 TCGA-60-2719 
        4.93        10.36        20.94        29.95        41.42        42.64 
TCGA-63-A5MW TCGA-66-2793 TCGA-77-6842 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
       53.88        10.06        29.56        39.09       104.09        11.54 
TCGA-77-A5G7 TCGA-85-8287 TCGA-85-8664 TCGA-85-A4JB TCGA-85-A510 TCGA-85-A5B5 
        5.92         0.76        18.08        30.97        15.85         3.65 
TCGA-94-7557 TCGA-94-8035 TCGA-96-8169 TCGA-NC-A5HF TCGA-NC-A5HP TCGA-NC-A5HT 
        0.16         4.01        18.31         4.54        25.32        26.43 
TCGA-O2-A52N 
       33.07 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.07     0.03     0.16     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  173.82   150.25   132.36   154.32   104.09 
subtype1 subtype2 subtype3 subtype4 subtype5 
   21.55    19.36    21.04    27.39    18.31 
[1] "0.1 - 173.8 (21.5)" "0.1 - 150.2 (19.4)" "0.0 - 132.4 (21.0)"
[4] "0.2 - 154.3 (27.4)" "0.2 - 104.1 (18.3)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       17       48        0         6        20         0
  subtype2       1       15       38        2        28        28         3
  subtype3       1       25       31        1        19        25         0
  subtype4       0       16       20        0         8        10         0
  subtype5       1       10        7        0         2         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         21          6        3
  subtype2         17          2        0
  subtype3         15          3        2
  subtype4          3          3        0
  subtype5          5          2        1
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        1        1        0        1
  STAGE IA         17       15       25       16       10
  STAGE IB         48       38       31       20        7
  STAGE II          0        2        1        0        0
  STAGE IIA         6       28       19        8        2
  STAGE IIB        20       28       25       10        9
  STAGE III         0        3        0        0        0
  STAGE IIIA       21       17       15        3        5
  STAGE IIIB        6        2        3        3        2
  STAGE IV          3        0        2        0        1
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 22 80 11  8
  subtype2 23 86 23  3
  subtype3 30 62 24  6
  subtype4 20 34  4  3
  subtype5 11 18  6  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       22       23       30       20       11
  T2       80       86       62       34       18
  T3       11       23       24        4        6
  T4        8        3        6        3        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 76 28 13  4
  subtype2 78 42 13  0
  subtype3 79 31  8  0
  subtype4 42 16  3  0
  subtype5 25  9  3  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       76       78       79       42       25
  N1       28       42       31       16        9
  N2       13       13        8        3        3
  N3        4        0        0        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 113   3
  subtype2 103   0
  subtype3  94   2
  subtype4  48   0
  subtype5  28   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    3
  subtype2  103    0
  subtype3   94    2
  subtype4   48    0
  subtype5   28    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      113      103       94       48       28
  1        3        0        2        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  31  90
  subtype2  30 105
  subtype3  33  89
  subtype4  15  46
  subtype5  14  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   90
  subtype2   30  105
  subtype3   33   89
  subtype4   15   46
  subtype5   14   23
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       31       30       33       15       14
  MALE         90      105       89       46       23
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1  74  11
  subtype2  99  14
  subtype3 101  12
  subtype4  50   6
  subtype5  34   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74   11
  subtype2   99   14
  subtype3  101   12
  subtype4   50    6
  subtype5   34    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        74       99      101       50       34
  YES       11       14       12        6        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     1
  subtype4                                     4
  subtype5                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      3
  subtype4                                      0
  subtype5                                      0
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
  subtype4                                       0
  subtype5                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         119
  subtype2                                                         125
  subtype3                                                         118
  subtype4                                                          57
  subtype5                                                          37
D9V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      119      125
                                                             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)      118       57
                                                             clus
vv                                                            subtype5
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       37
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   2   2   2
  subtype2 101   3   0   8
  subtype3  91   2   0   7
  subtype4  48   4   0   2
  subtype5  29   0   1   1
D9V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      109      101       91       48       29
  R1        2        3        2        4        0
  R2        2        0        0        0        1
  RX        2        8        7        2        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         4    74
  subtype2     2                         5   102
  subtype3     4                        13    86
  subtype4     0                         6    43
  subtype5     0                         2    27
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        4        0        0
  BLACK OR AFRICAN AMERICAN        4        5       13        6        2
  WHITE                           74      102       86       43       27
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
          cls
clus        0  1
  subtype1  3 67
  subtype2  1 88
  subtype3  2 83
  subtype4  1 41
  subtype5  0 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   67
  subtype2    1   88
  subtype3    2   83
  subtype4    1   41
  subtype5    0   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        2        1        0
  NOT HISPANIC OR LATINO       67       88       83       41       22
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  52  33
  subtype2  63  51
  subtype3 116  83
  subtype4  36  31
subtype1 subtype2 subtype3 subtype4 
      85      114      199       67 
subtype1 subtype2 subtype3 subtype4 
      33       51       83       31 
$subtype1
TCGA-18-3406 TCGA-18-3408 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 
       12.20        75.75         2.79       154.32        49.94        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-22-1012 TCGA-22-4609 TCGA-22-5471 TCGA-22-5473 
       60.89        34.78        14.10         9.57        60.66        63.55 
TCGA-22-5477 TCGA-22-5482 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-AAS8 
       44.25        11.74       151.27        14.07         1.55        36.62 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-39-5022 TCGA-43-6770 
       27.16         2.63        28.96        50.66        55.20        21.47 
TCGA-43-A474 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-7582 
       11.61         9.73         0.39         0.39        29.95         0.85 
TCGA-56-7730 TCGA-56-8309 TCGA-56-8622 TCGA-58-8391 TCGA-58-A46K TCGA-58-A46M 
        6.51        14.07         1.81        71.24        34.36        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-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2727 TCGA-66-2737 
      102.67        59.97        45.57        25.28        16.96         2.01 
TCGA-66-2758 TCGA-66-2770 TCGA-66-2787 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 
       21.01        23.01        40.01         5.03        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-7141 TCGA-77-7338 
       49.05         2.73        13.45        73.12         0.49         0.16 
TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
       55.73       150.25        22.29        27.62         6.41        36.53 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 
       29.95        18.94        24.13        26.79        30.64         5.29 
TCGA-85-A4CL TCGA-85-A4CN TCGA-90-7769 TCGA-90-A4EE TCGA-94-8491 TCGA-94-A5I6 
       30.28        34.13        11.77        22.62        26.63        17.69 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-LA-A446 
       21.34        18.15        18.58        20.71        19.10        13.18 
TCGA-O2-A52S 
       12.72 

$subtype2
TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        4.47         4.80        11.34        92.15        31.99        36.07 
TCGA-18-5595 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-22-0940 
       27.19        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-39-5011 TCGA-39-5021 TCGA-39-5036 TCGA-39-5039 
        4.01         0.39       133.25        68.58        71.18        17.88 
TCGA-43-2576 TCGA-43-2581 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-46-3765 
       40.21        38.66         5.46         7.76        78.18        13.02 
TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 
       12.00         9.99         3.98         5.46        30.35         0.10 
TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7823 TCGA-56-8201 TCGA-56-8307 
        2.04        31.27         1.32        33.24        13.05        26.89 
TCGA-56-8504 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-8388 TCGA-58-A46L TCGA-60-2695 
       16.77        19.23        18.74        13.55        56.65        21.11 
TCGA-60-2696 TCGA-60-2712 TCGA-60-2716 TCGA-60-2721 TCGA-63-A5MR TCGA-66-2734 
        3.58         9.01        48.49        32.32        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-77-6845 TCGA-77-7138 
        3.98        12.00        25.97        13.35        23.28        11.18 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 TCGA-77-A5G8 
       70.13       106.95        15.75        37.81        53.92        61.94 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-8048 TCGA-85-8276 TCGA-85-8288 
       34.95        31.30         1.38        25.15        34.52        13.22 
TCGA-85-8355 TCGA-85-8479 TCGA-85-A53L TCGA-90-7767 TCGA-90-A59Q TCGA-92-7341 
        2.01        15.39        12.39         2.93        10.59         3.48 
TCGA-92-8064 TCGA-94-7033 TCGA-94-8490 TCGA-94-A5I4 TCGA-96-7544 TCGA-L3-A524 
        5.26        21.04         5.03        16.14        71.01        16.11 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HR TCGA-NK-A5CX TCGA-O2-A52Q 
       76.80        64.54         2.89        40.90         3.65         3.72 

$subtype3
TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1075 TCGA-21-1079 
      117.57        23.54        92.42        86.96        70.16        31.73 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4593 
       31.63        88.11        10.82        32.19        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 
       16.64        22.06       129.01       133.74       103.53        54.44 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-34-2600 TCGA-34-2604 
        4.70         0.30         6.94       110.99        61.61        31.50 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
       31.27        65.23        16.93        44.75        39.32        38.79 
TCGA-34-8456 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
       26.43         0.43         8.12         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EM TCGA-37-A5EN TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
        3.39        28.50        21.70        82.52       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
        1.94        60.53        36.39        55.56        17.06        22.49 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 
       39.12        33.11        18.38        27.91        12.36        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V TCGA-46-3767 
       13.38        11.77         2.93        14.20        12.03        13.02 
TCGA-46-6026 TCGA-51-6867 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
       13.91        61.02        28.34         8.75        28.96        18.25 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 
        0.99         0.43         0.99         0.10        17.49        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8305 TCGA-56-8308 TCGA-56-8503 TCGA-56-8625 
        4.93         3.48         3.45        17.00         1.35        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY 
        9.93        20.25        15.81        20.94        13.32        17.85 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 TCGA-58-8392 TCGA-60-2703 
        0.13        14.47        13.25        29.95        16.47        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 
       37.94        92.71        80.45        41.42        50.33        42.64 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MS 
       23.57        26.83        66.61        58.65        11.34        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2754 
       16.37        25.41        36.16        53.88        34.59         2.01 
TCGA-66-2777 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
        2.01         1.97        22.98         4.04        22.98        30.02 
TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
       10.06         6.94         8.02        14.07        29.56        75.09 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7463 TCGA-77-8008 TCGA-77-8136 
      140.09        20.78        73.22        46.78        86.76        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 
       66.51        54.41        65.49        36.36       132.36         5.92 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7843 TCGA-85-8049 TCGA-85-8070 
       38.86        11.97        32.91         1.15        19.04        31.56 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        0.76        16.77        32.71         7.76        36.59        38.14 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 
       18.08        22.59        30.97        19.73        15.85        14.96 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-7557 
        3.65         9.50        20.22         4.01         2.30         0.16 
TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 
        4.01        14.14        18.31        19.36         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-LA-A7SW TCGA-MF-A522 
       30.67        27.16         5.69         2.01        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM 
        0.07         4.54         1.22        57.30         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W 
       65.49        16.80         0.43        33.07        43.89         8.58 
TCGA-O2-A5IB 
       11.18 

$subtype4
TCGA-21-5784 TCGA-22-4596 TCGA-22-5472 TCGA-33-4538 TCGA-33-6737 TCGA-33-6738 
       41.69         0.56        64.93        97.94        19.76        63.35 
TCGA-33-AASI TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       44.19        32.88        81.24        74.66         9.07        60.30 
TCGA-34-8455 TCGA-39-5019 TCGA-39-5028 TCGA-39-5035 TCGA-43-6647 TCGA-43-6773 
        4.04       111.35         1.71        68.38        24.89         3.81 
TCGA-46-6025 TCGA-52-7812 TCGA-56-6546 TCGA-56-8623 TCGA-56-8624 TCGA-56-A4ZJ 
       10.65        27.45         0.62        22.75         1.18        21.04 
TCGA-58-8386 TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2698 TCGA-60-2720 
        0.03        34.78        85.12        12.23        10.22         3.19 
TCGA-63-A5MG TCGA-63-A5MM TCGA-66-2783 TCGA-68-7756 TCGA-77-8007 TCGA-77-8130 
       70.62        14.99        24.95         6.64         6.51        82.92 
TCGA-77-8131 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5GA TCGA-77-A5GB 
       12.59       104.84        60.53       126.18        42.08        30.81 
TCGA-85-6175 TCGA-85-6561 TCGA-85-8350 TCGA-85-8353 TCGA-85-8584 TCGA-85-A4JC 
        9.67        12.99        22.45         3.09        12.59        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 
       24.36        30.48        27.16        16.21        29.92        24.92 
TCGA-90-7964 TCGA-92-7340 TCGA-94-7943 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
       14.07         2.70        18.38        57.07        17.46        27.68 
TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ 
       21.44        27.02        21.21        20.32        12.89        13.74 
TCGA-XC-AA0X 
        0.20 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.10     0.07     0.03 
subtype1 subtype2 subtype3 subtype4 
  154.32   173.82   140.09   126.18 
subtype1 subtype2 subtype3 subtype4 
   25.28    18.31    20.78    21.44 
[1] "0.2 - 154.3 (25.3)" "0.1 - 173.8 (18.3)" "0.1 - 140.1 (20.8)"
[4] "0.0 - 126.2 (21.4)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       14       30        0        12        18         1
  subtype2       0       17       41        1        17        24         1
  subtype3       3       40       54        2        22        35         1
  subtype4       0       12       19        0        12        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         30       41       54       19
  STAGE II          0        1        2        0
  STAGE IIA        12       17       22       12
  STAGE IIB        18       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  55   8   6
  subtype2  22  74  18   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       55       74      111       40
  T3        8       18       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  29   6   1
  subtype2  78  29   9   1
  subtype3 130  50  20   1
  subtype4  40  18   5   1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       52       78      130       40
  N1       29       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  75   0
  subtype2 100   2
  subtype3 157   2
  subtype4  54   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75    0
  subtype2  100    2
  subtype3  157    2
  subtype4   54    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       75      100      157       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  19  69
  subtype2  30  87
  subtype3  54 147
  subtype4  20  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   69
  subtype2   30   87
  subtype3   54  147
  subtype4   20   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       30       54       20
  MALE         69       87      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  67  11
  subtype2  78   7
  subtype3 154  21
  subtype4  59   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   11
  subtype2   78    7
  subtype3  154   21
  subtype4   59    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        67       78      154       59
  YES       11        7       21        5
[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                                                          84
  subtype2                                                         108
  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)       84      108
                                                             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   3
  subtype2  97   2   0   5
  subtype3 158   4   1   5
  subtype4  51   1   1   7
D10V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       72       97      158       51
  R1        4        2        4        1
  R2        1        0        1        1
  RX        3        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    82
  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       82      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  66
  subtype3   3 129
  subtype4   2  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    1   66
  subtype3    3  129
  subtype4    2   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        3        2
  NOT HISPANIC OR LATINO       58       66      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 50 36
  subtype2 72 56
  subtype3 72 41
subtype1 subtype2 subtype3 
      86      128      113 
subtype1 subtype2 subtype3 
      36       56       41 
$subtype1
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-5478 TCGA-22-A5C4 
       31.63        41.69        33.93        32.19         0.79        22.06 
TCGA-33-AASB TCGA-33-AASI TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 
        6.94        44.19        74.66         9.07        60.30        44.75 
TCGA-34-5928 TCGA-39-5019 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 
       39.32       111.35        24.89         5.46         3.81        13.38 
TCGA-43-A56V TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 TCGA-56-8083 TCGA-56-8201 
       12.03         0.10         1.32         0.10         4.93        13.05 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4ZJ 
        1.35         1.81         1.18        10.36        20.25        21.04 
TCGA-60-2697 TCGA-60-2709 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS 
       12.23        49.48        70.62        14.99        11.34        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
       16.37        36.16        53.88         6.94        13.35        14.07 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       70.13       106.95        86.76        37.81        82.92        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5GB 
       39.09        17.72       104.09        27.39         6.97        30.81 
TCGA-85-6175 TCGA-85-7950 TCGA-85-8049 TCGA-85-8276 TCGA-85-8481 TCGA-85-8582 
        9.67        18.94        19.04        34.52         7.76        38.14 
TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
       12.59        30.97        19.86        30.48        27.16        14.96 
TCGA-90-7964 TCGA-92-7340 TCGA-94-A4VJ TCGA-96-8170 TCGA-98-7454 TCGA-98-8020 
       14.07         2.70        14.14        17.46        21.44         2.76 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       21.34         5.69         2.01        27.02        21.21        20.32 
TCGA-LA-A7SW TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A7XE 
       13.41         4.21        25.32        26.43         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52V 
       33.07        43.89 

$subtype2
TCGA-21-5783 TCGA-22-4605 TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 TCGA-22-5483 
       88.11        32.02         9.57        14.63        86.30        18.84 
TCGA-22-5489 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASD 
       62.86        54.44        19.76        63.35        36.62       110.99 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       65.23        81.24         4.96         1.12        38.79         4.04 
TCGA-34-8456 TCGA-37-3783 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 
       26.43         4.01        55.20        82.52       102.18        17.06 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       27.91        12.36        21.47        19.59         7.76        78.18 
TCGA-43-8116 TCGA-43-8118 TCGA-46-6025 TCGA-46-6026 TCGA-51-6867 TCGA-52-7622 
       11.77         2.93        10.65        13.91        61.02        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 
        5.46        30.35         8.75        27.45         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 
        0.99         0.43         0.85         6.51        17.49         3.48 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8623 TCGA-56-8626 
        3.45        17.00        14.07        16.77        22.75         9.93 
TCGA-56-8629 TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       15.81         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-60-2703 TCGA-60-2704 TCGA-68-7755 TCGA-68-7756 
       16.47        34.78        96.82        37.94         2.73         6.64 
TCGA-68-8250 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 
        8.02        29.56        73.12        75.09        11.18        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        0.49        73.22         0.16        46.78        15.75         6.51 
TCGA-77-8009 TCGA-77-8133 TCGA-77-8143 TCGA-77-8146 TCGA-77-8156 TCGA-85-6560 
       55.73        53.92        26.40       104.84        36.36        11.97 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       12.99        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 
        1.15        29.95        25.15        24.13        30.64         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A513 
        2.01        15.39        36.59        22.59        24.36        29.92 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 
       24.92         9.50         2.93        11.77         3.48         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        18.38         4.01         5.03 
TCGA-94-8491 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-8021 
       26.63        71.01        57.07        18.31        27.68        30.81 
TCGA-98-8022 TCGA-XC-AA0X 
       30.67         0.20 

$subtype3
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       60.66        64.93        63.55        44.25        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-A4WN TCGA-33-A5GW 
       11.74        30.12        56.32        16.64         4.70         0.30 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-A5IX TCGA-37-5819 TCGA-37-A5EM TCGA-37-A5EN 
      118.36        27.16        33.90         3.39        28.50        21.70 
TCGA-43-5668 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-56-5898 TCGA-56-7223 
       18.38        11.61         9.73        14.20        18.25         0.99 
TCGA-56-7579 TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-A49D TCGA-56-A4BW 
       31.27        33.24        14.96        26.89        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-A46J 
       13.32        17.85        18.74         0.13        14.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-63-A5MB TCGA-63-A5MH 
       34.36        56.65        35.24        29.92       102.67        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU 
       58.65        59.97        45.57        25.28        89.29        25.41 
TCGA-63-A5MY TCGA-68-A59J TCGA-77-6845 TCGA-77-7139 TCGA-77-8140 TCGA-77-8148 
       34.59        13.45        23.28       140.09        11.54        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        60.53       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH 
       22.29         5.92        61.94        42.08        27.62        38.86 
TCGA-85-6798 TCGA-85-8070 TCGA-85-8071 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN 
        6.41        31.56        26.79        18.08        30.28        34.13 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED 
       19.73        16.21        15.85        12.39         3.65        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK 
       22.62        10.59         4.01        16.14        17.69        19.36 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       27.16        18.15        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       16.11        13.18        11.84         0.07        76.80         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM 
       64.54         1.22        57.30        13.74         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT 
       49.28        43.92        14.73        40.90        83.57        65.49 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
       16.80         3.72        12.72         8.58        11.18 

subtype1 subtype2 subtype3 
    0.10     0.03     0.07 
subtype1 subtype2 subtype3 
  111.35   110.99   150.25 
subtype1 subtype2 subtype3 
   19.45    18.61    22.62 
[1] "0.1 - 111.3 (19.4)" "0.0 - 111.0 (18.6)" "0.1 - 150.2 (22.6)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       13       27        1        11        22         0
  subtype2       1       34       37        1        21        20         0
  subtype3       1       17       26        1        24        23         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         10          3        1
  subtype2         13          0        2
  subtype3         17          3        0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         13       34       17
  STAGE IB         27       37       26
  STAGE II          1        1        1
  STAGE IIA        11       21       24
  STAGE IIB        22       20       23
  STAGE III         0        0        3
  STAGE IIIA       10       13       17
  STAGE IIIB        3        0        3
  STAGE IV          1        2        0
[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 15 50 20  4
  subtype2 43 71 14  3
  subtype3 22 67 22  4
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       15       43       22
  T2       50       71       67
  T3       20       14       22
  T4        4        3        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 60 21  6
  subtype2 89 30  8
  subtype3 66 37 12
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       60       89       66
  N1       21       30       37
  N2        6        8       12
[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"
D11V6, binary
          cls
clus        0  1
  subtype1 67  1
  subtype2 97  2
  subtype3 88  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    1
  subtype2   97    2
  subtype3   88    0
   clus
vv  subtype1 subtype2 subtype3
  0       67       97       88
  1        1        2        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1 27 62
  subtype2 32 99
  subtype3 25 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   62
  subtype2   32   99
  subtype3   25   90
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       32       25
  MALE         62       99       90
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus         0   1
  subtype1  74   6
  subtype2 102  12
  subtype3  91  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74    6
  subtype2  102   12
  subtype3   91   16
     clus
vv    subtype1 subtype2 subtype3
  NO        74      102       91
  YES        6       12       16
[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"
D11V9, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     7
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      1
  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                                                          87
  subtype2                                                         126
  subtype3                                                         106
D11V10, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       87      126
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      106
[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"
D11V11, continuous
D11V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 62  3  0  7
  subtype2 97  3  1  5
  subtype3 90  3  1  5
D11V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       62       97       90
  R1        3        3        3
  R2        0        1        1
  RX        7        5        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     2                         9    58
  subtype2     2                         9   109
  subtype3     2                         5    83
D11V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        2
  BLACK OR AFRICAN AMERICAN        9        9        5
  WHITE                           58      109       83
[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"
D11V15, binary
          cls
clus        0  1
  subtype1  1 59
  subtype2  3 96
  subtype3  0 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   59
  subtype2    3   96
  subtype3    0   68
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       59       96       68
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 26 13
  subtype2 87 62
  subtype3 81 58
subtype1 subtype2 subtype3 
      39      149      139 
subtype1 subtype2 subtype3 
      13       62       58 
$subtype1
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-5478 TCGA-22-A5C4 TCGA-34-5927 
       31.63        33.93        32.19         0.79        22.06        44.75 
TCGA-43-A56V TCGA-56-7223 TCGA-56-8083 TCGA-56-8503 TCGA-56-8625 TCGA-56-8628 
       12.03         0.99         4.93         1.35        10.36        20.25 
TCGA-56-A49D TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-68-7757 
       20.94        78.28        16.37        36.16        53.88         6.94 
TCGA-68-A59I TCGA-77-8008 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
       14.07        86.76        39.09        17.72       104.09        27.39 
TCGA-77-8145 TCGA-77-A5G6 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4JB TCGA-94-A4VJ 
        6.97        22.29         7.76        38.14        30.97        14.14 
TCGA-98-8020 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CX 
        2.76        13.41         0.07         1.22        26.43         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52V 
       16.80         0.43        43.89 

$subtype2
TCGA-21-5783 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 
       88.11        60.66        63.55        14.63        44.25        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       79.20        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
       54.44        19.76         4.70         0.30        36.62       110.99 
TCGA-33-AASL TCGA-34-5231 TCGA-34-8456 TCGA-37-5819 TCGA-37-A5EM TCGA-37-A5EN 
       27.16        65.23        26.43         3.39        28.50        21.70 
TCGA-39-5027 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7658 TCGA-43-8115 
      102.18        18.38        27.91        12.36        78.18        13.38 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-46-6026 TCGA-51-6867 TCGA-52-7809 
       11.77        11.61         9.73        13.91        61.02         5.46 
TCGA-52-7810 TCGA-56-5898 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       30.35        18.25         0.43        31.27         0.85         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8629 
       33.24        14.96         3.48        26.89        17.00        15.81 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       13.32        18.74         0.13        14.47        13.25        13.55 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       71.24        16.47        34.36        56.65        35.24        29.92 
TCGA-60-2703 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       96.82       102.67        66.61        58.65        59.97        45.57 
TCGA-63-A5MP TCGA-63-A5MU TCGA-63-A5MY TCGA-68-7755 TCGA-68-A59J TCGA-77-6842 
       25.28        25.41        34.59         2.73        13.45        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       73.12        75.09        23.28       140.09        20.78         0.49 
TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8140 TCGA-77-8143 
       73.22        46.78        15.75        55.73        11.54        26.40 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 
       66.51        54.41        65.49        36.36       150.25         5.92 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-8052 
       42.08        27.62         6.41        32.91         1.15        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
       31.56        26.79        30.64         5.29        32.71        15.39 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR 
       36.59        18.08        22.59        30.28        34.13        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       16.21        15.85        14.96         3.65         2.93        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7943 TCGA-94-8035 
       22.62        10.59         4.01         2.30        18.38         4.01 
TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A53A 
        5.03        16.14        17.69        19.36        27.16        18.15 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
        2.01        18.58        20.71        19.10        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL 
       11.84        76.80         4.54        64.54        57.30         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
       39.85        49.28        43.92        25.32        14.73        40.90 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
       83.57        65.49        12.72         8.58        11.18 

$subtype3
TCGA-21-5784 TCGA-22-4605 TCGA-22-4609 TCGA-22-5472 TCGA-22-5479 TCGA-22-5483 
       41.69        32.02         9.57        64.93        86.30        18.84 
TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-5232 TCGA-34-5234 
       63.35         6.94        44.19       118.36        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
        9.07        60.30        39.32         4.96         1.12        38.79 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
        4.04        33.90         4.01       111.35        55.20        82.52 
TCGA-39-5040 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       17.06        24.89        21.47         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A56U TCGA-46-6025 TCGA-52-7622 TCGA-52-7811 
        7.76         2.93        14.20        10.65        28.34         8.75 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7580 
       27.45         0.10         2.04         0.62         0.99         1.32 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8201 TCGA-56-8305 TCGA-56-8309 TCGA-56-8504 
        0.10        17.49        13.05         3.45        14.07        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BY 
        1.81        22.75         1.18         9.93        19.23        17.85 
TCGA-56-A4ZJ TCGA-58-8386 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 
       21.04         0.03        29.95        34.78        85.12        12.23 
TCGA-60-2704 TCGA-60-2709 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       37.94        49.48        70.62        14.99        11.34        89.29 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 
        6.64         8.02        13.35        11.18        70.13       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        0.16         6.51        37.81        82.92        12.59        53.92 
TCGA-77-8146 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GB 
      104.84        60.53       126.18       132.36        61.94        30.81 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
       38.86         9.67        11.97        12.99        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       31.30         1.38        29.95        18.94        25.15        19.04 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       34.52         0.76        13.22        22.45        16.77         3.09 
TCGA-85-8355 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
        2.01        12.59        19.86        24.36        30.48        27.16 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
       29.92        12.39        24.92         9.50        14.07        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8491 
        2.70         3.48         5.26        21.04         0.16        26.63 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       71.01        57.07        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D 
       30.81        30.67        21.34         5.69        27.02        21.21 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-O2-A52N TCGA-O2-A52Q 
       20.32        12.89        13.74         4.21        33.07         3.72 
TCGA-XC-AA0X 
        0.20 

subtype1 subtype2 subtype3 
    0.07     0.13     0.03 
subtype1 subtype2 subtype3 
  104.09   150.25   132.36 
subtype1 subtype2 subtype3 
   17.72    22.62    19.23 
[1] "0.1 - 104.1 (17.7)" "0.1 - 150.2 (22.6)" "0.0 - 132.4 (19.2)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        7        9        1         4         7         0
  subtype2       2       24       36        1        31        32         2
  subtype3       1       33       45        1        21        26         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          2        0
  subtype2         19          2        1
  subtype3         12          2        2
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        2        1
  STAGE IA          7       24       33
  STAGE IB          9       36       45
  STAGE II          1        1        1
  STAGE IIA         4       31       21
  STAGE IIB         7       32       26
  STAGE III         0        2        1
  STAGE IIIA        9       19       12
  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 18 12  2
  subtype2 32 92 23  4
  subtype3 41 78 21  5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7       32       41
  T2       18       92       78
  T3       12       23       21
  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 26  8  5
  subtype2 90 47 13
  subtype3 99 33  8
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       26       90       99
  N1        8       47       33
  N2        5       13        8
[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  30   0
  subtype2 117   1
  subtype3 105   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2  117    1
  subtype3  105    2
   clus
vv  subtype1 subtype2 subtype3
  0       30      117      105
  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   9  30
  subtype2  36 115
  subtype3  39 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   30
  subtype2   36  115
  subtype3   39  106
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       36       39
  MALE         30      115      106
[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  31   5
  subtype2 115  21
  subtype3 121   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    5
  subtype2  115   21
  subtype3  121    8
     clus
vv    subtype1 subtype2 subtype3
  NO        31      115      121
  YES        5       21        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                                                          36
  subtype2                                                         140
  subtype3                                                         143
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)       36      140
                                                             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)      143
[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  28   1   0   1
  subtype2 118   5   2   6
  subtype3 103   3   0  10
D12V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       28      118      103
  R1        1        5        3
  R2        0        2        0
  RX        1        6       10
[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    21
  subtype2     1                         6   123
  subtype3     5                        11   106
D12V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        5
  BLACK OR AFRICAN AMERICAN        6        6       11
  WHITE                           21      123      106
[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  22
  subtype2   0  98
  subtype3   4 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   22
  subtype2    0   98
  subtype3    4  103
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        4
  NOT HISPANIC OR LATINO       22       98      103
[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"
