[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/15084586/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/15114194/LUSC-TP.mergedcluster.txt"

nPatients in clinical file=495, in cluster file=504, common to both=495
[1]  12 495
[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 
181 162 150 
  1   2   3 
181 162 150 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
152 120  89 
  1   2   3 
152 120  89 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
60 73 62 
 1  2  3 
60 73 62 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
54 41 52 48 
 1  2  3  4 
54 41 52 48 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
111 150 151  80 
  1   2   3   4 
111 150 151  80 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
178 185 129 
  1   2   3 
178 185 129 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
121 130 122  61  35 
  1   2   3   4   5 
121 130 122  61  35 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 88 115 196  70 
  1   2   3   4 
 88 115 196  70 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 87 130 111 
  1   2   3 
 87 130 111 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 38 147 143 
  1   2   3 
 38 147 143 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 495 columns.

[1] "Batch" "23"   
[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=189,	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=325,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=106,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=36,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 495 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
113 290  69  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
113 290  69  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
113 290  69  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
113 290  69  23 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
314 131  39   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
314 131  39   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
314 131  39   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
314 131  39   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=106, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, 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 28 22
  subtype3 13 17
  subtype4 14 13
subtype1 subtype2 subtype3 subtype4 
      41       50       30       27 
subtype1 subtype2 subtype3 subtype4 
      17       22       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         1.64        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 
        3.95         0.43        24.33        33.11        28.96        21.93 
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 
        7.46        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         7.63        98.01 
TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 
        2.63        28.96        12.00        74.07        68.58        35.64 
TCGA-39-5037 TCGA-43-3394 TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       35.70        27.02         9.99         0.39         0.39        29.95 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-66-2727 
       66.54        41.42        56.91        29.85        35.90        16.96 
TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 
        2.01        21.01        25.05         1.02        23.01         3.02 
TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        2.01        24.95        40.01         5.03        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 
        4.01        49.05 

$subtype3
TCGA-18-3409 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       79.46        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       174.08        31.50        32.88 
TCGA-37-3792 TCGA-39-5030 TCGA-43-2576 TCGA-43-2581 TCGA-60-2696 TCGA-60-2698 
        0.39         1.94        40.21        38.66         3.58        10.22 
TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2725 TCGA-66-2744 
       92.71         9.01        50.33        35.34        26.83         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2767 TCGA-66-2769 TCGA-66-2785 TCGA-66-2786 
        1.02         0.92         2.01         7.07         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         6.58         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        47.80        36.39        15.58 
TCGA-43-2578 TCGA-60-2695 TCGA-60-2716 TCGA-60-2726 TCGA-66-2754 TCGA-66-2756 
       22.49        21.11        48.49        11.77         2.01         0.99 
TCGA-66-2757 TCGA-66-2790 TCGA-66-2793 
       43.99        22.98        10.06 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.39     0.39     0.39 
subtype1 subtype2 subtype3 subtype4 
  122.43   117.57   174.08   133.74 
subtype1 subtype2 subtype3 subtype4 
   21.07    29.90    23.98    15.58 
[1] "0.4 - 122.4 (21.1)" "0.4 - 117.6 (29.9)" "0.4 - 174.1 (24.0)"
[4] "0.4 - 133.7 (15.6)"
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        8       11         2         4          4          2        0
  subtype4        8        5         1         5          3          4        2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          2        2        8        8
  STAGE IB         21       24       11        5
  STAGE IIA         0        4        2        1
  STAGE IIB         9        9        4        5
  STAGE IIIA        6        6        4        3
  STAGE IIIB        2        7        2        4
  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, 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
D1V9, 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"
D1V10, binary
          cls
clus        0  1
  subtype1  1 41
  subtype2  0 52
  subtype3  1 31
  subtype4  0 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2    0   52
  subtype3    1   31
  subtype4    0   28
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        1        0
  YES       41       52       31       28
[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"
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    27
  subtype3     1                         1    21
  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       27       21       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 20
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   23
  subtype2    1   26
  subtype3    0   20
  subtype4    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        0        0
  NOT HISPANIC OR LATINO       23       26       20       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 30 24
  subtype3 25 23
subtype1 subtype2 subtype3 
      46       54       48 
subtype1 subtype2 subtype3 
      22       24       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         1.64        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         3.95         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        21.93        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 
        7.46        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 
        7.63        98.01         2.63        28.96        12.00         7.82 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-46-3768 
       74.07        68.58        35.64        35.70        27.02         9.99 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
        0.39         0.39        29.95        66.54        41.42        56.91 
TCGA-60-2722 TCGA-60-2723 TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 
       29.85        35.90        16.96         2.01        21.01        25.05 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 
        1.02         2.01        23.01         3.02         2.01        24.95 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       40.01         5.03        30.02        54.08         4.01        49.05 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-21-1083 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
       79.46         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 
      174.08        31.50        32.88        31.27         0.39         6.58 
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        47.80         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-60-2695 
       36.39        15.58        40.21        22.49        38.66        21.11 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2720 
       10.22        92.71         9.01        50.33        35.34         3.19 
TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       26.83         0.99         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
       43.99         7.07         1.97        25.97         4.04        22.98 

subtype1 subtype2 subtype3 
    0.43     0.39     0.39 
subtype1 subtype2 subtype3 
  122.43   117.57   174.08 
subtype1 subtype2 subtype3 
  20.775   27.990   21.550 
[1] "0.4 - 122.4 (20.8)" "0.4 - 117.6 (28.0)" "0.4 - 174.1 (21.5)"
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          6          9        0
  subtype3       14       16         1         8          6          4        1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          4        2       14
  STAGE IB         20       25       16
  STAGE IIA         2        4        1
  STAGE IIB         9       10        8
  STAGE IIIA        7        6        6
  STAGE IIIB        2        9        4
  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, 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
D2V9, 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"
D2V10, binary
          cls
clus        0  1
  subtype1  1 46
  subtype2  0 56
  subtype3  1 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    0   56
  subtype3    1   50
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        1
  YES       46       56       50
[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"
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    30
  subtype3     1                         2    34
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        1
  BLACK OR AFRICAN AMERICAN        2        3        2
  WHITE                           27       30       34
[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 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   25
  subtype2    1   29
  subtype3    0   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        0
  NOT HISPANIC OR LATINO       25       29       34
[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 95 80
  subtype2 96 61
  subtype3 90 55
subtype1 subtype2 subtype3 
     175      157      145 
subtype1 subtype2 subtype3 
      80       61       55 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       12.20         7.46        79.46         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        54.28        71.34 
TCGA-22-5481 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.20       174.08       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        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
        9.07        23.24        16.93        27.19        20.91         3.95 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        0.39         6.58         7.46        47.80        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
       70.03         1.71         1.94        36.39        15.58        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-52-7622 
        3.81        13.38         2.93         9.73        14.20        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7731 
        8.75        27.45         0.10         0.62         0.99         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8623 
        3.48        26.89        14.07         1.35        16.77        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A4ZJ TCGA-56-A5DS TCGA-56-A62T 
        1.18        10.36         9.93        21.04         0.26         2.76 
TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 
       13.25        34.78        85.12         3.58        12.23        37.94 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       21.93        49.48         9.01        50.33        35.34        48.49 
TCGA-60-2720 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
        3.19        26.83        70.62        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2734 TCGA-66-2737 TCGA-66-2755 
       89.29        78.28        16.37        43.10         2.01         0.92 
TCGA-66-2765 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00         3.02        19.00        12.00        24.95 
TCGA-66-2788 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-7138 
       22.98         6.64         6.94        13.35        16.18        11.18 
TCGA-77-7335 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       70.13         6.51        86.76        12.59        39.09        17.72 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
      104.09        27.39         6.97       126.18       132.36         5.92 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7844 
       30.81        38.86         9.67        12.99        34.95        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 
       18.94        25.15        19.04         3.09         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA 
       14.63        13.94        12.59        15.62        14.96        24.36 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED 
       12.56        16.21        14.96         0.79        24.92        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-96-8169 
       10.59         2.70         5.26         2.30         4.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D 
       17.46        16.57         8.42        21.34        27.02        21.21 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NK-A5CX TCGA-O2-A52V 
       20.32        12.89        64.08        13.74         3.65        43.89 
TCGA-XC-AA0X 
        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        31.73        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         7.63       133.74        98.01 
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        12.00        30.94 
TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        1.12        26.43         7.82         3.39        74.07        44.75 
TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 TCGA-43-6770 
       60.79        35.64        35.70        27.02        12.36        21.47 
TCGA-43-7657 TCGA-43-7658 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        7.76        66.51         9.99        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
        0.39        29.95         5.46         0.99         0.85         6.51 
TCGA-56-8308 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8392 
       17.00        13.32        17.85        18.74        71.24        16.47 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2710 
       34.36        56.65        35.24        29.92        10.22        66.54 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML 
       41.42        56.91        29.85       102.67        59.97        45.57 
TCGA-66-2742 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 
       21.07        21.01         1.02         2.01        23.01         2.01 
TCGA-66-2781 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        3.98        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        14.73        73.12        23.28        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 
       20.78         0.49        42.28         0.16        15.75        53.95 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       37.81        53.92         9.63        54.41        65.49         0.33 
TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
      117.57        42.41        42.08        27.62         6.41        36.53 
TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 
       31.30        24.13        31.56        16.87        10.09        32.71 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 
        0.10        25.68        19.33        12.39         3.65        11.77 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8063 TCGA-94-7943 TCGA-94-8490 TCGA-94-A5I4 
       22.62         3.48         4.01        11.70         5.03        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       17.69        57.07        19.36        18.58        20.71        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HN 
       16.11        13.18        13.41        11.84         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52S 
       30.58        24.00        14.73        29.75         0.43        12.72 
TCGA-O2-A5IB 
       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         1.64        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        27.02       110.99 
TCGA-33-AASI TCGA-34-2609 TCGA-34-5928 TCGA-34-5929 TCGA-34-8455 TCGA-37-3789 
       44.19        31.27        18.15         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        27.39        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-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
       30.35        28.96        18.25         2.04         0.43         1.45 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.32        17.49         1.81        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 
       19.23         0.13         0.03        13.55        29.95        21.11 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 
       96.82        92.71        80.45        42.64        32.32        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MU TCGA-63-A5MV 
       23.57        11.77        66.61        58.65        25.41        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       53.88        34.59        16.96         0.99         1.02         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2768 TCGA-66-2769 
        0.99        43.99        25.05         0.99         2.01         7.07 
TCGA-66-2780 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
       12.03         1.97        25.97         4.04        22.98        10.06 
TCGA-68-8250 TCGA-77-6842 TCGA-77-6844 TCGA-77-7337 TCGA-77-7463 TCGA-77-8130 
        8.02        29.56        75.09       106.95        46.78        82.92 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8154 TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7699 
       11.54        26.40        35.90        22.29        11.97        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
        1.38         1.15        14.07        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-A4JB TCGA-85-A4QQ 
       22.45        16.77         5.29         0.72        17.72        18.18 
TCGA-85-A4QR TCGA-85-A510 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-94-7033 
       19.73        15.85         9.50         2.93        14.07        21.04 
TCGA-94-7557 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8020 TCGA-98-8021 
        0.16        26.63        14.14        49.87         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-NC-A5HD 
       30.67        27.16         3.88        18.15         2.01         0.07 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM 
        4.54        51.78         1.22        45.37         4.21        39.85 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       22.78        83.57        65.49        16.80        33.07         3.72 
TCGA-O2-A52W 
        8.58 

subtype1 subtype2 subtype3 
    0.10     0.10     0.03 
subtype1 subtype2 subtype3 
  174.08   133.74   122.43 
subtype1 subtype2 subtype3 
   16.93    23.01    19.59 
[1] "0.1 - 174.1 (16.9)" "0.1 - 133.7 (23.0)" "0.0 - 122.4 (19.6)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       34       63        1        21        36         0
  subtype2       0       22       48        1        26        29         2
  subtype3       2       31       40        0        16        27         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         17          6        1
  subtype2         22          9        3
  subtype3         23          6        3
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        2
  STAGE IA         34       22       31
  STAGE IB         63       48       40
  STAGE II          1        1        0
  STAGE IIA        21       26       16
  STAGE IIB        36       29       27
  STAGE III         0        2        1
  STAGE IIIA       17       22       23
  STAGE IIIB        6        9        6
  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  30   6
  subtype2  31 100  23   8
  subtype3  39  86  16   9
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       41       31       39
  T2      104      100       86
  T3       30       23       16
  T4        6        8        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 128  37  10   2
  subtype2  88  56  15   2
  subtype3  96  38  14   1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      128       88       96
  N1       37       56       38
  N2       10       15       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 132   3
  subtype3 125   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  147    1
  subtype2  132    3
  subtype3  125    3
   clus
vv  subtype1 subtype2 subtype3
  0      147      132      125
  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  63 118
  subtype2  33 129
  subtype3  31 119
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  118
  subtype2   33  129
  subtype3   31  119
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       63       33       31
  MALE        118      129      119
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     9
  subtype3                                     5
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
          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                                                         175
  subtype2                                                         152
  subtype3                                                         143
D3V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             4        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      175      152
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      143
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus         0   1
  subtype1   5 176
  subtype2   6 156
  subtype3   2 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  176
  subtype2    6  156
  subtype3    2  148
     clus
vv    subtype1 subtype2 subtype3
  NO         5        6        2
  YES      176      156      148
[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"
D3V11, continuous
D3V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 140   5   2  11
  subtype2 130   5   2   9
  subtype3 124   2   0   2
D3V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      140      130      124
  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   126
  subtype2     2                        11   113
  subtype3     1                        12   101
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        2        1
  BLACK OR AFRICAN AMERICAN        8       11       12
  WHITE                          126      113      101
[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   6 120
  subtype2   1  96
  subtype3   1  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  120
  subtype2    1   96
  subtype3    1   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        1        1
  NOT HISPANIC OR LATINO      120       96       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(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2       0  1
  subtype1 84 64
  subtype2 71 45
  subtype3 54 31
subtype1 subtype2 subtype3 
     148      116       85 
subtype1 subtype2 subtype3 
      64       45       31 
$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       174.08         1.55        19.76        27.02 
TCGA-33-AASB TCGA-33-AASI TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
        6.94        44.19        67.79        56.38         9.07        16.93 
TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-39-5011 TCGA-39-5022 
       18.15        27.19         4.04        20.91        47.80        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 
       70.03         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        66.51 
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-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 
        1.32         0.10        26.89        14.07         1.35        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ 
        1.18        10.36         9.93        20.25        20.94        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8393 
        0.13         0.26         0.03        13.25        13.55        34.78 
TCGA-58-A46J TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-63-A5MG 
       85.12        12.23        96.82        37.94        49.48        70.62 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        89.29        78.28        16.37        36.16 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-7138 
        6.64         6.94        13.35        16.18        29.56        11.18 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 
        6.51        86.76        12.59        39.09        17.72         6.97 
TCGA-77-8146 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH 
       71.77         0.33       126.18       132.36        30.81        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        9.67        11.97        34.95        18.94        25.15        19.04 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
        0.76        22.45         2.01         7.76        13.94        12.59 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       15.62        17.72        14.96        24.36        12.56        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 
       15.85        14.96         0.79        12.39        24.92         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
       20.22        22.62        10.59         2.70         4.01         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8491 TCGA-96-8169 
       21.04         0.16        11.70         4.01        26.63        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
       17.46        16.57         8.42        30.67        21.34         3.88 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW 
        2.01        27.02        21.21        20.32        12.89        13.41 
TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       64.08        13.74         4.21        65.49         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       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        31.73        63.55        14.63        44.25        54.28 
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-39-5016 TCGA-39-5019 
       27.16        12.00         1.12        26.43        74.07        44.75 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-6770 
       68.58        60.79        27.39        35.64        35.70        21.47 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-46-6025 TCGA-51-6867 
        7.76        13.38         2.93         9.73        10.65        61.02 
TCGA-52-7622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       28.34        18.25         0.99         1.45         0.85         6.51 
TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 
       15.81        17.85        18.74         2.76        71.24        16.47 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-63-A5MB TCGA-63-A5MJ 
       34.36        56.65        35.24        29.92       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 
       45.57        25.28         2.73        14.73        73.12        23.28 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 TCGA-77-8133 
        0.49        42.28        70.13         0.16        53.95        53.92 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
       54.41        65.49       117.57        42.41        42.08        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8052 
       12.99         6.41        36.53        31.30        29.95        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 
       31.56        16.87        34.52        10.09         3.09        32.71 
TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 
       14.63        25.68        19.33         3.65        11.77         3.48 
TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK 
        5.26         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-A5HD TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR 
       11.84         0.07         2.89        30.58        24.00        29.75 
TCGA-NK-A5D1 TCGA-O2-A52S 
       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        23.24        30.94 
TCGA-34-5929 TCGA-37-5819 TCGA-39-5029 TCGA-39-5035 TCGA-43-5670 TCGA-43-6143 
        4.96         3.39        24.33        15.58        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-56-8304 TCGA-56-8308 TCGA-56-8504 
        0.99         0.43        17.49         3.48        17.00        16.77 
TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX TCGA-58-8390 TCGA-63-A5MH TCGA-63-A5MI 
        1.81        19.23        13.32        29.95        66.61        58.65 
TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-68-8250 TCGA-77-6844 TCGA-77-7139 
       25.41        53.88        34.59         8.02        75.09        89.98 
TCGA-77-7140 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 TCGA-77-8130 
       20.78       106.95        46.78        15.75        37.81        82.92 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 
      104.09        11.54        26.40        27.39         9.63        35.90 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 
       22.29         5.92        32.91         1.38         1.15        14.07 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QQ 
       13.22        16.77         5.29         0.72         0.10        18.18 
TCGA-85-A4QR TCGA-90-7766 TCGA-90-7964 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8020 
       19.73         9.50        14.07        14.14        49.87         2.76 
TCGA-98-8021 TCGA-98-A538 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       30.81        27.16         4.54        51.78         1.22        45.37 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52W 
       39.85        37.22        14.73        22.78        83.57         8.58 
TCGA-O2-A5IB 
       11.18 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  174.08   154.32   106.95 
subtype1 subtype2 subtype3 
  16.470   24.705   19.230 
[1] "0.0 - 174.1 (16.5)" "0.1 - 154.3 (24.7)" "0.1 - 107.0 (19.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       31       37        1        22        36         1
  subtype2       1       22       39        1        23        18         1
  subtype3       1       19       20        0        13        15         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         17          3        3
  subtype2         13          1        1
  subtype3         16          2        0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         31       22       19
  STAGE IB         37       39       20
  STAGE II          1        1        0
  STAGE IIA        22       23       13
  STAGE IIB        36       18       15
  STAGE III         1        1        1
  STAGE IIIA       17       13       16
  STAGE IIIB        3        1        2
  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 29  6
  subtype2 31 67 19  3
  subtype3 22 54 10  3
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       36       31       22
  T2       81       67       54
  T3       29       19       10
  T4        6        3        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 97 39 11
  subtype2 79 34  6
  subtype3 54 24 11
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       97       79       54
  N1       39       34       24
  N2       11        6       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  96   1
  subtype3  73   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110    3
  subtype2   96    1
  subtype3   73    0
   clus
vv  subtype1 subtype2 subtype3
  0      110       96       73
  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  45 107
  subtype2  29  91
  subtype3  19  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45  107
  subtype2   29   91
  subtype3   19   70
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       29       19
  MALE        107       91       70
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     4
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          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                                                         147
  subtype2                                                         112
  subtype3                                                          83
D4V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      147      112
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       83
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus         0   1
  subtype1   5 147
  subtype2   2 118
  subtype3   4  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  147
  subtype2    2  118
  subtype3    4   85
     clus
vv    subtype1 subtype2 subtype3
  NO         5        2        4
  YES      147      118       85
[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"
D4V11, continuous
D4V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   3   0   9
  subtype2  97   5   1   6
  subtype3  68   1   1   2
D4V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      109       97       68
  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   109
  subtype2     1                         7    96
  subtype3     0                         6    61
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        1        0
  BLACK OR AFRICAN AMERICAN       11        7        6
  WHITE                          109       96       61
[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   4 104
  subtype2   1  78
  subtype3   1  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  104
  subtype2    1   78
  subtype3    1   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        1
  NOT HISPANIC OR LATINO      104       78       49
[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 38 19
  subtype2 36 33
  subtype3 29 30
subtype1 subtype2 subtype3 
      57       69       59 
subtype1 subtype2 subtype3 
      19       33       30 
$subtype1
TCGA-18-4721 TCGA-21-1072 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-22-5483 
      154.32        99.16        60.89       122.43        43.23        18.84 
TCGA-22-5489 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       62.86         7.63       174.08       103.53        14.07        27.02 
TCGA-34-2605 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-37-4133 
       28.96        65.23        23.24        30.94         4.96         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5034 
        6.81         0.39         3.39        74.07        55.20        36.39 
TCGA-39-5040 TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 
       17.06        22.49        12.36         5.46        19.59        66.51 
TCGA-46-6026 TCGA-52-7810 TCGA-52-7812 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 
       13.91        30.35        27.45        80.45        49.48        41.42 
TCGA-60-2714 TCGA-60-2716 TCGA-66-2727 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 
       50.33        48.49        16.96        21.01         1.02         2.01 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-77-6842 
       24.95         1.97        22.98        54.08         4.01        29.56 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7465 TCGA-85-7698 TCGA-85-7699 
       73.12        89.98         0.49        15.75        31.30        32.91 
TCGA-85-7950 TCGA-90-7767 TCGA-96-7544 
       18.94         2.93        49.87 

$subtype2
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1081 
       49.94        27.19       119.54        46.88        70.16         9.34 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-4607 TCGA-22-5471 
       41.69        33.93        10.82        21.99        19.30        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5492 
       64.93        63.55        44.25        54.28        71.34        16.64 
TCGA-33-4547 TCGA-33-4589 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       79.53         1.55        31.27        67.79        56.38         9.07 
TCGA-34-5241 TCGA-34-5928 TCGA-37-3789 TCGA-37-3792 TCGA-39-5011 TCGA-39-5019 
       16.93        18.15         0.43         0.39        47.80        44.75 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 
       68.58        70.03        60.79         1.71        24.33        15.58 
TCGA-39-5037 TCGA-43-5670 TCGA-43-6770 TCGA-46-6025 TCGA-52-7811 TCGA-56-6545 
       35.70        27.91        21.47        10.65         8.75         2.04 
TCGA-56-6546 TCGA-56-7222 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
        0.62         0.43         3.58        12.23        10.22        96.82 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-66-2768 TCGA-66-2769 
        3.19        32.32        23.57        11.77         2.01         7.07 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-77-6845 
       19.00         3.98        12.00        22.98         5.03        23.28 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 
      106.95         0.16        46.78        12.99         6.41         1.15 
TCGA-85-7844 TCGA-92-7340 TCGA-94-7033 
       29.95         2.70        21.04 

$subtype3
TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 TCGA-22-1000 TCGA-22-1011 
       15.58        31.73       119.80        31.63        14.93         1.74 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 TCGA-22-5474 TCGA-22-5478 
       20.48         0.56        32.02         9.57        14.63         0.79 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-33-6737 TCGA-34-2596 TCGA-34-2604 
       11.74        30.12        56.32        19.76         2.63        31.50 
TCGA-34-2608 TCGA-34-7107 TCGA-37-4129 TCGA-39-5030 TCGA-39-5031 TCGA-43-2581 
       32.88         1.12         6.58         1.94        27.39        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-51-6867 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 
       27.02        18.38        61.02         0.10        18.25         0.99 
TCGA-56-7730 TCGA-60-2695 TCGA-60-2704 TCGA-60-2706 TCGA-60-2710 TCGA-60-2712 
        6.51        21.11        37.94        92.71        66.54         9.01 
TCGA-60-2713 TCGA-60-2719 TCGA-60-2725 TCGA-66-2737 TCGA-66-2770 TCGA-66-2773 
       56.91        42.64        26.83         2.01        23.01         3.02 
TCGA-66-2777 TCGA-66-2800 TCGA-68-7756 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 
        2.01        49.05         6.64        75.09        42.28        70.13 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-90-6837 
        9.67        11.97        36.53        34.95         1.38        24.92 
TCGA-90-7766 TCGA-90-7769 TCGA-94-7557 TCGA-94-7943 TCGA-98-7454 
        9.50        11.77         0.16        11.70         8.42 

subtype1 subtype2 subtype3 
    0.39     0.16     0.10 
subtype1 subtype2 subtype3 
  174.08   119.54   119.80 
subtype1 subtype2 subtype3 
   27.45    21.47    18.38 
[1] "0.4 - 174.1 (27.4)" "0.2 - 119.5 (21.5)" "0.1 - 119.8 (18.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       11       16        0         7        11          7
  subtype2       0        7       28        0        10        15          9
  subtype3       1       12       25        1         5         8          7
          vv
clus       STAGE IIIB
  subtype1          8
  subtype2          3
  subtype3          2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        1
  STAGE IA         11        7       12
  STAGE IB         16       28       25
  STAGE II          0        0        1
  STAGE IIA         7       10        5
  STAGE IIB        11       15        8
  STAGE IIIA        7        9        7
  STAGE IIIB        8        3        2
[1] 8 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 35  4  6
  subtype2 11 51  9  2
  subtype3 19 33  7  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       15       11       19
  T2       35       51       33
  T3        4        9        7
  T4        6        2        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 34 17  7  2
  subtype2 44 21  5  2
  subtype3 46 11  4  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       34       44       46
  N1       17       21       11
  N2        7        5        4
  N3        2        2        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0
  subtype1 54
  subtype2 67
  subtype3 55
[1] "NOT AVAILABLE: table only has an event [0]"
D5V7, binary
          cls
clus        0  1
  subtype1 12 48
  subtype2 17 56
  subtype3 20 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   48
  subtype2   17   56
  subtype3   20   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       17       20
  MALE         48       56       42
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     0
  subtype3                                     1
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      0
  subtype3                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          56
  subtype2                                                          73
  subtype3                                                          61
D5V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       56       73
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       61
[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"
D5V10, binary
          cls
clus        0  1
  subtype1  4 56
  subtype2  3 70
  subtype3  3 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   56
  subtype2    3   70
  subtype3    3   59
     clus
vv    subtype1 subtype2 subtype3
  NO         4        3        3
  YES       56       70       59
[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"
D5V11, continuous
D5V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 43  0  2  5
  subtype2 55  4  2  4
  subtype3 51  1  0  0
D5V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       43       55       51
  R1        0        4        1
  R2        2        2        0
  RX        5        4        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    46
  subtype2     0                         6    53
  subtype3     1                         2    48
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        1
  BLACK OR AFRICAN AMERICAN        1        6        2
  WHITE                           46       53       48
[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"
D5V15, binary
          cls
clus        0  1
  subtype1  1 37
  subtype2  3 45
  subtype3  0 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   37
  subtype2    3   45
  subtype3    0   38
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       37       45       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 31 20
  subtype2 17 22
  subtype3 27 22
  subtype4 28 18
subtype1 subtype2 subtype3 subtype4 
      51       39       49       46 
subtype1 subtype2 subtype3 subtype4 
      20       22       22       18 
$subtype1
TCGA-18-4721 TCGA-18-5592 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
      154.32        49.94        60.89       122.43       119.80        43.23 
TCGA-21-5787 TCGA-22-1000 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-33-4566 
       10.82        14.93        71.34        18.84        62.86       174.08 
TCGA-33-4582 TCGA-34-2608 TCGA-34-5239 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 
      103.53        32.88        23.24         0.39         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
        0.39         3.39        74.07        70.03        24.33         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 
       36.39        15.58        38.66        12.36         5.46        19.59 
TCGA-43-7658 TCGA-52-7812 TCGA-60-2695 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 
       66.51        27.45        21.11        49.48        41.42         9.01 
TCGA-60-2714 TCGA-60-2716 TCGA-66-2773 TCGA-66-2785 TCGA-66-2794 TCGA-77-6842 
       50.33        48.49         3.02         1.97        54.08        29.56 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7465 TCGA-85-7699 
       73.12        89.98         0.49        70.13        15.75        32.91 
TCGA-85-7950 TCGA-90-7767 TCGA-96-7544 
       18.94         2.93        49.87 

$subtype2
TCGA-18-5595 TCGA-21-5784 TCGA-22-1011 TCGA-22-4596 TCGA-22-5472 TCGA-22-5473 
       27.19        41.69         1.74         0.56        64.93        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5485 TCGA-33-6737 TCGA-34-2596 
       44.25         0.79        11.74        30.12        19.76         2.63 
TCGA-34-2604 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 
       31.50        31.27        65.23        56.38        16.93        30.94 
TCGA-34-7107 TCGA-39-5027 TCGA-39-5037 TCGA-39-5040 TCGA-52-7811 TCGA-56-6546 
        1.12        60.79        35.70        17.06         8.75         0.62 
TCGA-56-7221 TCGA-60-2696 TCGA-60-2697 TCGA-60-2706 TCGA-60-2725 TCGA-66-2727 
        0.99         3.58        12.23        92.71        26.83        16.96 
TCGA-66-2737 TCGA-66-2795 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-90-6837 
        2.01         4.01        34.95         1.38        29.95        24.92 
TCGA-90-7769 TCGA-94-7033 TCGA-98-7454 
       11.77        21.04         8.42 

$subtype3
TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 TCGA-21-5782 TCGA-21-5786 TCGA-22-0940 
      119.54        46.88         9.34        31.63        33.93        21.99 
TCGA-22-4607 TCGA-22-5471 TCGA-22-5474 TCGA-22-5479 TCGA-22-5492 TCGA-33-4547 
       19.30        31.73        14.63        54.28        16.64        79.53 
TCGA-33-4589 TCGA-34-5232 TCGA-34-5236 TCGA-34-5928 TCGA-37-3789 TCGA-39-5011 
        1.55        67.79         9.07        18.15         0.43        47.80 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-43-5670 TCGA-46-6025 TCGA-56-5897 
       44.75        68.58         1.71        27.91        10.65         0.10 
TCGA-56-6545 TCGA-56-7222 TCGA-60-2698 TCGA-60-2703 TCGA-60-2720 TCGA-60-2721 
        2.04         0.43        10.22        96.82         3.19        32.32 
TCGA-60-2724 TCGA-60-2726 TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2781 
       23.57        11.77         2.01         7.07        19.00         3.98 
TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-68-7756 TCGA-77-6845 TCGA-77-7337 
       12.00        22.98         5.03         6.64        23.28       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 
        0.16        46.78        11.97        12.99         6.41         1.15 
TCGA-92-7340 
        2.70 

$subtype4
TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-22-4591 TCGA-22-4605 
       99.16        70.16        15.58        31.73        20.48        32.02 
TCGA-22-4609 TCGA-22-5491 TCGA-33-4532 TCGA-33-4586 TCGA-33-6738 TCGA-34-2605 
        9.57        56.32         7.63        14.07        27.02        28.96 
TCGA-34-5929 TCGA-37-4129 TCGA-39-5022 TCGA-39-5031 TCGA-43-2578 TCGA-43-3394 
        4.96         6.58        55.20        27.39        22.49        27.02 
TCGA-43-5668 TCGA-43-6770 TCGA-46-6026 TCGA-51-6867 TCGA-52-7810 TCGA-56-5898 
       18.38        21.47        13.91        61.02        30.35        18.25 
TCGA-56-7730 TCGA-60-2704 TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 
        6.51        37.94        80.45        66.54        56.91        42.64 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 
       21.01         1.02         2.01        23.01         2.01        24.95 
TCGA-66-2790 TCGA-66-2800 TCGA-77-6844 TCGA-77-7142 TCGA-85-6175 TCGA-85-7696 
       22.98        49.05        75.09        42.28         9.67        36.53 
TCGA-85-7698 TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 
       31.30         9.50         0.16        11.70 

subtype1 subtype2 subtype3 subtype4 
    0.39     0.56     0.10     0.16 
subtype1 subtype2 subtype3 subtype4 
  174.08    92.71   119.54    99.16 
subtype1 subtype2 subtype3 subtype4 
   32.88    19.76    14.63    23.98 
[1] "0.4 - 174.1 (32.9)" "0.6 - 92.7 (19.8)"  "0.1 - 119.5 (14.6)"
[4] "0.2 - 99.2 (24.0)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0        9       16        0         7         9          8
  subtype2       0        7       17        1         5         6          3
  subtype3       0        4       19        0         7        12          6
  subtype4       1       10       17        0         3         7          6
          vv
clus       STAGE IIIB
  subtype1          5
  subtype2          1
  subtype3          3
  subtype4          4
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        0        1
  STAGE IA          9        7        4       10
  STAGE IB         16       17       19       17
  STAGE II          0        1        0        0
  STAGE IIA         7        5        7        3
  STAGE IIB         9        6       12        7
  STAGE IIIA        8        3        6        6
  STAGE IIIB        5        1        3        4
[1] 8 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 13 32  4  5
  subtype2  9 26  5  1
  subtype3  7 36  6  3
  subtype4 16 25  5  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       13        9        7       16
  T2       32       26       36       25
  T3        4        5        6        5
  T4        5        1        3        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 32 14  8  0
  subtype2 31  7  3  0
  subtype3 29 19  1  2
  subtype4 32  9  4  2
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       32       31       29       32
  N1       14        7       19        9
  N2        8        3        1        4
  N3        0        0        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0
  subtype1 49
  subtype2 36
  subtype3 47
  subtype4 44
[1] "NOT AVAILABLE: table only has an event [0]"
D6V7, binary
          cls
clus        0  1
  subtype1 14 40
  subtype2  9 32
  subtype3 11 41
  subtype4 15 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   40
  subtype2    9   32
  subtype3   11   41
  subtype4   15   33
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       14        9       11       15
  MALE         40       32       41       33
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     3
  subtype2                                     0
  subtype3                                     0
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      1
  subtype3                                      0
  subtype4                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          50
  subtype2                                                          40
  subtype3                                                          52
  subtype4                                                          48
D6V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       50       40
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       52       48
[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"
D6V10, binary
          cls
clus        0  1
  subtype1  3 51
  subtype2  1 40
  subtype3  3 49
  subtype4  3 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    1   40
  subtype3    3   49
  subtype4    3   45
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        1        3        3
  YES       51       40       49       45
[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"
D6V11, continuous
D6V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 46  0  0  4
  subtype2 29  0  0  3
  subtype3 37  4  2  1
  subtype4 37  1  2  1
D6V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       46       29       37       37
  R1        0        0        4        1
  R2        0        0        2        2
  RX        4        3        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    43
  subtype2     1                         2    32
  subtype3     0                         2    39
  subtype4     0                         3    33
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        0
  BLACK OR AFRICAN AMERICAN        2        2        2        3
  WHITE                           43       32       39       33
[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"
D6V15, binary
          cls
clus        0  1
  subtype1  2 34
  subtype2  1 26
  subtype3  1 30
  subtype4  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   34
  subtype2    1   26
  subtype3    1   30
  subtype4    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        1        0
  NOT HISPANIC OR LATINO       34       26       30       30
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 71 38
  subtype2 89 56
  subtype3 83 62
  subtype4 39 38
subtype1 subtype2 subtype3 subtype4 
     109      145      145       77 
subtype1 subtype2 subtype3 subtype4 
      38       56       62       38 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-21-1070 
       12.20         7.46        11.34        23.54         1.64       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        31.73        56.32        79.53         1.55 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       67.79         9.07        16.93        20.91         3.95         0.43 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-43-6771 TCGA-43-8118 
       70.03         1.71        24.33        27.39         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-56-8304 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BW 
        1.45        17.49         3.48        16.77         1.81        19.23 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-A46L TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 
        0.13         0.26        56.65        21.93        80.45        48.49 
TCGA-60-2721 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MY 
       32.32        23.57        70.62        89.29        25.41        34.59 
TCGA-66-2734 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2778 
       43.10        25.05         0.99         2.01        19.00        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-68-7757 TCGA-77-6844 
       12.03         3.98        12.00        22.98         6.94        75.09 
TCGA-77-7138 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
       11.18       106.95        46.78        86.76        82.92        12.59 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5G7 
       11.54        26.40        27.39         6.97        35.90         5.92 
TCGA-77-A5GB TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8479 
       30.81        34.95         1.38         1.15        14.07         0.72 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-90-6837 
       13.94        15.62        14.96        18.18        16.21        24.92 
TCGA-90-7766 TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-A4VJ 
        9.50         2.70         2.30        21.04         4.01        14.14 
TCGA-96-7544 TCGA-96-8170 TCGA-98-8020 TCGA-98-A538 TCGA-NC-A5HF TCGA-NC-A5HG 
       49.87        17.46         2.76        27.16         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-O2-A52V 
       45.37        30.58        14.73        65.49         3.65        43.89 
TCGA-O2-A52W 
        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        54.28        11.74        30.12 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW 
        7.63        98.01       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        12.00 
TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        1.12        26.43         7.82        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 
       55.20        60.79        35.64        35.70        27.02        21.47 
TCGA-43-A474 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       11.61         9.73         9.99        10.65         0.39         0.39 
TCGA-51-4081 TCGA-51-6867 TCGA-56-5898 TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 
       29.95        61.02        18.25         0.85         6.51        17.00 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K 
       13.32        17.85        18.74        71.24        16.47        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 
       35.24        29.92        49.48        66.54        41.42        29.85 
TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2727 
       35.90       102.67        59.97        45.57        25.28        16.96 
TCGA-66-2737 TCGA-66-2758 TCGA-66-2766 TCGA-66-2770 TCGA-66-2787 TCGA-66-2791 
        2.01        21.01         1.02        23.01        40.01         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J 
       30.02        54.08         4.01        49.05         2.73        14.73 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       73.12        23.28        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 
       70.13         0.16        53.95        37.81        53.92         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA 
       54.41        65.49         0.33       117.57        42.41        42.08 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 
       27.62        12.99         6.41        36.53        31.30        29.95 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8354 
       24.13        31.56        16.87        34.52        10.09        32.71 
TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A5B5 
        2.01        14.63        25.68        19.33        19.73         3.65 
TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 
       11.77         3.48         5.26         5.03        16.14        17.69 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 
       57.07        19.36        18.58        20.71        19.10        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NK-A5CR 
       13.18        11.84         2.89        37.22        29.75        83.57 
TCGA-O2-A52S 
       12.72 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-18-3417 TCGA-21-1078 TCGA-21-1079 TCGA-21-1083 
       79.46         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       174.08       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        23.24        30.94        18.15 
TCGA-34-5929 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        4.96         0.39         6.58         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
        0.39         3.39         1.94        36.39        15.58        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
       24.89        19.59         7.76        66.51        13.38        11.77 
TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7580 
       13.91         5.46         2.04         0.62         0.99         1.32 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       26.89        14.07         1.35        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 
       15.81         2.76        13.25        13.55        29.95        21.11 
TCGA-60-2703 TCGA-60-2712 TCGA-60-2713 TCGA-60-2720 TCGA-60-2726 TCGA-63-A5MH 
       96.82         9.01        56.91         3.19        11.77        66.61 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       58.65        14.99        78.28        16.37        36.16        53.88 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 
        0.99         2.01         0.92         0.99        43.99         2.01 
TCGA-66-2769 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-8251 
        7.07         1.97         4.04        22.98        10.06        13.35 
TCGA-68-A59I TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 TCGA-77-8139 
       16.18        29.56        15.75         6.51        39.09       104.09 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7950 
      132.36        22.29        38.86        11.97        32.91        18.94 
TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8481 
       25.15         0.76        13.22        22.45         5.29         7.76 
TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
        0.10        17.72        24.36        15.85        14.96        12.39 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-94-7557 
        2.93        20.22        22.62        10.59         4.01         0.16 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       16.57        30.81        30.67        21.34        18.15         2.01 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HM 
       13.41         0.07        64.08         1.22         4.21        39.85 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       24.00        22.78        16.80         0.43        33.07         3.72 
TCGA-O2-A5IB 
       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        27.02        32.88        56.38 
TCGA-34-8454 TCGA-34-8455 TCGA-39-5011 TCGA-39-5039 TCGA-43-2578 TCGA-43-6773 
       27.19         4.04        47.80        17.88        22.49         3.81 
TCGA-52-7622 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7731 TCGA-56-8623 
       28.34        27.45        28.96         0.43         0.10        22.75 
TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZJ TCGA-58-8386 TCGA-58-8393 TCGA-58-A46J 
        1.18        20.94        21.04         0.03        34.78        85.12 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2714 
        3.58        12.23        10.22        37.94        92.71        50.33 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2725 TCGA-63-A5MN TCGA-66-2742 TCGA-66-2753 
       35.34        42.64        26.83        11.34        21.07         1.02 
TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2786 TCGA-68-7756 
        2.01         3.02         2.01        24.95        25.97         6.64 
TCGA-68-8250 TCGA-77-8138 TCGA-77-8146 TCGA-77-A5FZ TCGA-85-6175 TCGA-85-8049 
        8.02        17.72        71.77       126.18         9.67        19.04 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8584 TCGA-85-A50M TCGA-85-A513 TCGA-90-7964 
       16.77         3.09        12.59        12.56         0.79        14.07 
TCGA-94-7943 TCGA-94-8491 TCGA-96-8169 TCGA-98-7454 TCGA-98-A539 TCGA-98-A53C 
       11.70        26.63        18.31         8.42         3.88        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ TCGA-XC-AA0X 
       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   174.08   126.18 
subtype1 subtype2 subtype3 subtype4 
   16.77    27.02    16.80    19.04 
[1] "0.1 - 122.4 (16.8)" "0.2 - 154.3 (27.0)" "0.1 - 174.1 (16.8)"
[4] "0.0 - 126.2 (19.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       21       37        1         8        22         0
  subtype2       1       19       55        1        23        29         1
  subtype3       1       26       37        0        24        29         2
  subtype4       0       22       21        0         8        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         16          3        1
  subtype2         14          7        0
  subtype3         21          7        3
  subtype4         11          3        3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        1        0
  STAGE IA         21       19       26       22
  STAGE IB         37       55       37       21
  STAGE II          1        1        0        0
  STAGE IIA         8       23       24        8
  STAGE IIB        22       29       29       11
  STAGE III         0        1        2        0
  STAGE IIIA       16       14       21       11
  STAGE IIIB        3        7        7        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 66 17  4
  subtype2 28 97 17  8
  subtype3 36 85 23  7
  subtype4 25 40 12  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       24       28       36       25
  T2       66       97       85       40
  T3       17       17       23       12
  T4        4        8        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 72 26 10  1
  subtype2 93 45 10  1
  subtype3 95 45 10  1
  subtype4 53 13  9  2
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       72       93       95       53
  N1       26       45       45       13
  N2       10       10       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  89   1
  subtype2 126   0
  subtype3 122   3
  subtype4  66   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89    1
  subtype2  126    0
  subtype3  122    3
  subtype4   66    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       89      126      122       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  27  84
  subtype2  33 117
  subtype3  42 109
  subtype4  25  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   84
  subtype2   33  117
  subtype3   42  109
  subtype4   25   55
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       27       33       42       25
  MALE         84      117      109       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, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     6
  subtype3                                     7
  subtype4                                     0
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  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                                                         107
  subtype2                                                         143
  subtype3                                                         141
  subtype4                                                          78
D7V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      107      143
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7        0
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      141       78
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
          cls
clus         0   1
  subtype1   2 109
  subtype2   2 148
  subtype3   6 145
  subtype4   3  77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  109
  subtype2    2  148
  subtype3    6  145
  subtype4    3   77
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        2        6        3
  YES      109      148      145       77
[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"
D7V11, continuous
D7V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  84   2   2   3
  subtype2 128   6   0   7
  subtype3 118   3   1   7
  subtype4  63   1   1   5
D7V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       84      128      118       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    71
  subtype2     1                         9   104
  subtype3     3                        10   107
  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                           71      104      107       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  64
  subtype2   1  92
  subtype3   1 101
  subtype4   2  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   64
  subtype2    1   92
  subtype3    1  101
  subtype4    2   50
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        1        1        2
  NOT HISPANIC OR LATINO       64       92      101       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 108  65
  subtype2 109  69
  subtype3  65  60
subtype1 subtype2 subtype3 
     173      178      125 
subtype1 subtype2 subtype3 
      65       69       60 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1078 
       12.20        23.54         1.64        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 
        7.63        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 
       67.79        56.38        16.93        30.94         4.96        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-39-5024 TCGA-39-5028 
        4.04        20.91         3.95         0.43        70.03         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-52-7810 TCGA-52-7811 TCGA-56-1622 
       13.38        14.20        12.03        30.35         8.75        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
        0.10         2.04         0.43         1.32         0.10        17.49 
TCGA-56-8304 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-A49D 
        3.48         1.35         1.81         1.18        10.36        20.94 
TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       19.23        21.04         0.13         0.26         0.03        13.25 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       34.78        85.12         3.58        10.22        21.93        80.45 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       35.34        48.49        42.64         3.19        32.32        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MR TCGA-63-A5MT 
       26.83        11.77        70.62        58.65        89.29        16.37 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 TCGA-66-2763 
       36.16        34.59        43.10        21.07         1.02         0.99 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         2.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 TCGA-66-2793 
       12.03         3.98        12.00        25.97        22.98        10.06 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6844 TCGA-77-7138 
        6.64         6.94         8.02        16.18        75.09        11.18 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
       42.28       106.95        46.78        86.76        82.92        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       39.09        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        6.97        71.77        35.90       132.36        22.29         5.92 
TCGA-77-A5GB TCGA-85-6175 TCGA-85-8276 TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 
       30.81         9.67        34.52        16.77         0.72         7.76 
TCGA-85-8582 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-90-6837 
       13.94        14.96        18.18        19.73        16.21        24.92 
TCGA-90-7766 TCGA-90-7964 TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-8491 
        9.50        14.07         2.70         2.30        21.04        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8020 
       14.14        49.87        18.31        17.46        16.57         2.76 
TCGA-98-8021 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW 
       30.81        27.16         3.88        20.32        12.89        13.41 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HO 
        0.07         4.54        51.78        45.37        39.85        30.58 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52V TCGA-O2-A52W 
       14.73        22.78         3.65        43.89         8.58 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
        7.46        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        31.73        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 
       14.63        44.25        54.28        11.74        30.12        56.32 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       98.01       151.27        14.07        27.02         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-39-5016 
        9.07        12.00         1.12        26.43         7.82        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 
       44.75        68.58        55.20        60.79        27.39        35.64 
TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-6773 TCGA-43-8118 TCGA-43-A474 
       35.70        27.02        21.47         3.81         2.93        11.61 
TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.73         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7579 
       29.95        61.02        28.34        18.25         0.99         1.45 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX 
        0.85         6.51        17.00        16.77        15.81        13.32 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K 
       17.85        18.74         2.76        71.24        16.47        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       56.65        35.24        29.92        49.48        66.54        41.42 
TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML 
       56.91        29.85        35.90       102.67        59.97        45.57 
TCGA-63-A5MP TCGA-63-A5MU TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 
       25.28        25.41        16.96         2.01        21.01        25.05 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 
        1.02         2.01        23.01        24.95        40.01         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J 
       30.02        54.08         4.01        49.05         2.73        14.73 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 
       73.12        23.28        89.98        20.78         0.49        70.13 
TCGA-77-7338 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 
        0.16        53.95        37.81        53.92         9.63        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
       65.49         0.33       117.57        42.41        42.08        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 
       12.99         6.41        36.53        34.95        31.30         1.15 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       29.95        19.04        24.13        31.56        14.07        16.87 
TCGA-85-8277 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL 
       10.09        32.71         2.01        14.63        15.62        25.68 
TCGA-85-A4CN TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 
       19.33        14.96         3.65        11.77         3.48         4.01 
TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
        5.26         4.01         5.03        16.14        17.69        57.07 
TCGA-96-A4JK TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 
       19.36        18.15        18.58        20.71        19.10        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HR 
       13.18        11.84        64.08         2.89        37.22        29.75 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52S TCGA-XC-AA0X 
       83.57         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 
       79.46         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       174.08        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        23.24        18.15         0.39         6.58         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        47.80         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       36.39        15.58        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        66.51        11.77 
TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7223 TCGA-56-8307 TCGA-56-8309 
        5.46        27.45         0.62         0.99        26.89        14.07 
TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 
       22.75         9.93        20.25        13.55        29.95        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 
       12.23        96.82        37.94        92.71         9.01        50.33 
TCGA-63-A5MH TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2744 
       66.61        14.99        11.34        78.28        53.88         0.99 
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-66-2789 TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 
        4.04        22.98        13.35        29.56        15.75         6.51 
TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 
      126.18        38.86        11.97        32.91         1.38        18.94 
TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
       25.15         0.76        13.22        22.45         5.29         3.09 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 
       12.59         0.10        17.72        24.36        12.56        15.85 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        0.79        12.39         2.93        20.22        22.62        10.59 
TCGA-94-7557 TCGA-94-7943 TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B 
        0.16        11.70         8.42        30.67        21.34         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP 
       27.02        21.21         1.22        13.74         4.21        24.00 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       65.49        16.80        33.07         3.72        11.18 

subtype1 subtype2 subtype3 
    0.03     0.16     0.10 
subtype1 subtype2 subtype3 
  132.36   154.32   174.08 
subtype1 subtype2 subtype3 
  18.180   23.145   17.720 
[1] "0.0 - 132.4 (18.2)" "0.2 - 154.3 (23.1)" "0.1 - 174.1 (17.7)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       30       59        1        19        31         0
  subtype2       1       27       62        1        26        37         1
  subtype3       1       31       29        0        18        23         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         28          4        4
  subtype2         19         10        0
  subtype3         15          6        3
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         30       27       31
  STAGE IB         59       62       29
  STAGE II          1        1        0
  STAGE IIA        19       26       18
  STAGE IIB        31       37       23
  STAGE III         0        1        2
  STAGE IIIA       28       19       15
  STAGE IIIB        4       10        6
  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  35 104  32   7
  subtype2  37 118  21   9
  subtype3  41  66  16   6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       35       37       41
  T2      104      118       66
  T3       32       21       16
  T4        7        9        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 117  43  14   1
  subtype2 113  53  15   3
  subtype3  83  33  10   1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      117      113       83
  N1       43       53       33
  N2       14       15       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 153   0
  subtype3 106   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144    4
  subtype2  153    0
  subtype3  106    3
   clus
vv  subtype1 subtype2 subtype3
  0      144      153      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  55 123
  subtype2  36 149
  subtype3  36  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55  123
  subtype2   36  149
  subtype3   36   93
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       55       36       36
  MALE        123      149       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"
D8V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     7
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          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                                                         173
  subtype2                                                         177
  subtype3                                                         119
D8V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      173      177
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      119
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus         0   1
  subtype1   4 174
  subtype2   6 179
  subtype3   3 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  174
  subtype2    6  179
  subtype3    3  126
     clus
vv    subtype1 subtype2 subtype3
  NO         4        6        3
  YES      174      179      126
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 141   2   1   9
  subtype2 151   7   3   8
  subtype3 101   3   0   5
D8V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      141      151      101
  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   115
  subtype2     2                        13   127
  subtype3     4                         6    97
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        4
  BLACK OR AFRICAN AMERICAN       11       13        6
  WHITE                          115      127       97
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
          cls
clus         0   1
  subtype1   4 103
  subtype2   2 114
  subtype3   2  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  103
  subtype2    2  114
  subtype3    2   90
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO      103      114       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"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 61 55
  subtype2 86 40
  subtype3 68 49
  subtype4 37 23
  subtype5 20 15
subtype1 subtype2 subtype3 subtype4 subtype5 
     116      126      117       60       35 
subtype1 subtype2 subtype3 subtype4 subtype5 
      55       40       49       23       15 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        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         1.64        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        31.73        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         7.63       133.74        98.01        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2605 TCGA-34-5241 
      174.08       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        47.80        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        15.58        35.64        17.88        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-46-3768 TCGA-51-4081 TCGA-56-1622 
       27.02        33.11        18.38         9.99        29.95        28.96 
TCGA-56-5897 TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 
        0.10        21.11         3.58        92.71        80.45         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       56.91        50.33        48.49        32.32        35.90        23.57 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.92        21.01        25.05         0.99         2.01         2.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
       19.00         2.01        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-77-8007 TCGA-77-8144 TCGA-85-7699 
        5.03        30.02         4.01         6.51        27.39        32.91 
TCGA-90-A59Q TCGA-94-7033 
       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 
       18.15         4.96         1.12        26.43        20.91         3.95 
TCGA-39-5037 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       35.70        27.91        12.36         7.76        66.51        13.38 
TCGA-43-A474 TCGA-46-6025 TCGA-51-6867 TCGA-52-7809 TCGA-56-7222 TCGA-56-7223 
       11.61        10.65        61.02         5.46         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        1.45         1.32         0.85         3.48        26.89        17.00 
TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
       16.77        15.81        19.23        13.32        17.85        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46N 
        0.13         2.76        13.25        71.24        16.47        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-A5MR TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2766 TCGA-66-2768 TCGA-68-7755 
       89.29        25.41        34.59         1.02         2.01         2.73 
TCGA-68-8251 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 
       13.35        23.28        11.18        89.98        20.78        70.13 
TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       15.75        37.81        53.92        26.40         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
       65.49        35.90         0.33       117.57        22.29        42.41 
TCGA-85-6561 TCGA-85-7710 TCGA-85-7843 TCGA-85-8070 TCGA-85-8276 TCGA-85-8288 
       12.99         1.38         1.15        31.56        34.52        13.22 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CN 
        5.29        32.71         0.72        14.63        15.62        19.33 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 
       19.73        16.21        14.96        12.39         2.93        11.77 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-94-8490 
        3.48         4.01         5.26         2.30        11.70         5.03 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A53A TCGA-98-A53J 
       16.14        17.69        19.36        27.16        18.15        20.71 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG 
       19.10        16.11        11.84         0.07        64.08        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        45.37         2.89        39.85        37.22        30.58 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       29.75        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 
       54.28        18.84        22.06        27.02        44.19        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-8454 TCGA-34-8455 
       67.79        56.38         9.07        23.24        27.19         4.04 
TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 TCGA-43-6647 TCGA-43-6771 
       44.75        70.03        60.79        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        16.18        75.09        42.28       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 
       71.77       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        13.94        12.59        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
       24.36        18.18        12.56         0.79        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        49.87        57.07 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 
       17.46        16.57         8.42         2.76        30.67        21.34 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 
        3.88         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        12.00        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        14.73        73.12         0.49         0.16 
TCGA-77-8009 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 
       53.95        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        14.07        16.87        25.68 
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        30.94        27.39 
TCGA-43-2578 TCGA-43-8116 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-56-8625 
       22.49        11.77        14.20        12.03        13.91        10.36 
TCGA-56-A49D TCGA-58-8390 TCGA-60-2711 TCGA-60-2719 TCGA-63-A5MW TCGA-66-2793 
       20.94        29.95        41.42        42.64        53.88        10.06 
TCGA-77-6842 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-A5G7 TCGA-85-8287 
       29.56        39.09       104.09        11.54         5.92         0.76 
TCGA-85-8664 TCGA-85-A4JB TCGA-85-A510 TCGA-85-A5B5 TCGA-94-7557 TCGA-94-8035 
        0.10        17.72        15.85         3.65         0.16         4.01 
TCGA-96-8169 TCGA-NC-A5HF TCGA-NC-A5HP TCGA-NC-A5HT TCGA-O2-A52N 
       18.31         4.54        24.00        22.78        33.07 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.07     0.03     0.16     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  174.08   118.36   132.36   154.32   104.09 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.090   17.770   18.180   24.705   18.310 
[1] "0.1 - 174.1 (21.1)" "0.1 - 118.4 (17.8)" "0.0 - 132.4 (18.2)"
[4] "0.2 - 154.3 (24.7)" "0.1 - 104.1 (18.3)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       16       48        0         6        19         0
  subtype2       1       15       37        1        27        27         3
  subtype3       1       25       31        1        19        25         0
  subtype4       0       17       20        0         7        10         0
  subtype5       1       10        6        0         1         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1         21          8        3
  subtype2         17          1        0
  subtype3         14          4        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         16       15       25       17       10
  STAGE IB         48       37       31       20        6
  STAGE II          0        1        1        0        0
  STAGE IIA         6       27       19        7        1
  STAGE IIB        19       27       25       10        9
  STAGE III         0        3        0        0        0
  STAGE IIIA       21       17       14        3        5
  STAGE IIIB        8        1        4        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 22 84 22  2
  subtype3 30 62 24  6
  subtype4 20 34  4  3
  subtype5 11 16  6  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       22       22       30       20       11
  T2       80       84       62       34       16
  T3       11       22       24        4        6
  T4        8        2        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 75 41 12  0
  subtype3 79 31  8  0
  subtype4 42 16  3  0
  subtype5 23  9  3  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       76       75       79       42       23
  N1       28       41       31       16        9
  N2       13       12        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  99   0
  subtype3  94   2
  subtype4  48   0
  subtype5  28   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    3
  subtype2   99    0
  subtype3   94    2
  subtype4   48    0
  subtype5   28    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      113       99       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  29 101
  subtype3  33  89
  subtype4  15  46
  subtype5  13  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   90
  subtype2   29  101
  subtype3   33   89
  subtype4   15   46
  subtype5   13   22
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       31       29       33       15       13
  MALE         90      101       89       46       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"
D9V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     7
  subtype3                                     1
  subtype4                                     4
  subtype5                                     0
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       0
  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                                                         120
  subtype3                                                         117
  subtype4                                                          57
  subtype5                                                          35
D9V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      119      120
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      117       57
                                                             clus
vv                                                            subtype5
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG CLEAR CELL 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)       35
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus         0   1
  subtype1   4 117
  subtype2   3 127
  subtype3   4 118
  subtype4   0  61
  subtype5   1  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  117
  subtype2    3  127
  subtype3    4  118
  subtype4    0   61
  subtype5    1   34
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         4        3        4        0        1
  YES      117      127      118       61       34
[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"
D9V11, continuous
D9V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   2   2   2
  subtype2  99   3   0   8
  subtype3  91   2   0   7
  subtype4  48   4   0   2
  subtype5  27   0   1   1
D9V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      109       99       91       48       27
  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    73
  subtype2     2                         5    97
  subtype3     4                        13    86
  subtype4     0                         6    43
  subtype5     0                         2    25
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                           73       97       86       43       25
[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 83
  subtype3  2 83
  subtype4  1 41
  subtype5  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   67
  subtype2    1   83
  subtype3    2   83
  subtype4    1   41
  subtype5    0   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        2        1        0
  NOT HISPANIC OR LATINO       67       83       83       41       20
[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  54  31
  subtype2  63  46
  subtype3 116  77
  subtype4  39  28
subtype1 subtype2 subtype3 subtype4 
      85      109      193       67 
subtype1 subtype2 subtype3 subtype4 
      31       46       77       28 
$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        31.73        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        12.00        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        14.73        73.12         0.49         0.16 
TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
       53.95       117.57        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        14.07        16.87         5.29 
TCGA-85-A4CL TCGA-85-A4CN TCGA-90-7769 TCGA-90-A4EE TCGA-94-8491 TCGA-94-A5I6 
       25.68        19.33        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 
        7.46         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        54.28        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       174.08       118.36         4.96         1.12        20.91 
TCGA-37-3783 TCGA-37-3792 TCGA-39-5011 TCGA-39-5021 TCGA-39-5036 TCGA-39-5039 
        3.95         0.39        47.80        68.58        35.64        17.88 
TCGA-43-2576 TCGA-43-2581 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-46-3768 
       40.21        38.66         5.46         7.76        66.51         9.99 
TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 
        5.46        30.35         0.10         2.04         1.45         1.32 
TCGA-56-8307 TCGA-56-8504 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-8388 TCGA-58-A46L 
       26.89        16.77        19.23        18.74        13.55        56.65 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2712 TCGA-60-2716 TCGA-60-2721 TCGA-63-A5MR 
       21.11         3.58         9.01        48.49        32.32        89.29 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 
       43.10        21.07         0.99         1.02         0.92        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 
        0.99         2.01         1.02         2.01         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-68-8251 TCGA-77-6845 
       12.03         3.98        12.00        25.97        13.35        23.28 
TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 
       11.18        70.13       106.95        15.75        37.81        53.92 
TCGA-77-A5G8 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-8048 TCGA-85-8276 
       42.41        34.95        31.30         1.38        25.15        34.52 
TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 TCGA-85-A53L TCGA-90-7767 TCGA-90-A59Q 
       13.22         2.01         0.72        12.39         2.93        10.59 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-8490 TCGA-94-A5I4 TCGA-96-7544 
        3.48         5.26        21.04         5.03        16.14        49.87 
TCGA-L3-A524 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HR TCGA-NK-A5CX 
       16.11        64.08        51.78         2.89        29.75         3.65 
TCGA-O2-A52Q 
        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         1.64        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         7.63       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        30.94        18.15        27.19 
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-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        3.39        70.03        60.79        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 
       36.39        35.70        17.06        22.49        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       18.38        27.91        12.36        19.59        13.38        11.77 
TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-6867 TCGA-52-7622 
        2.93        14.20        12.03        13.91        61.02        28.34 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
        8.75        28.96        18.25         0.99         0.43         0.99 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 TCGA-56-8625 
        0.10        17.49         3.48        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         2.76        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        16.18        29.56        75.09 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7463 TCGA-77-8008 TCGA-77-8136 
       89.98        20.78        42.28        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 
        9.63        54.41        65.49         0.33       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        14.63        13.94 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 
        0.10        15.62        17.72        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         3.88         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        45.37         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        30.58        24.00        14.73        22.78        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        98.01        19.76        27.02 
TCGA-33-AASI TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       44.19        32.88        67.79        56.38         9.07        23.24 
TCGA-34-8455 TCGA-39-5019 TCGA-39-5028 TCGA-39-5035 TCGA-43-6647 TCGA-43-6773 
        4.04        44.75         1.71        15.58        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        71.77        35.90       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        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 
       24.36        18.18        12.56        16.21         0.79        24.92 
TCGA-90-7964 TCGA-92-7340 TCGA-94-7943 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
       14.07         2.70        11.70        57.07        17.46        16.57 
TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HJ 
        8.42        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   174.08   133.74   126.18 
subtype1 subtype2 subtype3 subtype4 
   22.29    18.74    18.84    17.46 
[1] "0.2 - 154.3 (22.3)" "0.1 - 174.1 (18.7)" "0.1 - 133.7 (18.8)"
[4] "0.0 - 126.2 (17.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0       15       30        0        11        18         1
  subtype2       0       17       41        1        16        22         1
  subtype3       3       39       52        1        21        35         1
  subtype4       0       12       19        0        12        15         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          7          6        0
  subtype2         13          2        2
  subtype3         33          7        2
  subtype4          7          3        2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        3        0
  STAGE IA         15       17       39       12
  STAGE IB         30       41       52       19
  STAGE II          0        1        1        0
  STAGE IIA        11       16       21       12
  STAGE IIB        18       22       35       15
  STAGE III         1        1        1        0
  STAGE IIIA        7       13       33        7
  STAGE IIIB        6        2        7        3
  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  21  74  17   3
  subtype3  49 107  33   7
  subtype4  16  40   9   5
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       19       21       49       16
  T2       55       74      107       40
  T3        8       17       33        9
  T4        6        3        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        N0  N1  N2  N3
  subtype1  52  29   6   1
  subtype2  77  28   9   1
  subtype3 126  50  19   1
  subtype4  40  18   5   1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       52       77      126       40
  N1       29       28       50       18
  N2        6        9       19        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  99   2
  subtype3 154   2
  subtype4  54   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75    0
  subtype2   99    2
  subtype3  154    2
  subtype4   54    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       75       99      154       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  29  86
  subtype3  53 143
  subtype4  20  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   69
  subtype2   29   86
  subtype3   53  143
  subtype4   20   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       29       53       20
  MALE         69       86      143       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, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     4
  subtype2                                     6
  subtype3                                     3
  subtype4                                     0
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  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                                                         106
  subtype3                                                         190
  subtype4                                                          68
D10V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4        6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       84      106
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3        0
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      190       68
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus         0   1
  subtype1   1  87
  subtype2   1 114
  subtype3   8 188
  subtype4   2  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   87
  subtype2    1  114
  subtype3    8  188
  subtype4    2   68
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        8        2
  YES       87      114      188       68
[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"
D10V11, continuous
D10V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  72   4   1   3
  subtype2  96   2   0   5
  subtype3 155   4   1   5
  subtype4  51   1   1   7
D10V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       72       96      155       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    80
  subtype3     2                        17   136
  subtype4     4                         4    48
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        3        2        4
  BLACK OR AFRICAN AMERICAN        7        2       17        4
  WHITE                           60       80      136       48
[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  64
  subtype3   3 124
  subtype4   2  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    1   64
  subtype3    3  124
  subtype4    2   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        3        2
  NOT HISPANIC OR LATINO       58       64      124       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 53 31
  subtype2 76 51
  subtype3 71 38
subtype1 subtype2 subtype3 
      84      127      109 
subtype1 subtype2 subtype3 
      31       51       38 
$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        56.38         9.07        23.24        30.94 
TCGA-34-5928 TCGA-39-5019 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 
       18.15        44.75        24.89         5.46         3.81        13.38 
TCGA-43-A56V TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 TCGA-56-8503 TCGA-56-8622 
       12.03         0.10         1.32         0.10         1.35         1.81 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4ZJ TCGA-60-2697 TCGA-60-2709 
        1.18        10.36        20.25        21.04        12.23        49.48 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       70.62        14.99        11.34        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-7335 TCGA-77-7337 
       53.88         6.94        13.35        16.18        70.13       106.95 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       86.76        37.81        82.92        12.59        39.09        17.72 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5GB TCGA-85-6175 TCGA-85-7950 
      104.09        27.39         6.97        30.81         9.67        18.94 
TCGA-85-8049 TCGA-85-8276 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
       19.04        34.52         7.76        13.94        12.59        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-90-7964 TCGA-92-7340 
       14.96        18.18        12.56        14.96        14.07         2.70 
TCGA-94-A4VJ TCGA-96-8170 TCGA-98-7454 TCGA-98-8020 TCGA-98-8023 TCGA-98-A539 
       14.14        17.46         8.42         2.76        21.34         3.88 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-LA-A7SW TCGA-NC-A5HK 
        2.01        27.02        21.21        20.32        13.41         4.21 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V 
       24.00        22.78         3.65         0.43        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        54.28        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        27.02        36.62       110.99 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       65.23        67.79         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-37-3783 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 
       26.43         3.95        55.20        70.03        60.79        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        66.51 
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-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8623 TCGA-56-8626 TCGA-56-8629 
       17.00        14.07        16.77        22.75         9.93        15.81 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-60-2703 TCGA-60-2704 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 
       34.78        96.82        37.94         2.73         6.64         8.02 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 
       29.56        73.12        75.09        11.18        20.78         0.49 
TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
       42.28         0.16        46.78        15.75         6.51        53.95 
TCGA-77-8133 TCGA-77-8143 TCGA-77-8146 TCGA-77-8156 TCGA-85-6560 TCGA-85-6561 
       53.92        26.40        71.77         0.33        11.97        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       36.53        34.95        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 
       29.95        25.15        24.13        16.87         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A513 TCGA-90-6837 
        0.72        14.63        15.62        24.36         0.79        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 
        9.50         2.93        11.77         3.48         5.26         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       21.04         0.16        11.70         4.01         5.03        26.63 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 
       49.87        57.07        18.31        16.57        30.81        30.67 
TCGA-XC-AA0X 
        0.20 

$subtype3
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       31.73        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-43-5668 TCGA-43-A474 
      118.36        27.16        20.91         3.39        18.38        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 TCGA-56-8307 
        9.73        14.20        18.25         0.99         1.45        26.89 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
       20.94        19.23        13.32        17.85        18.74         0.13 
TCGA-56-A62T TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2.76        85.12        34.36        56.65        35.24        29.92 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
      102.67        66.61        58.65        59.97        45.57        25.28 
TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MY TCGA-68-A59J TCGA-77-6845 TCGA-77-7139 
       89.29        25.41        34.59        14.73        23.28        89.98 
TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
       11.54         9.63        54.41        65.49        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-8070 TCGA-85-8071 TCGA-85-8664 
       27.62        38.86         6.41        31.56        14.07         0.10 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L 
       25.68        19.33        19.73        16.21        15.85        12.39 
TCGA-85-A5B5 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-94-A5I4 
        3.65        20.22        22.62        10.59         4.01        16.14 
TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J 
       17.69        19.36        27.16        18.15        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD 
       19.10        12.89        16.11        13.18        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       64.08         4.54        51.78         1.22        45.37        13.74 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        39.85        37.22        30.58        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W 
       83.57        65.49        16.80         3.72        12.72         8.58 
TCGA-O2-A5IB 
       11.18 

subtype1 subtype2 subtype3 
    0.10     0.03     0.07 
subtype1 subtype2 subtype3 
  106.95   110.99   132.36 
subtype1 subtype2 subtype3 
   17.59    16.77    20.22 
[1] "0.1 - 107.0 (17.6)" "0.0 - 111.0 (16.8)" "0.1 - 132.4 (20.2)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       13       26        1        11        21         0
  subtype2       1       34       36        1        21        20         0
  subtype3       1       18       26        0        21        23         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          4        1
  subtype2         13          0        2
  subtype3         17          2        0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        1
  STAGE IA         13       34       18
  STAGE IB         26       36       26
  STAGE II          1        1        0
  STAGE IIA        11       21       21
  STAGE IIB        21       20       23
  STAGE III         0        0        3
  STAGE IIIA        9       13       17
  STAGE IIIB        4        0        2
  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 49 19  4
  subtype2 43 70 14  3
  subtype3 21 65 22  3
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       15       43       21
  T2       49       70       65
  T3       19       14       22
  T4        4        3        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 58 21  6
  subtype2 88 30  8
  subtype3 64 36 11
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       58       88       64
  N1       21       30       36
  N2        6        8       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"
D11V6, binary
          cls
clus        0  1
  subtype1 67  1
  subtype2 96  2
  subtype3 85  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    1
  subtype2   96    2
  subtype3   85    0
   clus
vv  subtype1 subtype2 subtype3
  0       67       96       85
  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 60
  subtype2 32 98
  subtype3 23 88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   60
  subtype2   32   98
  subtype3   23   88
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       32       23
  MALE         60       98       88
[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, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     7
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          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                                                          84
  subtype2                                                         125
  subtype3                                                         102
D11V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       84      125
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              7
  LUNG CLEAR CELL 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)      102
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
          cls
clus         0   1
  subtype1   0  87
  subtype2   6 124
  subtype3   3 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   87
  subtype2    6  124
  subtype3    3  108
     clus
vv    subtype1 subtype2 subtype3
  NO         0        6        3
  YES       87      124      108
[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"
D11V11, continuous
D11V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 60  3  0  7
  subtype2 96  3  1  5
  subtype3 89  3  1  5
D11V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       60       96       89
  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    56
  subtype2     2                         9   108
  subtype3     2                         5    79
D11V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        2
  BLACK OR AFRICAN AMERICAN        9        9        5
  WHITE                           56      108       79
[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 57
  subtype2  3 95
  subtype3  0 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   57
  subtype2    3   95
  subtype3    0   64
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       57       95       64
[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 25 13
  subtype2 90 55
  subtype3 85 52
subtype1 subtype2 subtype3 
      38      145      137 
subtype1 subtype2 subtype3 
      13       55       52 
$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        30.94 
TCGA-43-A56V TCGA-56-7223 TCGA-56-8503 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D 
       12.03         0.99         1.35        10.36        20.25        20.94 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-68-7757 TCGA-68-A59I 
       78.28        16.37        36.16        53.88         6.94        16.18 
TCGA-77-8008 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
       86.76        39.09        17.72       104.09        27.39         6.97 
TCGA-77-A5G6 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4JB TCGA-94-A4VJ TCGA-98-8020 
       22.29         7.76        13.94        17.72        14.14         2.76 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A5D1 
       13.41         0.07         1.22        22.78         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52V 
        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        31.73        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-39-5027 TCGA-43-5668 
       27.16        65.23        26.43         3.39        60.79        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
       27.91        12.36        66.51        13.38        11.77        11.61 
TCGA-43-A475 TCGA-46-6026 TCGA-51-6867 TCGA-52-7809 TCGA-52-7810 TCGA-56-5898 
        9.73        13.91        61.02         5.46        30.35        18.25 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8307 
        0.43         1.45         0.85         6.51         3.48        26.89 
TCGA-56-8308 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T 
       17.00        15.81        13.32        18.74         0.13         2.76 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L 
       13.25        13.55        71.24        16.47        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
       35.24        29.92        96.82       102.67        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MU TCGA-63-A5MY TCGA-68-7755 
       59.97        45.57        25.28        25.41        34.59         2.73 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
       14.73        29.56        73.12        75.09        23.28        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 
       20.78         0.49        42.28        46.78        15.75        53.95 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       11.54        26.40         9.63        54.41        65.49         0.33 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6798 TCGA-85-7699 
      117.57         5.92        42.08        27.62         6.41        32.91 
TCGA-85-7843 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 
        1.15        24.13        31.56        14.07        16.87         5.29 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       32.71         0.72        14.63         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       19.33        19.73        16.21        15.85        14.96         3.65 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 
        2.93        11.77        22.62        10.59         4.01         2.30 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK 
       11.70         4.01         5.03        16.14        17.69        19.36 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.16        18.15         2.01        18.58        20.71        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        11.84        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT TCGA-O2-A52S TCGA-O2-A52W 
       14.73        29.75        83.57        65.49        12.72         8.58 
TCGA-O2-A5IB 
       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        54.28        18.84 
TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-5232 TCGA-34-5234 
       27.02         6.94        44.19       118.36        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
        9.07        23.24        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
        4.04        20.91         3.95        44.75        55.20        70.03 
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-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
        0.10        17.49        14.07        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8386 
        1.18         9.93        19.23        17.85        21.04         0.03 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 
       29.95        34.78        85.12        12.23        37.94        49.48 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-68-7756 TCGA-68-8250 
       70.62        14.99        11.34        89.29         6.64         8.02 
TCGA-68-8251 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
       13.35        11.18        70.13       106.95         0.16         6.51 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8146 TCGA-77-8154 
       37.81        82.92        12.59        53.92        71.77        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
      126.18       132.36        42.41        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       11.97        12.99        36.53        34.95        31.30         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8276 TCGA-85-8287 
       29.95        18.94        25.15        19.04        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8584 
       13.22        22.45        16.77         3.09         2.01        12.59 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-85-A53L 
       14.96        24.36        18.18        12.56         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 
       24.92         9.50        14.07        20.22         2.70         3.48 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8491 TCGA-96-7544 TCGA-96-7545 
        5.26        21.04         0.16        26.63        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        16.57         8.42        30.81        30.67 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 
       21.34         3.88        27.02        21.21        20.32        12.89 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       13.74         4.21        33.07         3.72         0.20 

subtype1 subtype2 subtype3 
    0.07     0.10     0.03 
subtype1 subtype2 subtype3 
  104.09   117.57   132.36 
subtype1 subtype2 subtype3 
   17.26    19.10    18.15 
[1] "0.1 - 104.1 (17.3)" "0.1 - 117.6 (19.1)" "0.0 - 132.4 (18.1)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        7        8        1         4         7         0
  subtype2       2       25       36        0        28        32         2
  subtype3       1       33       44        1        21        25         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IV
  subtype1          9          2        0
  subtype2         19          1        1
  subtype3         11          3        2
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        2        1
  STAGE IA          7       25       33
  STAGE IB          8       36       44
  STAGE II          1        0        1
  STAGE IIA         4       28       21
  STAGE IIB         7       32       25
  STAGE III         0        2        1
  STAGE IIIA        9       19       11
  STAGE IIIB        2        1        3
  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 17 12  2
  subtype2 31 90 23  3
  subtype3 41 77 20  5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        7       31       41
  T2       17       90       77
  T3       12       23       20
  T4        2        3        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 25  8  5
  subtype2 88 46 12
  subtype3 97 33  8
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       25       88       97
  N1        8       46       33
  N2        5       12        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 114   1
  subtype3 104   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2  114    1
  subtype3  104    2
   clus
vv  subtype1 subtype2 subtype3
  0       30      114      104
  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  29
  subtype2  34 113
  subtype3  39 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   29
  subtype2   34  113
  subtype3   39  104
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       34       39
  MALE         29      113      104
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     8
  subtype3                                     0
          vv
clus       LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          34
  subtype2                                                         136
  subtype3                                                         141
D12V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       34      136
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG CLEAR CELL 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)      141
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
          cls
clus         0   1
  subtype1   0  38
  subtype2   5 142
  subtype3   4 139
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   38
  subtype2    5  142
  subtype3    4  139
     clus
vv    subtype1 subtype2 subtype3
  NO         0        5        4
  YES       38      142      139
[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"
D12V11, continuous
D12V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  27   1   0   1
  subtype2 117   5   2   6
  subtype3 101   3   0  10
D12V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       27      117      101
  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    20
  subtype2     1                         6   119
  subtype3     5                        11   104
D12V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        5
  BLACK OR AFRICAN AMERICAN        6        6       11
  WHITE                           20      119      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"
D12V15, binary
          cls
clus         0   1
  subtype1   0  21
  subtype2   0  94
  subtype3   4 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   21
  subtype2    0   94
  subtype3    4  101
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        4
  NOT HISPANIC OR LATINO       21       94      101
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
