[1] "ofn"        "-oTLUAD-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/LUAD-TP/22506767/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/22552673/LUAD-TP.mergedcluster.txt"

nPatients in clinical file=522, in cluster file=520, common to both=520
[1]  12 520
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
15 10  7 
 1  2  3 
15 10  7 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
14 11  7 
 1  2  3 
14 11  7 
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
172 138 132  74 
  1   2   3   4 
172 138 132  74 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
156 172 130 
  1   2   3 
156 172 130 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5 
 91  23  67  75 109 
  1   2   3   4   5 
 91  23  67  75 109 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
167 135  63 
  1   2   3 
167 135  63 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
132 120  90 115  58 
  1   2   3   4   5 
132 120  90 115  58 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 79 112  97  48  53  49  77 
  1   2   3   4   5   6   7 
 79 112  97  48  53  49  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
187 221 105 
  1   2   3 
187 221 105 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 72  39 145 131  96  30 
  1   2   3   4   5   6 
 72  39 145 131  96  30 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
59 90 97 44 70 77 
 1  2  3  4  5  6 
59 90 97 44 70 77 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
104 238  95 
  1   2   3 
104 238  95 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 520 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=176,	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=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 520 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
172 279  47  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
172 279  47  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
172 279  47  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
172 279  47  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
335  97  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  335    97    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
335  97  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  335    97    76 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=12, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=94, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 11  3
  subtype2  8  2
  subtype3  5  2
subtype1 subtype2 subtype3 
      14       10        7 
subtype1 subtype2 subtype3 
       3        2        2 
$subtype1
TCGA-44-2655 TCGA-44-2661 TCGA-35-3615 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       43.53        38.10         0.46        46.98        44.42        44.94 
TCGA-44-2666 TCGA-44-3919 TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 
        3.19        33.73        26.56        37.02        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 
       14.04        12.66 

$subtype2
TCGA-44-2662 TCGA-05-4249 TCGA-05-4250 TCGA-35-4122 TCGA-35-4123 TCGA-44-2665 
       42.08        50.07         3.98         7.40         5.98        42.77 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-64-1676 
       25.02        38.24        34.06        56.81 

$subtype3
TCGA-55-1592 TCGA-55-1595 TCGA-64-1677 TCGA-55-1594 TCGA-55-1596 TCGA-64-1678 
       23.05        48.62        20.65        38.73        67.89        39.09 
TCGA-67-3771 
       20.05 

subtype1 subtype2 subtype3 
    0.46     3.98    20.05 
subtype1 subtype2 subtype3 
   46.98    56.81    67.89 
subtype1 subtype2 subtype3 
  30.145   36.150   38.730 
[1] "0.5 - 47.0 (30.1)"  "4.0 - 56.8 (36.2)"  "20.1 - 67.9 (38.7)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIB STAGE IIIA STAGE IV
  subtype1        4        8         1          0        2
  subtype2        5        3         1          1        0
  subtype3        3        0         1          2        0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          4        5        3
  STAGE IB          8        3        0
  STAGE IIB         1        1        1
  STAGE IIIA        0        1        2
  STAGE IV          2        0        0
[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"
          vv
clus       T1 T2 T3
  subtype1  5 10  0
  subtype2  5  4  1
  subtype3  2  5  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5        5        2
  T2       10        4        5
  T3        0        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 11  1     2
  subtype2  8  2     0
  subtype3  4  1     2
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          11        8        4
  N1           1        2        1
  N2+N3        2        0        2
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 13  2
  subtype2 10  0
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    2
  subtype2   10    0
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0       13       10        7
  1        2        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 10  5
  subtype2  4  6
  subtype3  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    5
  subtype2    4    6
  subtype3    4    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10        4        4
  MALE          5        6        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"
D1V8, binary
          cls
clus       0 1
  subtype1 8 1
  subtype2 7 0
  subtype3 5 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2    7    0
  subtype3    5    0
     clus
vv    subtype1 subtype2 subtype3
  NO         8        7        5
  YES        1        0        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"
D1V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        3        1 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                                 1
  subtype2                                 0
  subtype3                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 14
  subtype2                                                 10
  subtype3                                                  6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA
  subtype1                              0
  subtype2                              0
  subtype3                              1
D1V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         1        0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       14       10        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        1
[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"
D1V11, continuous
D1V12, continuous
          vv
clus       R0 R2 RX
  subtype1 11  0  2
  subtype2  9  1  0
  subtype3  6  0  0
D1V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       11        9        6
  R2        0        1        0
  RX        2        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    14
  subtype2     0                         0     8
  subtype3     2                         1     4
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        2
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                           14        8        4
[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"
D1V15, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  0  8
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    0    8
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       13        8        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  8  3
  subtype3  5  2
subtype1 subtype2 subtype3 
      13       11        7 
subtype1 subtype2 subtype3 
       2        3        2 
$subtype1
TCGA-44-2655 TCGA-44-2661 TCGA-35-3615 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       43.53        38.10         0.46        46.98        44.42        44.94 
TCGA-44-2666 TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        3.19        26.56        37.02        20.05        18.84        14.04 
TCGA-67-3774 
       12.66 

$subtype2
TCGA-44-2662 TCGA-05-4249 TCGA-05-4250 TCGA-35-4122 TCGA-35-4123 TCGA-44-2665 
       42.08        50.07         3.98         7.40         5.98        42.77 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-64-1676 
       25.02        38.24        34.06        33.73        56.81 

$subtype3
TCGA-55-1592 TCGA-55-1595 TCGA-64-1677 TCGA-55-1594 TCGA-55-1596 TCGA-64-1678 
       23.05        48.62        20.65        38.73        67.89        39.09 
TCGA-67-3771 
       20.05 

subtype1 subtype2 subtype3 
    0.46     3.98    20.05 
subtype1 subtype2 subtype3 
   46.98    56.81    67.89 
subtype1 subtype2 subtype3 
   26.56    34.06    38.73 
[1] "0.5 - 47.0 (26.6)"  "4.0 - 56.8 (34.1)"  "20.1 - 67.9 (38.7)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIB STAGE IIIA STAGE IV
  subtype1        3        8         1          0        2
  subtype2        6        3         1          1        0
  subtype3        3        0         1          2        0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          3        6        3
  STAGE IB          8        3        0
  STAGE IIB         1        1        1
  STAGE IIIA        0        1        2
  STAGE IV          2        0        0
[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"
          vv
clus       T1 T2 T3
  subtype1  4 10  0
  subtype2  6  4  1
  subtype3  2  5  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        6        2
  T2       10        4        5
  T3        0        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 10  1     2
  subtype2  9  2     0
  subtype3  4  1     2
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          10        9        4
  N1           1        2        1
  N2+N3        2        0        2
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 12  2
  subtype2 11  0
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    2
  subtype2   11    0
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0       12       11        7
  1        2        0        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"
D2V7, binary
          cls
clus       0 1
  subtype1 9 5
  subtype2 5 6
  subtype3 4 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    5
  subtype2    5    6
  subtype3    4    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        5        4
  MALE          5        6        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"
D2V8, binary
          cls
clus       0 1
  subtype1 7 1
  subtype2 8 0
  subtype3 5 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2    8    0
  subtype3    5    0
     clus
vv    subtype1 subtype2 subtype3
  NO         7        8        5
  YES        1        0        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"
D2V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        3        1 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                                 1
  subtype2                                 0
  subtype3                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 13
  subtype2                                                 11
  subtype3                                                  6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA
  subtype1                              0
  subtype2                              0
  subtype3                              1
D2V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         1        0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       13       11        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
          vv
clus       R0 R2 RX
  subtype1 10  0  2
  subtype2 10  1  0
  subtype3  6  0  0
D2V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       10       10        6
  R2        0        1        0
  RX        2        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    13
  subtype2     0                         0     9
  subtype3     2                         1     4
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        2
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                           13        9        4
[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  1 12
  subtype2  0  9
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   12
  subtype2    0    9
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       12        9        7
[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 104  64
  subtype2  78  58
  subtype3  91  36
  subtype4  50  23
subtype1 subtype2 subtype3 subtype4 
     168      136      127       73 
subtype1 subtype2 subtype3 subtype4 
      64       58       36       23 
$subtype1
TCGA-05-4402 TCGA-05-4405 TCGA-38-4629 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
        8.02        20.05        28.41        14.73        42.08        27.78 
TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       46.72       156.66        37.32        21.47        41.69        23.05 
TCGA-55-6979 TCGA-55-7573 TCGA-55-8091 TCGA-55-8207 TCGA-55-8511 TCGA-67-6217 
        7.79        16.01        19.73        32.12        18.15        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-80-5611 TCGA-91-A4BC TCGA-95-7562 TCGA-95-7947 
       52.60        82.68        85.32         1.45         2.86        15.68 
TCGA-95-7948 TCGA-J2-8192 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
       15.65        24.30        21.83        27.19         5.29         2.43 
TCGA-05-5423 TCGA-05-5715 TCGA-38-4627 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 
        4.96         2.04        37.71        44.61        46.98        44.42 
TCGA-44-2659 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6775 TCGA-44-6777 
       44.94        33.73        26.56        28.01        23.18        32.45 
TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 
        7.17        12.66         8.55        13.45        28.57        12.66 
TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR4 
       14.07        29.75        53.29        55.33        22.26        28.90 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
      221.33        71.47       101.72        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
       78.67        48.46        57.53        53.16         3.91        11.05 
TCGA-50-6594 TCGA-53-7626 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
       12.16        30.54        14.30         5.62        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 
       45.34        32.71        40.54        28.67        20.02         3.91 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 
       23.64        29.19         0.36        17.72        17.10        17.62 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        1.58        21.40         3.25        19.99        17.95         4.57 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46R TCGA-62-A46Y TCGA-64-1676 TCGA-64-1679 
       42.38        88.64        56.71        13.61        56.81        81.80 
TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-69-7765 TCGA-69-7974 
       38.37        42.90        20.05        18.84         5.42         6.05 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-5147 
       19.43         8.42        15.35         9.24        50.33        43.82 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7147 TCGA-78-7155 TCGA-78-7163 
       36.66       108.66       163.10        19.27        38.50       238.29 
TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 
       31.20        26.01        10.55       232.18        77.59       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       27.09        12.36         5.88        19.89        35.24         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       24.33         0.79        22.82        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-91-6835 TCGA-91-6847 TCGA-93-7348 
       14.60        13.91        28.34         2.60        27.68        17.46 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 
       19.00        41.82        27.29         2.76        42.25        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
       25.48        18.54        18.12        21.60        21.44        19.76 
TCGA-97-A4M6 TCGA-99-8025 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A5IP 
       18.67        34.85        18.08        35.47        19.00         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
       18.58        15.65        38.63         2.76        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A7XG TCGA-O1-A52J 
       86.04        58.85        41.59        19.13        20.28        59.11 

$subtype2
TCGA-05-4382 TCGA-05-4418 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-44-7670 
       19.96         9.01        15.02        35.28        11.64        29.00 
TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8205 
       48.62         5.79         7.99        23.18        21.44        19.69 
TCGA-55-A491 TCGA-55-A492 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       20.58        19.59        10.55        13.71        16.18         6.12 
TCGA-93-A4JQ TCGA-97-A4M7 TCGA-L9-A443 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       17.29        20.68         6.35        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       45.01         0.00        47.05         2.99        14.96        29.98 
TCGA-05-4432 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 
       25.02        29.00         7.40         5.98         8.68        49.05 
TCGA-44-2668 TCGA-44-5643 TCGA-44-5644 TCGA-44-6779 TCGA-44-7667 TCGA-44-7669 
       25.02        33.30        28.37        16.44        36.07        18.87 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS TCGA-49-4487 TCGA-49-4506 
       23.64        15.98         9.44        13.64        28.11        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 
        8.81        29.46        55.89        22.26        73.12        62.24 
TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-6590 
        8.55       123.58         8.22        14.27         8.45        42.35 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-53-7624 TCGA-55-1594 TCGA-55-1596 
       25.55         6.21         0.72        34.29        38.73        67.89 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6987 TCGA-55-7570 TCGA-55-7576 TCGA-55-7815 
       46.03         3.88        70.26        27.09        22.03        25.41 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 
       11.28        34.19        18.44        19.82        29.23        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-A493 
        5.06        17.79        17.56        15.72        14.47         0.92 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       14.60        49.25        47.80        40.96        29.92        39.09 
TCGA-64-5781 TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
       51.25         6.64         6.12         4.41        13.51         4.24 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-A9RS TCGA-75-5125 TCGA-75-7027 
       23.38        26.30         4.31        11.18        66.64       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7161 
       27.16         5.69        20.58        21.90        19.50         9.57 
TCGA-78-7220 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8669 
       26.53        31.13        34.39        38.04        32.78        30.84 
TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 
       24.23        41.36         1.97        10.19        12.23         7.36 
TCGA-91-8499 TCGA-95-7567 TCGA-95-7944 TCGA-97-8176 TCGA-99-8032 TCGA-99-8033 
        1.18        18.67        12.39        15.39         1.45        21.57 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ 
       86.14        49.35         5.49        29.46        11.05        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-S2-AA1A 
       71.05         0.13        47.08        16.87 

$subtype3
TCGA-05-4384 TCGA-05-4434 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       14.01        15.02        26.30        43.53        38.10        23.93 
TCGA-44-6776 TCGA-44-7661 TCGA-49-6742 TCGA-49-6745 TCGA-50-5932 TCGA-55-7725 
       86.01        18.31        16.04        17.16        40.60        14.53 
TCGA-55-8090 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-73-7498 TCGA-78-7166 
       19.66        13.68        16.93        22.65        39.09         8.48 
TCGA-78-7633 TCGA-95-A4VK TCGA-97-A4LX TCGA-97-A4M2 TCGA-J2-8194 TCGA-MP-A4TA 
       50.24        21.40        20.19        20.52        23.80        31.23 
TCGA-05-4403 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5429 
       19.00        12.00        21.99        26.01        24.00         9.04 
TCGA-35-3615 TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
        0.46       120.79         4.37        42.77         3.19        37.15 
TCGA-44-3398 TCGA-44-6145 TCGA-44-6148 TCGA-44-7659 TCGA-44-A47A TCGA-44-A47G 
       38.24        19.56        23.15        22.72        15.32        11.54 
TCGA-49-4486 TCGA-49-4494 TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 TCGA-50-5939 
       76.21        35.54       164.12        20.52        60.16        15.12 
TCGA-50-5942 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-55-6642 TCGA-55-6983 
       60.72        36.99        36.79        27.25        80.52        92.81 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7574 TCGA-55-7728 TCGA-55-7911 TCGA-55-8087 
       24.99       107.21        32.71        23.15        17.65        15.19 
TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8512 TCGA-55-8513 TCGA-62-8395 
       15.65        22.16        15.42        19.96        26.01        39.98 
TCGA-62-A46U TCGA-62-A46V TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3773 
       67.96        72.30        37.02         2.04        28.47        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-8253 
       12.66        14.73         5.72         4.64        22.68        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-75-6212 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       13.45        26.73        49.84        39.95       119.51        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 
        5.88        22.92       104.19        53.33        39.35        39.75 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8671 TCGA-86-8674 
       20.55         4.57        32.65        31.04        27.58        26.50 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       29.46        13.64        26.47         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       19.82        22.45        23.61        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M5 TCGA-99-7458 
       15.91         5.39        16.41        20.58        20.84        24.56 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4TH 
       36.76        21.63        32.48        14.30        14.53        24.36 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       14.10        73.91        74.33         1.64         0.49         0.43 
TCGA-NJ-A55R 
       19.82 

$subtype4
TCGA-05-4396 TCGA-05-4427 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6761 
        9.96        26.01        29.23         9.37        11.08        11.64 
TCGA-55-7914 TCGA-55-8203 TCGA-55-8204 TCGA-55-A4DF TCGA-64-1677 TCGA-95-7043 
        6.15        17.98        16.93        20.19        20.65        16.54 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M3 TCGA-L9-A444 TCGA-05-4390 TCGA-05-4397 
       18.18        17.92        17.75        10.09        37.02        24.03 
TCGA-05-4424 TCGA-05-4430 TCGA-05-5428 TCGA-38-4625 TCGA-44-3917 TCGA-44-3918 
       30.02        25.02        22.03        97.74        38.89        34.06 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-49-AARE TCGA-4B-A93V 
       23.77        21.63        61.28        19.46        40.41         9.86 
TCGA-50-5051 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 
       15.72        10.13        13.94        35.21        30.58        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-7903 TCGA-55-8085 TCGA-55-8507 TCGA-55-8508 
       40.73        15.25        18.64        29.72        13.74        20.28 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A494 TCGA-62-A46P TCGA-62-A46S 
       14.66        12.33        20.71        15.81        19.53        54.35 
TCGA-62-A470 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-69-7764 TCGA-69-7973 
       39.25        87.98        28.41        20.05        13.61         7.56 
TCGA-69-7979 TCGA-73-4675 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 TCGA-78-7149 
       13.41        30.31         1.25        77.85        85.15       129.53 
TCGA-78-7159 TCGA-78-7167 TCGA-78-7536 TCGA-80-5608 TCGA-86-8054 TCGA-86-8585 
       64.90        88.14         8.02        93.11        37.74        11.61 
TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6828 TCGA-93-A4JO TCGA-95-A4VP TCGA-97-8171 
        0.62         3.81        10.62         1.08        19.89        18.67 
TCGA-97-8179 
       14.30 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.00     0.43     0.62 
subtype1 subtype2 subtype3 subtype4 
  238.29   123.58   164.12   129.53 
subtype1 subtype2 subtype3 subtype4 
   23.41    19.89    22.68    19.89 
[1] "0.4 - 238.3 (23.4)" "0.0 - 123.6 (19.9)" "0.4 - 164.1 (22.7)"
[4] "0.6 - 129.5 (19.9)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       2       40       53        1        22        16         27
  subtype2       2       31       32        0        11        29         21
  subtype3       1       41       34        0        10        20         14
  subtype4       0       21       20        0         7         7         10
          vv
clus       STAGE IIIB STAGE IV
  subtype1          3        6
  subtype2          3        8
  subtype3          2        7
  subtype4          3        4
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           2        2        1        0
  STAGE IA         40       31       41       21
  STAGE IB         53       32       34       20
  STAGE II          1        0        0        0
  STAGE IIA        22       11       10        7
  STAGE IIB        16       29       20        7
  STAGE IIIA       27       21       14       10
  STAGE IIIB        3        3        2        3
  STAGE IV          6        8        7        4
[1] 9 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  54 102  11   4
  subtype2  38  78  17   4
  subtype3  51  60  13   8
  subtype4  28  38   5   3
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       54       38       51       28
  T2      102       78       60       38
  T3       11       17       13        5
  T4        4        4        8        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 102  33    31
  subtype2  90  26    21
  subtype3  91  24    14
  subtype4  50  13    10
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0         102       90       91       50
  N1          33       26       24       13
  N2+N3       31       21       14       10
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 113   6
  subtype2  91   8
  subtype3  93   7
  subtype4  52   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113    6
  subtype2   91    8
  subtype3   93    7
  subtype4   52    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      113       91       93       52
  1        6        8        7        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1 107  65
  subtype2  62  76
  subtype3  76  56
  subtype4  31  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107   65
  subtype2   62   76
  subtype3   76   56
  subtype4   31   43
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      107       62       76       31
  MALE         65       76       56       43
[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"
D3V8, binary
          cls
clus         0   1
  subtype1 139  20
  subtype2 108  19
  subtype3 105  10
  subtype4  58  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139   20
  subtype2  108   19
  subtype3  105   10
  subtype4   58   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       139      108      105       58
  YES       20       19       10       11
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          4                                30
  subtype2                          4                                23
  subtype3                          2                                37
  subtype4                          8                                17
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                117
  subtype2                                                100
  subtype3                                                 64
  subtype4                                                 40
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          1
  subtype3                                          2
  subtype4                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             9
  subtype2                                             2
  subtype3                                             7
  subtype4                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  2
  subtype2                              1                                  0
  subtype3                              0                                  1
  subtype4                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             5
  subtype2                            0                             4
  subtype3                            2                             9
  subtype4                            0                             5
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
  subtype4                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             2
  subtype2                                             1
  subtype3                                             0
  subtype4                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            1
  subtype3                            8
  subtype4                            1
D3V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4        4        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        30       23       37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      117      100       64
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        1        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             9        2        7
  LUNG CLEAR CELL ADENOCARCINOMA                            1        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        2
  LUNG PAPILLARY ADENOCARCINOMA                             5        4        9
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        1        0
  MUCINOUS (COLLOID) CARCINOMA                              0        1        8
                                                    clus
vv                                                   subtype4
  LUNG ACINAR ADENOCARCINOMA                                8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       40
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1
  LUNG CLEAR CELL ADENOCARCINOMA                            0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0
  LUNG MUCINOUS ADENOCARCINOMA                              0
  LUNG PAPILLARY ADENOCARCINOMA                             5
  LUNG SIGNET RING ADENOCARCINOMA                           0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2
  MUCINOUS (COLLOID) CARCINOMA                              1
[1] 12  4
[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 113   4   1  10
  subtype2  96   4   1   6
  subtype3  86   3   2   6
  subtype4  49   2   0   4
D3V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      113       96       86       49
  R1        4        4        3        2
  R2        1        1        2        0
  RX       10        6        6        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        23
  subtype2                                0     3                        15
  subtype3                                0     1                         8
  subtype4                                0     1                         6
          vv
clus       WHITE
  subtype1   128
  subtype2    98
  subtype3   108
  subtype4    56
D3V14, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   2        3        1        1
  BLACK OR AFRICAN AMERICAN              23       15        8        6
  WHITE                                 128       98      108       56
[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"
D3V15, binary
          cls
clus         0   1
  subtype1   1 131
  subtype2   4  97
  subtype3   1 102
  subtype4   1  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  131
  subtype2    4   97
  subtype3    1  102
  subtype4    1   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        4        1        1
  NOT HISPANIC OR LATINO      131       97      102       54
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1  90  64
  subtype2 109  59
  subtype3  87  38
subtype1 subtype2 subtype3 
     154      168      125 
subtype1 subtype2 subtype3 
      64       59       38 
$subtype1
TCGA-05-4384 TCGA-05-5420 TCGA-38-4631 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       14.01        15.02        11.64        86.01        29.00        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-49-AAR0 TCGA-55-A492 TCGA-55-A4DF 
        9.37        11.08        16.04       156.66        19.59        20.19 
TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7043 
        8.48        50.24        85.32        16.18         1.45        16.54 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-A4M3 TCGA-L9-A443 TCGA-MP-A4TA TCGA-05-4390 
       15.68        21.40        17.75         6.35        31.23        37.02 
TCGA-05-4415 TCGA-05-4424 TCGA-05-5425 TCGA-35-5375 TCGA-44-5643 TCGA-44-6144 
        2.99        30.02        29.00         8.68        33.30        23.77 
TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-A4SS 
       21.63        61.28        19.46        36.07        18.87        13.64 
TCGA-44-A4SU TCGA-49-4490 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 
       13.45        12.66        55.89        53.29        22.26        73.12 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5072 TCGA-50-5930 
        8.55        40.41       221.33         9.86         8.22         9.27 
TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       14.27         8.45        15.12        53.16         3.91        25.55 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 
        0.72        10.13        34.29        35.21        30.58        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-7570 TCGA-55-7910 
       40.73        15.25        53.65         3.88        27.09        34.19 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8096 TCGA-55-8505 
       18.44        29.23        29.72        17.79        23.64        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       13.74        20.28        17.72        17.10        17.62        14.66 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 TCGA-62-8398 
       12.33        20.71        21.40         3.25         4.57        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 
       88.64        49.25        47.80        54.35        39.25        40.96 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-69-7764 
       81.80        38.37        87.98        42.90        28.41        13.61 
TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-73-7499 
        7.56        13.41        13.51        14.01         4.24        50.33 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 
       11.18        77.85        43.82        85.15        36.66       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 
       27.16         5.69        20.58       129.53        21.90        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7162 TCGA-78-7220 TCGA-78-7536 TCGA-78-8640 
       38.50        32.09       104.19        26.53         8.02       232.18 
TCGA-78-8662 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
      110.50        12.36        34.39        38.04        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8585 
       35.24        37.74         4.08        22.82        21.47        11.61 
TCGA-86-8669 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
       30.84        26.50         3.81        41.36        10.19        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-93-A4JP TCGA-95-A4VP 
       27.68         7.36         1.15         1.18        19.00        19.89 
TCGA-97-8171 TCGA-97-8176 TCGA-97-8179 TCGA-99-8032 TCGA-J2-A4AD TCGA-L4-A4E5 
       18.67        15.39        14.30         1.45        18.08        19.00 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4TF TCGA-NJ-A55R 
        1.91        18.58        11.05        19.82 

$subtype2
TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-38-6178 TCGA-44-6146 TCGA-44-6147 
        9.96        20.05        26.01        14.73        23.93        27.78 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-7284 
       17.16        11.64        37.32        40.60        41.69         7.99 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.66        17.98        19.69        32.12        18.15 
TCGA-55-A491 TCGA-73-4658 TCGA-78-8660 TCGA-91-6836 TCGA-93-8067 TCGA-95-7562 
       20.58        52.60        10.55        13.71         6.12         2.86 
TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A444 
       15.65        18.18        17.92        20.68        23.80        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4417 TCGA-05-4425 
       27.19         5.29         2.43        10.09        14.96        21.99 
TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-38-4632 TCGA-44-2656 
       24.00        22.03         9.04         2.04        44.61        46.98 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 
        3.19        25.02        38.89        34.06        26.56        28.37 
TCGA-44-6775 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 
       23.18        16.44        22.72         7.17        23.64        12.66 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 TCGA-50-5051 TCGA-50-5933 
        8.55        15.32         9.44        28.57        15.72        78.67 
TCGA-50-5941 TCGA-50-6593 TCGA-50-6594 TCGA-53-7813 TCGA-55-6642 TCGA-55-6712 
       48.46        11.05        12.16        13.94        80.52         5.62 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 
       45.34        32.71        92.81        40.54       107.21        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
       28.67        20.02        22.03         3.91        25.41        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8092 TCGA-55-8301 
       11.28        17.65        19.82        23.08         5.06        17.56 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8616 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       15.72         0.36         1.58         0.92        15.81        19.99 
TCGA-62-8395 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       39.98        19.53        56.71        67.96        72.30        13.61 
TCGA-62-A472 TCGA-64-5775 TCGA-64-5815 TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 
       29.92         2.04        28.47        14.73         5.72         6.64 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-A59K TCGA-71-6725 
       22.68         5.42         6.05         4.41        19.43         8.42 
TCGA-71-8520 TCGA-73-4676 TCGA-75-5125 TCGA-78-7143 TCGA-78-7147 TCGA-78-7152 
        6.90         9.24        66.64       163.10        19.27        39.95 
TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 
      119.51         5.88        64.90         9.57        88.14        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-80-5608 
       53.33        26.01        39.35        10.55        77.59        93.11 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       27.09         5.88        31.13         4.57        24.33         0.79 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
       31.04        31.20        14.60         0.62        28.34        29.46 
TCGA-86-A4JF TCGA-91-6828 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
       24.23        10.62        23.61        41.82        18.67        27.29 
TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M0 
        2.76        25.48        18.54        18.12        21.60        21.44 
TCGA-99-8025 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       34.85        35.47        32.48        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TK 
       58.45        49.35        58.85         5.49        29.46        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
       73.91        71.05        74.33         0.13         1.64        20.28 

$subtype3
TCGA-38-7271 TCGA-44-7661 TCGA-50-5935 TCGA-55-6978 TCGA-55-6979 TCGA-55-7573 
       26.30        18.31        21.47         5.79         7.79        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 TCGA-55-8619 
       23.18        14.53        21.44        19.73        16.93        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-67-6217 TCGA-73-7498 TCGA-93-A4JQ TCGA-97-A4LX 
       16.93        22.65        13.87        39.09        17.29        20.19 
TCGA-97-A4M2 TCGA-J2-8192 TCGA-L9-A743 TCGA-05-5423 TCGA-38-A44F TCGA-44-2665 
       20.52        24.30        21.83         4.96         4.37        42.77 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6777 TCGA-44-A479 TCGA-44-A47G 
       28.01        19.56        23.15        32.45        15.98        11.54 
TCGA-49-4487 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
       28.11        29.75        55.33        22.26        62.24        28.90 
TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
      123.58       164.12        20.52        71.47       101.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6595 
       47.41        49.28        60.72        57.53        42.35         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-6543 TCGA-55-6971 
       36.99        36.79        27.25        30.54        14.30        46.03 
TCGA-55-6980 TCGA-55-6984 TCGA-55-6987 TCGA-55-7574 TCGA-55-7728 TCGA-55-7816 
       69.34        24.99        70.26        32.71        23.15        15.39 
TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8512 
       15.19        15.65        29.19        22.16        15.42        19.96 
TCGA-55-8513 TCGA-55-A57B TCGA-62-8397 TCGA-64-5781 TCGA-67-6216 TCGA-69-7761 
       26.01        17.95        42.38        51.25         4.64         6.12 
TCGA-69-8254 TCGA-69-8453 TCGA-75-6212 TCGA-75-7025 TCGA-78-7160 TCGA-78-7163 
       13.45        26.73        49.84       108.66        22.92       238.29 
TCGA-78-8648 TCGA-86-7714 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 
       39.75        20.55        32.65        23.05        13.91        27.58 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-8496 TCGA-91-8497 
       13.64        26.47         1.97         2.60        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7944 TCGA-97-7546 
       19.82        22.45        17.46         1.08        12.39        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 
       64.60        63.52        61.48         0.59        15.91         5.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       16.41        20.58        19.76        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 
       36.76        21.57        21.63        14.30        14.53        15.65 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       37.35        86.04        41.59        24.36        14.10        11.15 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J TCGA-S2-AA1A 
       47.08         0.49         0.43        59.11        16.87 

subtype1 subtype2 subtype3 
    0.72     0.13     0.43 
subtype1 subtype2 subtype3 
  232.18   163.10   238.29 
subtype1 subtype2 subtype3 
   20.04    20.43    22.16 
[1] "0.7 - 232.2 (20.0)" "0.1 - 163.1 (20.4)" "0.4 - 238.3 (22.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       4       36       39        0        19        15         28
  subtype2       0       29       58        0        15        31         27
  subtype3       1       54       27        1        15        16          9
          vv
clus       STAGE IIIB STAGE IV
  subtype1          4       10
  subtype2          4        6
  subtype3          1        4
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           4        0        1
  STAGE IA         36       29       54
  STAGE IB         39       58       27
  STAGE II          0        0        1
  STAGE IIA        19       15       15
  STAGE IIB        15       31       16
  STAGE IIIA       28       27        9
  STAGE IIIB        4        4        1
  STAGE IV         10        6        4
[1] 9 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  51  87  12   5
  subtype2  39 104  21   8
  subtype3  65  52   8   3
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       51       39       65
  T2       87      104       52
  T3       12       21        8
  T4        5        8        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  97  25    32
  subtype2 112  33    25
  subtype3  90  25     9
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          97      112       90
  N1          25       33       25
  N2+N3       32       25        9
[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 102  10
  subtype2 118   6
  subtype3  75   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102   10
  subtype2  118    6
  subtype3   75    3
   clus
vv  subtype1 subtype2 subtype3
  0      102      118       75
  1       10        6        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"
D4V7, binary
          cls
clus        0  1
  subtype1 63 93
  subtype2 90 82
  subtype3 91 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   93
  subtype2   90   82
  subtype3   91   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       63       90       91
  MALE         93       82       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus         0   1
  subtype1 120  26
  subtype2 146  12
  subtype3 111  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  120   26
  subtype2  146   12
  subtype3  111   17
     clus
vv    subtype1 subtype2 subtype3
  NO       120      146      111
  YES       26       12       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          9                                30
  subtype2                          4                                40
  subtype3                          5                                22
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 98
  subtype2                                                109
  subtype3                                                 74
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          1
  subtype3                                          4
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             3
  subtype2                                             7
  subtype3                                             9
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  0
  subtype2                              0                                  1
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             9
  subtype2                            1                             6
  subtype3                            1                             7
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             3
  subtype2                                             2
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            3
  subtype2                            1
  subtype3                            6
D4V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                9        4        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        30       40       22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       98      109       74
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             3        7        9
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1        1
  LUNG MUCINOUS ADENOCARCINOMA                              0        1        1
  LUNG PAPILLARY ADENOCARCINOMA                             9        6        7
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             3        2        0
  MUCINOUS (COLLOID) CARCINOMA                              3        1        6
[1] 12  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  98   4   0   8
  subtype2 117   5   0   9
  subtype3  80   2   1   6
D4V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       98      117       80
  R1        4        5        2
  R2        0        0        1
  RX        8        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        20   119
  subtype2     4                        12   132
  subtype3     0                        18   102
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        4        0
  BLACK OR AFRICAN AMERICAN       20       12       18
  WHITE                          119      132      102
[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   5 113
  subtype2   2 120
  subtype3   0 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  113
  subtype2    2  120
  subtype3    0  110
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        0
  NOT HISPANIC OR LATINO      113      120      110
[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 54 32
  subtype2 15  7
  subtype3 33 33
  subtype4 43 30
  subtype5 68 39
subtype1 subtype2 subtype3 subtype4 subtype5 
      86       22       66       73      107 
subtype1 subtype2 subtype3 subtype4 subtype5 
      32        7       33       30       39 
$subtype1
TCGA-05-4405 TCGA-38-6178 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-49-4501 
       20.05        14.73        38.10        23.93        27.78        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 
       17.16        11.64        41.69        23.05         7.79        16.01 
TCGA-67-6217 TCGA-93-A4JQ TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       13.87        17.29        20.68         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-35-4123 TCGA-44-2656 
       27.19        25.02         4.96         9.04         5.98        46.98 
TCGA-44-2665 TCGA-44-3918 TCGA-44-3919 TCGA-44-5645 TCGA-44-6775 TCGA-44-6777 
       42.77        34.06        33.73        28.01        23.18        32.45 
TCGA-44-A4SS TCGA-49-4488 TCGA-49-4505 TCGA-49-4512 TCGA-49-6767 TCGA-49-AARO 
       13.64        28.57        14.07        29.75        22.26       123.58 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       71.47       101.72        49.28        14.27        78.67         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6593 TCGA-50-6673 
       48.46        60.72        57.53        42.35        11.05         0.72 
TCGA-50-8457 TCGA-50-8460 TCGA-55-6712 TCGA-55-6969 TCGA-55-6981 TCGA-55-6982 
       36.99        27.25         5.62        40.73        45.34        32.71 
TCGA-55-7911 TCGA-62-A46R TCGA-62-A46V TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
       17.65        56.71        72.30        56.81        81.80        38.37 
TCGA-64-5778 TCGA-64-5815 TCGA-67-6215 TCGA-67-6216 TCGA-71-6725 TCGA-73-4676 
       42.90        28.47         5.72         4.64         8.42         9.24 
TCGA-75-6206 TCGA-78-7535 TCGA-86-6562 TCGA-86-6851 TCGA-86-8055 TCGA-86-8075 
       85.15        31.20        12.36         5.88         4.08        22.82 
TCGA-86-8279 TCGA-86-8668 TCGA-86-8671 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       31.20        13.91        27.58        10.62        41.36         1.97 
TCGA-91-6835 TCGA-91-6840 TCGA-91-8496 TCGA-93-A4JO TCGA-95-7039 TCGA-97-A4M0 
        2.60        12.23        16.60         1.08        41.82        21.44 
TCGA-J2-A4AG TCGA-MP-A4TK 
       32.48        19.13 

$subtype2
TCGA-05-4384 TCGA-05-4402 TCGA-05-4434 TCGA-95-7947 TCGA-05-4249 TCGA-05-4250 
       14.01         8.02        15.02        15.68        50.07         3.98 
TCGA-44-2664 TCGA-44-8117 TCGA-49-4510 TCGA-49-6744 TCGA-50-5066 TCGA-86-8073 
       41.13        12.66        29.46        55.33        47.41        24.33 
TCGA-93-A4JP TCGA-97-7546 TCGA-97-7941 TCGA-97-A4M6 TCGA-J2-A4AD TCGA-L4-A4E6 
       19.00        42.25        15.91        18.67        18.08        14.30 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YI 
       41.59        24.36        73.91         0.13 

$subtype3
TCGA-05-4396 TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F TCGA-49-AAR0 TCGA-73-7498 
        9.96        86.01        29.23        11.08       156.66        39.09 
TCGA-78-7633 TCGA-91-7771 TCGA-95-7948 TCGA-95-A4VK TCGA-MP-A4T8 TCGA-MP-A4TD 
       50.24        16.18        15.65        21.40         5.29        10.09 
TCGA-05-4417 TCGA-05-4422 TCGA-35-3615 TCGA-44-4112 TCGA-44-A47A TCGA-44-A4SU 
       14.96        12.00         0.46        26.56        15.32        13.45 
TCGA-49-4486 TCGA-50-5051 TCGA-55-8507 TCGA-55-A494 TCGA-62-8395 TCGA-62-A46O 
       76.21        15.72        13.74        15.81        39.98        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-64-1680 TCGA-69-7760 TCGA-71-8520 TCGA-73-4675 
       19.53        54.35        37.02         6.64         6.90        30.31 
TCGA-75-6212 TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
       49.84       163.10        19.27        20.58       129.53       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
       38.50        32.09         5.88         9.57       104.19        88.14 
TCGA-78-7537 TCGA-78-7539 TCGA-78-8662 TCGA-86-7713 TCGA-86-7954 TCGA-86-8056 
       53.33        26.01       110.50        38.04        19.89         4.57 
TCGA-86-8074 TCGA-86-8278 TCGA-86-8280 TCGA-86-8669 TCGA-86-A4D0 TCGA-93-A4JN 
        0.79        31.04        23.05        30.84         3.81        23.61 
TCGA-99-7458 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T2 
       24.56        14.53         1.91        18.58        58.45        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-NJ-A4YG TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       58.85         5.49        74.33         0.43        20.28        59.11 

$subtype4
TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-55-6978 TCGA-80-5611 TCGA-91-6836 
        9.01        26.01        28.41         5.79        85.32        13.71 
TCGA-95-7043 TCGA-95-A4VN TCGA-05-4397 TCGA-05-4398 TCGA-05-4420 TCGA-05-5715 
       16.54        18.18        24.03        47.05        29.98         2.04 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 
        7.40         8.68        97.74        38.89        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 TCGA-44-A479 
       23.77        19.56        16.44        19.46        18.87        15.98 
TCGA-49-4487 TCGA-49-4507 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
       28.11         8.81        53.29        22.26        62.24        28.90 
TCGA-49-AARE TCGA-4B-A93V TCGA-50-5044 TCGA-50-5072 TCGA-50-5946 TCGA-50-6591 
       40.41         9.86        20.52         8.22        53.16         3.91 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 
       34.29        35.21        38.73        67.89        30.58        46.03 
TCGA-55-8620 TCGA-62-8394 TCGA-62-8398 TCGA-62-A471 TCGA-64-5774 TCGA-64-5779 
       12.33         4.57        14.60        40.96        87.98        28.41 
TCGA-64-5781 TCGA-69-8255 TCGA-69-A59K TCGA-73-A9RS TCGA-75-5125 TCGA-75-7027 
       51.25         4.24        19.43        11.18        66.64       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7150 TCGA-78-7536 TCGA-83-5908 TCGA-86-8054 
       27.16         5.69        21.90         8.02        27.09        37.74 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-91-6847 TCGA-91-8499 TCGA-95-7567 
       21.47        14.60        11.61        27.68         1.18        18.67 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4TE TCGA-NJ-A4YF 
       15.65        38.63        86.14        86.04        29.46        71.05 
TCGA-NJ-A55R 
       19.82 

$subtype5
TCGA-05-5420 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 TCGA-49-AARN 
       15.02        18.31        29.00         9.37        16.04        37.32 
TCGA-50-5932 TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-91-A4BC TCGA-97-A4M2 
       40.60        20.65        52.60         8.48         1.45        20.52 
TCGA-J2-8192 TCGA-J2-8194 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4426 TCGA-05-5425 
       24.30        23.80        31.23         2.43        26.01        29.00 
TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 TCGA-44-2668 TCGA-44-3396 
      120.79        37.71         4.37        44.42        25.02        37.15 
TCGA-44-3398 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-7659 TCGA-44-7662 
       38.24        23.15        21.63        61.28        22.72         7.17 
TCGA-44-7667 TCGA-44-7672 TCGA-44-A47G TCGA-49-4494 TCGA-49-4506 TCGA-49-4514 
       36.07        23.64        11.54        35.54        32.84        55.89 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARR TCGA-50-5930 TCGA-50-5939 TCGA-50-6592 
       73.12         8.55       164.12         9.27        15.12        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-53-7626 TCGA-53-7813 
       12.16         6.21        10.13        36.79        30.54        13.94 
TCGA-55-6543 TCGA-55-6970 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 
       14.30        15.25        32.71        23.15        25.41        34.19 
TCGA-55-8505 TCGA-55-8506 TCGA-64-1678 TCGA-67-3771 TCGA-69-7761 TCGA-69-7763 
       14.47         0.36        39.09        20.05         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-73-4659 TCGA-73-4670 TCGA-73-7499 TCGA-75-6214 
       13.61         5.42        23.38         4.31        50.33        36.66 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7540 
       39.95        19.50        64.90        22.92       238.29        39.35 
TCGA-78-7542 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7955 
       10.55        93.11        31.13        34.39        32.78        35.24 
TCGA-86-8076 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       32.65        28.34        29.46        24.23        13.64        26.47 
TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 
       10.19         7.36         1.15        14.27        19.82        17.46 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       12.39        19.89        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-8179 TCGA-97-A4M5 TCGA-99-8028 TCGA-L4-A4E5 TCGA-MP-A4SY 
        0.59        14.30        20.84        36.76        19.00        49.35 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A55A TCGA-S2-AA1A 
       11.05        14.10        11.15         0.49        16.87 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.72     0.13     0.43     1.18     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 
  123.58    73.91   163.10   100.57   238.29 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.555   18.835   23.330   24.030   23.150 
[1] "0.7 - 123.6 (23.6)" "0.1 - 73.9 (18.8)"  "0.4 - 163.1 (23.3)"
[4] "1.2 - 100.6 (24.0)" "0.4 - 238.3 (23.1)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       30       23        0        10        13         11
  subtype2       0        8        6        0         1         1          4
  subtype3       0       11       20        0         8        10          9
  subtype4       0       14       20        1         5        14         13
  subtype5       1       31       26        0        11        13         20
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        1
  subtype2          0        3
  subtype3          3        6
  subtype4          3        4
  subtype5          1        3
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        0        0        1
  STAGE IA         30        8       11       14       31
  STAGE IB         23        6       20       20       26
  STAGE II          0        0        0        1        0
  STAGE IIA        10        1        8        5       11
  STAGE IIB        13        1       10       14       13
  STAGE IIIA       11        4        9       13       20
  STAGE IIIB        1        0        3        3        1
  STAGE IV          1        3        6        4        3
[1] 9 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 35 50  5  1
  subtype2  8 12  1  1
  subtype3 15 39  6  7
  subtype4 19 46  6  4
  subtype5 40 56 10  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       35        8       15       19       40
  T2       50       12       39       46       56
  T3        5        1        6        6       10
  T4        1        1        7        4        3
[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 54 20    13
  subtype2 14  4     3
  subtype3 44 14     8
  subtype4 41 20    14
  subtype5 72 14    21
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          54       14       44       41       72
  N1          20        4       14       20       14
  N2+N3       13        3        8       14       21
[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"
D5V6, binary
          cls
clus        0  1
  subtype1 67  1
  subtype2 15  3
  subtype3 51  6
  subtype4 50  4
  subtype5 76  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    1
  subtype2   15    3
  subtype3   51    6
  subtype4   50    4
  subtype5   76    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       67       15       51       50       76
  1        1        3        6        4        3
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 57 34
  subtype2 15  8
  subtype3 32 35
  subtype4 35 40
  subtype5 57 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   34
  subtype2   15    8
  subtype3   32   35
  subtype4   35   40
  subtype5   57   52
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       57       15       32       35       57
  MALE         34        8       35       40       52
[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"
D5V8, binary
          cls
clus        0  1
  subtype1 72 12
  subtype2 16  4
  subtype3 55  4
  subtype4 54 14
  subtype5 87 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   12
  subtype2   16    4
  subtype3   55    4
  subtype4   54   14
  subtype5   87   12
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        72       16       55       54       87
  YES       12        4        4       14       12
[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"
D5V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          2                                12
  subtype2                          2                                 8
  subtype3                          1                                22
  subtype4                          3                                17
  subtype5                          4                                15
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 67
  subtype2                                                 10
  subtype3                                                 35
  subtype4                                                 50
  subtype5                                                 71
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          1
  subtype2                                          0
  subtype3                                          0
  subtype4                                          0
  subtype5                                          4
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             3
  subtype2                                             1
  subtype3                                             5
  subtype4                                             0
  subtype5                                             4
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              0                                  0
  subtype3                              0                                  1
  subtype4                              1                                  0
  subtype5                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             4
  subtype2                            0                             2
  subtype3                            0                             2
  subtype4                            0                             0
  subtype5                            1                             5
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             0
  subtype3                                             0
  subtype4                                             4
  subtype5                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            1
  subtype2                            0
  subtype3                            1
  subtype4                            0
  subtype5                            3
D5V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                2        2        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        12        8       22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       67       10       35
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                1        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             3        1        5
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             4        2        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        0
  MUCINOUS (COLLOID) CARCINOMA                              1        0        1
                                                    clus
vv                                                   subtype4 subtype5
  LUNG ACINAR ADENOCARCINOMA                                3        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        17       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       50       71
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             0        4
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              0        1
  LUNG PAPILLARY ADENOCARCINOMA                             0        5
  LUNG SIGNET RING ADENOCARCINOMA                           0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             4        0
  MUCINOUS (COLLOID) CARCINOMA                              0        3
[1] 12  5
[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 59  3  0  5
  subtype2 12  0  3  5
  subtype3 50  3  0  4
  subtype4 50  1  0  3
  subtype5 64  3  0  4
D5V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       59       12       50       50       64
  R1        3        0        3        1        3
  R2        0        3        0        0        0
  RX        5        5        4        3        4
[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     1                         6    73
  subtype2     1                         3    13
  subtype3     1                         6    52
  subtype4     1                        12    50
  subtype5     1                        12    87
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        1        1        1
  BLACK OR AFRICAN AMERICAN        6        3        6       12       12
  WHITE                           73       13       52       50       87
[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"
D5V15, binary
          cls
clus        0  1
  subtype1  1 68
  subtype2  0 15
  subtype3  0 42
  subtype4  3 51
  subtype5  2 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   68
  subtype2    0   15
  subtype3    0   42
  subtype4    3   51
  subtype5    2   85
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        0        3        2
  NOT HISPANIC OR LATINO       68       15       42       51       85
[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(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 96 65
  subtype2 75 55
  subtype3 42 21
subtype1 subtype2 subtype3 
     161      130       63 
subtype1 subtype2 subtype3 
      65       55       21 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96         8.02        20.05        15.02        15.02 
TCGA-38-6178 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       14.73        38.10        23.93        27.78        86.01        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5932 
       11.08        46.72        16.04        11.64       156.66        40.60 
TCGA-50-6597 TCGA-55-1592 TCGA-55-7573 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 
       41.69        23.05        16.01        13.87        52.60        39.09 
TCGA-78-7633 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7948 TCGA-97-A4M7 
       50.24        16.18         1.45        17.29        15.65        20.68 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4398 
        6.35        21.83         2.43        10.09        50.07        47.05 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       12.00        26.01        25.02         4.96        29.00         9.04 
TCGA-35-3615 TCGA-38-4626 TCGA-38-A44F TCGA-44-2656 TCGA-44-3918 TCGA-44-3919 
        0.46       120.79         4.37        46.98        34.06        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6777 TCGA-44-8117 TCGA-44-A47A 
       26.56        28.01        23.77        32.45        12.66        15.32 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 
       13.45        76.21        28.57        35.54        14.07        29.46 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-AARO TCGA-49-AARR TCGA-50-5045 
       29.75        53.29        55.33       123.58       164.12        71.47 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5936 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 
       15.72        49.28         8.45        60.72        57.53        11.05 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8460 TCGA-55-6970 TCGA-55-6981 TCGA-55-6982 
        0.72        36.99        27.25        15.25        45.34        32.71 
TCGA-55-7815 TCGA-55-8505 TCGA-55-8507 TCGA-55-A494 TCGA-62-8395 TCGA-62-A46P 
       25.41        14.47        13.74        15.81        39.98        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
       56.71        72.30        81.80        37.02        38.37        42.90 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-71-6725 TCGA-73-4659 
        5.72         4.64         6.64        22.68         8.42        23.38 
TCGA-73-4675 TCGA-73-4676 TCGA-75-6206 TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 
       30.31         9.24        85.15        49.84       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
       19.27        20.58       129.53       119.51        32.09         5.88 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-8662 
        9.57       104.19        88.14        53.33        26.01       110.50 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       12.36        38.04        19.89         4.57        24.33        22.82 
TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6828 
       23.05        13.91        30.84        27.58        26.47        10.62 
TCGA-91-6835 TCGA-91-6840 TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-93-A4JO 
        2.60        12.23        16.60        14.27        23.61         1.08 
TCGA-93-A4JP TCGA-95-7944 TCGA-97-7937 TCGA-97-7941 TCGA-97-8179 TCGA-97-A4M0 
       19.00        12.39        18.54        15.91        14.30        21.44 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-J2-A4AD TCGA-L4-A4E6 
       20.84        18.67        24.56        36.76        18.08        14.30 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 
       14.53        18.58        58.45        37.35        58.85        41.59 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        14.10        11.15        73.91        74.33         0.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

$subtype2
TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-44-8119 TCGA-49-6745 TCGA-49-AARN 
        9.01        26.01        28.41         9.37        17.16        37.32 
TCGA-55-6978 TCGA-55-6979 TCGA-80-5611 TCGA-91-6836 TCGA-95-7043 TCGA-95-A4VN 
        5.79         7.79        85.32        13.71        16.54        18.18 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4397 
       10.09        27.19         5.29        31.23         3.98        24.03 
TCGA-05-4417 TCGA-05-4420 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       14.96        29.98         2.04         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-44-2664 TCGA-44-2665 TCGA-44-3917 TCGA-44-5643 
       97.74        37.71        41.13        42.77        38.89        33.30 
TCGA-44-5644 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
       28.37        19.56        23.15        23.18        61.28        16.44 
TCGA-44-7660 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4506 
       19.46        15.98        11.54        13.64        28.11        32.84 
TCGA-49-4507 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE 
        8.81        22.26        22.26        62.24        28.90        40.41 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 
        9.86        20.52       101.72        47.41         8.22        14.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       78.67        15.12        48.46        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-8459 TCGA-53-7624 TCGA-53-A4EZ 
       25.55        12.16         6.21        36.79        34.29        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
       38.73        67.89        30.58         5.62        40.73        46.03 
TCGA-55-7911 TCGA-55-8506 TCGA-55-8620 TCGA-62-8394 TCGA-62-8398 TCGA-62-A46O 
       17.65         0.36        12.33         4.57        14.60        47.80 
TCGA-62-A471 TCGA-64-1676 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       40.96        56.81        87.98        28.41        51.25        28.47 
TCGA-67-3771 TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 TCGA-73-A9RS TCGA-75-5125 
       20.05         4.24        19.43         6.90        11.18        66.64 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7535 
      100.57         5.69        21.90        19.50        38.50        31.20 
TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        8.02        27.09         5.88        35.24        37.74         4.08 
TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-A456 TCGA-86-A4D0 
        0.79        31.20        21.47        11.61        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6847 
       24.23        13.64        41.36         1.97        10.19        27.68 
TCGA-91-6848 TCGA-91-8499 TCGA-95-7039 TCGA-95-7567 TCGA-J2-A4AG TCGA-L4-A4E5 
        7.36         1.18        41.82        18.67        32.48        19.00 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 
        1.91        15.65        38.63        86.14        49.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TK TCGA-NJ-A4YF 
        5.49        29.46        19.13        71.05 

$subtype3
TCGA-44-7661 TCGA-44-7670 TCGA-64-1677 TCGA-78-7166 TCGA-95-7947 TCGA-95-A4VK 
       18.31        29.00        20.65         8.48        15.68        21.40 
TCGA-97-A4M2 TCGA-J2-8192 TCGA-J2-8194 TCGA-44-2657 TCGA-44-2668 TCGA-44-3396 
       20.52        24.30        23.80        44.42        25.02        37.15 
TCGA-44-3398 TCGA-44-6774 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       38.24        21.63        22.72         7.17        36.07        18.87 
TCGA-44-7672 TCGA-49-4514 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-50-5930 TCGA-50-7109 
       23.64        55.89        73.12         8.55         9.27        10.13 
TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 TCGA-55-7574 TCGA-55-7728 TCGA-55-7910 
       30.54        13.94        14.30        32.71        23.15        34.19 
TCGA-62-A46S TCGA-64-1678 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-73-4670 
       54.35        39.09         6.12        13.61         5.42         4.31 
TCGA-73-7499 TCGA-75-6214 TCGA-78-7152 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 
       50.33        36.66        39.95        64.90        22.92       238.29 
TCGA-78-7540 TCGA-78-7542 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 
       39.35        10.55        93.11        31.13        34.39        32.78 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8673 TCGA-91-6849 TCGA-91-A4BD 
       32.65        31.04        14.60        28.34         1.15        19.82 
TCGA-93-7348 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       17.46        19.89        42.25        63.52        61.48        25.48 
TCGA-97-7938 TCGA-MP-A4TF TCGA-NJ-A55A 
        0.59        11.05         0.49 

subtype1 subtype2 subtype3 
    0.13     0.36     0.49 
subtype1 subtype2 subtype3 
  164.12   101.72   238.29 
subtype1 subtype2 subtype3 
  23.050   22.705   23.800 
[1] "0.1 - 164.1 (23.1)" "0.4 - 101.7 (22.7)" "0.5 - 238.3 (23.8)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       50       40        0        14        20         27
  subtype2       1       27       38        1        13        26         20
  subtype3       0       17       17        0         8         5         10
          vv
clus       STAGE IIIB STAGE IV
  subtype1          4        9
  subtype2          3        5
  subtype3          1        3
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA         50       27       17
  STAGE IB         40       38       17
  STAGE II          0        1        0
  STAGE IIA        14       13        8
  STAGE IIB        20       26        5
  STAGE IIIA       27       20       10
  STAGE IIIB        4        3        1
  STAGE IV          9        5        3
[1] 9 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 61 86  9 10
  subtype2 34 83 15  3
  subtype3 22 34  4  3
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       61       34       22
  T2       86       83       34
  T3        9       15        4
  T4       10        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+N3
  subtype1 102  31    27
  subtype2  81  33    21
  subtype3  42   8    11
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         102       81       42
  N1          31       33        8
  N2+N3       27       21       11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1 121   9
  subtype2  97   5
  subtype3  41   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  121    9
  subtype2   97    5
  subtype3   41    3
   clus
vv  subtype1 subtype2 subtype3
  0      121       97       41
  1        9        5        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"
D6V7, binary
          cls
clus        0  1
  subtype1 91 76
  subtype2 68 67
  subtype3 37 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91   76
  subtype2   68   67
  subtype3   37   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       91       68       37
  MALE         76       67       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1 133  17
  subtype2  98  22
  subtype3  53   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  133   17
  subtype2   98   22
  subtype3   53    7
     clus
vv    subtype1 subtype2 subtype3
  NO       133       98       53
  YES       17       22        7
[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"
D6V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                42
  subtype2                          3                                21
  subtype3                          4                                11
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 94
  subtype2                                                103
  subtype3                                                 36
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          0
  subtype3                                          3
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             8
  subtype2                                             1
  subtype3                                             4
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  2
  subtype2                              0                                  0
  subtype3                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             8
  subtype2                            1                             1
  subtype3                            0                             4
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             4
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            3
  subtype2                            1
  subtype3                            1
D6V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        3        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        42       21       11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       94      103       36
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             8        1        4
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             8        1        4
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        4        0
  MUCINOUS (COLLOID) CARCINOMA                              3        1        1
[1] 12  3
[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 110   6   2  13
  subtype2  88   3   1   5
  subtype3  37   1   0   3
D6V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      110       88       37
  R1        6        3        1
  R2        2        1        0
  RX       13        5        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        14   126
  subtype2     3                        19    94
  subtype3     0                         6    55
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        3        0
  BLACK OR AFRICAN AMERICAN       14       19        6
  WHITE                          126       94       55
[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"
D6V15, binary
          cls
clus         0   1
  subtype1   0 117
  subtype2   4  95
  subtype3   2  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  117
  subtype2    4   95
  subtype3    2   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        4        2
  NOT HISPANIC OR LATINO      117       95       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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 80 49
  subtype2 87 30
  subtype3 34 55
  subtype4 78 35
  subtype5 41 14
subtype1 subtype2 subtype3 subtype4 subtype5 
     129      117       89      113       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      49       30       55       35       14 
$subtype1
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 TCGA-38-6178 
       19.96         8.02        20.05        26.01        28.41        14.73 
TCGA-44-2662 TCGA-49-6761 TCGA-55-1595 TCGA-55-6979 TCGA-55-8511 TCGA-55-A491 
       42.08        11.64        48.62         7.79        18.15        20.58 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-91-6836 TCGA-95-7562 TCGA-95-7948 
       20.65        52.60        82.68        13.71         2.86        15.65 
TCGA-97-A4LX TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TC 
       20.19        24.30         6.35        10.09        27.19         2.43 
TCGA-05-4398 TCGA-05-4426 TCGA-05-5428 TCGA-35-4123 TCGA-38-4628 TCGA-38-4632 
       47.05        26.01        22.03         5.98        49.05        44.61 
TCGA-44-2656 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       46.98        42.77        37.15        34.06        33.73        26.56 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7662 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4488 
       23.18        32.45         7.17        12.66        13.45        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 
       12.66        14.07        29.75        22.26        22.26        62.24 
TCGA-49-AAR4 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5933 TCGA-50-5941 
       28.90        71.47       101.72        47.41        78.67        48.46 
TCGA-50-5946 TCGA-50-6594 TCGA-55-6712 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       53.16        12.16         5.62        69.34        45.34        32.71 
TCGA-55-7281 TCGA-55-7576 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
       28.67        22.03        15.39        18.64        11.28        17.65 
TCGA-55-7994 TCGA-55-8096 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-A48Z 
       19.82        23.64        17.56         0.36        17.72        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-62-8394 TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
        3.25         0.92         4.57        56.71        67.96        72.30 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-5778 TCGA-69-7760 TCGA-69-7765 
       29.92        56.81        81.80        42.90         6.64         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
        4.41        13.41        13.51        19.43         8.42         6.90 
TCGA-73-4668 TCGA-73-4676 TCGA-75-5125 TCGA-78-7143 TCGA-78-7145 TCGA-78-7535 
       15.35         9.24        66.64       163.10        27.16        31.20 
TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-8055 TCGA-86-8073 
       77.59        27.09        12.36         5.88         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8673 TCGA-86-A4JF 
        0.79        22.82        31.04        31.20        28.34        24.23 
TCGA-91-6829 TCGA-91-6847 TCGA-91-6848 TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 
       41.36        27.68         7.36        41.82        18.67         2.76 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8547 TCGA-99-8028 TCGA-L4-A4E5 TCGA-L9-A7SV 
       25.48        18.54        21.60        36.76        19.00        18.58 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       38.63         2.76        86.14        58.45        49.35        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A4YQ 
       41.59        19.13        47.08 

$subtype2
TCGA-05-4384 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       14.01        26.30        43.53        38.10        23.93        86.01 
TCGA-49-4501 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-7725 TCGA-55-7914 
       46.72        40.60        21.47        41.69        14.53         6.15 
TCGA-55-8090 TCGA-55-8207 TCGA-55-8619 TCGA-55-A492 TCGA-67-6217 TCGA-73-7498 
       19.66        32.12        13.68        19.59        13.87        39.09 
TCGA-78-7633 TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-05-4249 TCGA-05-4425 
       50.24        17.92        20.52        17.75        50.07        21.99 
TCGA-05-5423 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-44-2657 TCGA-44-2659 
        4.96         2.04         0.46       120.79        44.42        44.94 
TCGA-44-2666 TCGA-44-3398 TCGA-44-8120 TCGA-44-A47A TCGA-49-4486 TCGA-49-6744 
        3.19        38.24         8.55        15.32        76.21        55.33 
TCGA-50-5942 TCGA-50-5944 TCGA-50-8457 TCGA-50-8460 TCGA-53-7626 TCGA-55-6543 
       60.72        57.53        36.99        27.25        30.54        14.30 
TCGA-55-6970 TCGA-55-6986 TCGA-55-7227 TCGA-55-7283 TCGA-55-7574 TCGA-55-7727 
       15.25       107.21        31.30        20.02        32.71         3.91 
TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 TCGA-55-8514 TCGA-55-A4DG TCGA-55-A57B 
       15.19        15.65        29.19        17.10        19.99        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
       39.98        42.38        88.64        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 
       12.66        14.73         5.72         4.64        22.68        13.61 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 
       14.01        13.45         1.25        77.85        85.15        49.84 
TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7537 TCGA-78-8648 
       39.95        32.09         5.88       104.19        53.33        39.75 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8668 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P7 
       20.55         4.57        13.91        27.58        29.46        13.64 
TCGA-86-A4P8 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
       26.47         1.15        16.60        14.27        19.82        22.45 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
       23.61        19.00        27.29        42.25        64.60        61.48 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M1 
        0.59         5.39        16.41        14.30        21.44        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       18.67        24.56        21.63        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-MP-A4T6 TCGA-MP-A4TH TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A55O 
       14.53        58.85        24.36        74.33         0.13         0.43 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

$subtype3
TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-44-7661 TCGA-49-6742 TCGA-49-6745 
        9.01        15.02        15.02        18.31        16.04        17.16 
TCGA-49-AARN TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8205 
       37.32         5.79         7.99        23.18        21.44        19.69 
TCGA-78-7166 TCGA-78-8660 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-A4VK TCGA-MP-A4TA 
        8.48        10.55         6.12        17.29        21.40        31.23 
TCGA-05-4250 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4433 TCGA-05-5425 
        3.98         0.00        19.00         2.99        24.00        29.00 
TCGA-05-5429 TCGA-35-4122 TCGA-38-4625 TCGA-44-2668 TCGA-44-5643 TCGA-44-6145 
        9.04         7.40        97.74        25.02        33.30        19.56 
TCGA-44-6779 TCGA-44-A4SS TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 
       16.44        13.64        35.54        32.84         8.81        53.29 
TCGA-49-AAR9 TCGA-50-5044 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 
        8.55        20.52         8.22         9.27         8.45        15.12 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 TCGA-53-7624 
       42.35        25.55         6.21         0.72        36.79        34.29 
TCGA-55-6975 TCGA-55-6984 TCGA-55-6987 TCGA-55-7728 TCGA-55-8089 TCGA-55-8092 
        3.88        24.99        70.26        23.15        23.08         5.06 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-62-8398 TCGA-62-A46O TCGA-62-A471 
       15.42        15.72        14.47        14.60        47.80        40.96 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-69-7761 TCGA-73-4666 TCGA-73-4670 
        2.04        51.25        28.47         6.12        26.30         4.31 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 
       36.66       100.57         5.69        20.58        21.90        19.50 
TCGA-78-7160 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-86-7711 TCGA-86-8585 
       22.92        26.53        39.35        10.55        34.39        11.61 
TCGA-86-8672 TCGA-91-6830 TCGA-95-7944 TCGA-97-8175 TCGA-97-8176 TCGA-99-8033 
        0.62         1.97        12.39        18.12        15.39        21.57 
TCGA-L9-A5IP TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YP 
        1.91         5.49        11.05        14.10         1.64 

$subtype4
TCGA-05-4396 TCGA-38-4630 TCGA-38-4631 TCGA-44-8119 TCGA-49-AAR0 TCGA-55-1592 
        9.96        35.28        11.64         9.37       156.66        23.05 
TCGA-55-8203 TCGA-55-A4DF TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7043 
       17.98        20.19        85.32        16.18         1.45        16.54 
TCGA-J2-8194 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 
       23.80         5.29        10.09        45.01        37.02        24.03 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-35-5375 
       14.96        29.98        12.00        30.02        25.02         8.68 
TCGA-44-5644 TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       28.37        21.63        61.28        19.46        36.07        18.87 
TCGA-44-A479 TCGA-44-A47B TCGA-49-4487 TCGA-49-4510 TCGA-49-4514 TCGA-49-AAR2 
       15.98         9.44        28.11        29.46        55.89        73.12 
TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5051 TCGA-50-5931 TCGA-50-6591 TCGA-50-7109 
      221.33         9.86        15.72        14.27         3.91        10.13 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       13.94        35.21        38.73        67.89        30.58        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-7570 TCGA-55-7815 
       42.51        40.73        46.03        53.65        27.09        25.41 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8507 
       34.19        18.44        29.23        29.72        17.79        13.74 
TCGA-55-8508 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A494 TCGA-62-8402 
       20.28        14.66        12.33        20.71        15.81        49.25 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 
       19.53        54.35        39.25        39.09        87.98        28.41 
TCGA-67-3771 TCGA-69-7973 TCGA-69-8255 TCGA-73-4659 TCGA-73-A9RS TCGA-75-5147 
       20.05         7.56         4.24        23.38        11.18        43.82 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 
      129.53       119.51        38.50        64.90         9.57       238.29 
TCGA-78-7167 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 
       88.14         8.02        26.01       232.18       110.50        93.11 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       31.13        38.04        32.78        19.89        35.24        37.74 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6828 
       21.47        14.60        30.84        26.50         3.81        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-95-A4VP TCGA-97-8171 TCGA-99-8032 
       10.19        12.23         1.18        19.89        18.67         1.45 
TCGA-L9-A8F4 TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A55R 
       15.65        29.46        73.91        71.05        19.82 

$subtype5
TCGA-44-6147 TCGA-44-7670 TCGA-44-7671 TCGA-55-7573 TCGA-55-8091 TCGA-55-8204 
       27.78        29.00        29.23        16.01        19.73        16.93 
TCGA-55-8621 TCGA-55-A48X TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4M7 TCGA-L9-A743 
       16.93        22.65        15.68        18.18        20.68        21.83 
TCGA-05-4430 TCGA-38-4627 TCGA-38-A44F TCGA-44-5645 TCGA-44-6148 TCGA-44-7659 
       25.02        37.71         4.37        28.01        23.15        22.72 
TCGA-44-7672 TCGA-44-A47G TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-50-5055 
       23.64        11.54        40.41       123.58       164.12        60.16 
TCGA-50-5068 TCGA-50-6593 TCGA-55-6983 TCGA-55-6985 TCGA-55-8208 TCGA-55-8512 
       49.28        11.05        92.81        40.54        22.16        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-62-A46Y TCGA-64-1680 TCGA-64-1681 
       26.01        17.62         1.58        13.61        37.02        38.37 
TCGA-69-7974 TCGA-69-8453 TCGA-73-4675 TCGA-73-7499 TCGA-75-7025 TCGA-78-7147 
        6.05        26.73        30.31        50.33       108.66        19.27 
TCGA-86-8076 TCGA-86-8280 TCGA-91-6835 TCGA-93-7348 TCGA-93-A4JO TCGA-97-7552 
       32.65        23.05         2.60        17.46         1.08        63.52 
TCGA-97-7941 TCGA-97-8552 TCGA-97-A4M5 TCGA-99-8025 TCGA-J2-A4AD TCGA-MP-A4TJ 
       15.91        20.58        20.84        34.85        18.08        11.15 
TCGA-NJ-A55A 
        0.49 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.36     0.13     0.00     1.18     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 
  163.10   120.79   100.57   238.29   164.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
   23.18    21.44    16.44    25.02    22.65 
[1] "0.4 - 163.1 (23.2)" "0.1 - 120.8 (21.4)" "0.0 - 100.6 (16.4)"
[4] "1.2 - 238.3 (25.0)" "0.5 - 164.1 (22.6)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       2       23       37        1        15        26         17
  subtype2       0       46       30        0         9        11         15
  subtype3       1       11       22        0         7        16         22
  subtype4       1       28       37        0        12        12         13
  subtype5       1       23       13        0         7         6          6
          vv
clus       STAGE IIIB STAGE IV
  subtype1          4        5
  subtype2          1        4
  subtype3          3        8
  subtype4          3        7
  subtype5          0        2
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           2        0        1        1        1
  STAGE IA         23       46       11       28       23
  STAGE IB         37       30       22       37       13
  STAGE II          1        0        0        0        0
  STAGE IIA        15        9        7       12        7
  STAGE IIB        26       11       16       12        6
  STAGE IIIA       17       15       22       13        6
  STAGE IIIB        4        1        3        3        0
  STAGE IV          5        4        8        7        2
[1] 9 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 33 82 11  5
  subtype2 57 49  8  5
  subtype3 16 54 13  6
  subtype4 33 70  9  3
  subtype5 30 22  6  0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       33       57       16       33       30
  T2       82       49       54       70       22
  T3       11        8       13        9        6
  T4        5        5        6        3        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"
          vv
clus       N0 N1 N2+N3
  subtype1 72 35    22
  subtype2 86 17    12
  subtype3 47 20    22
  subtype4 87 13    14
  subtype5 39 11     6
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          72       86       47       87       39
  N1          35       17       20       13       11
  N2+N3       22       12       22       14        6
[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"
D7V6, binary
          cls
clus        0  1
  subtype1 86  4
  subtype2 81  4
  subtype3 65  8
  subtype4 79  7
  subtype5 35  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86    4
  subtype2   81    4
  subtype3   65    8
  subtype4   79    7
  subtype5   35    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       86       81       65       79       35
  1        4        4        8        7        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 76 56
  subtype2 79 41
  subtype3 39 51
  subtype4 47 68
  subtype5 36 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76   56
  subtype2   79   41
  subtype3   39   51
  subtype4   47   68
  subtype5   36   22
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       76       79       39       47       36
  MALE         56       41       51       68       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"
D7V8, binary
          cls
clus         0   1
  subtype1 110  15
  subtype2  99   8
  subtype3  60  17
  subtype4  89  16
  subtype5  50   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110   15
  subtype2   99    8
  subtype3   60   17
  subtype4   89   16
  subtype5   50    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO       110       99       60       89       50
  YES       15        8       17       16        5
[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"
D7V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          1                                25
  subtype2                          7                                29
  subtype3                          3                                18
  subtype4                          6                                21
  subtype5                          1                                14
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 95
  subtype2                                                 61
  subtype3                                                 59
  subtype4                                                 75
  subtype5                                                 30
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          3
  subtype3                                          1
  subtype4                                          0
  subtype5                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             6
  subtype2                                             7
  subtype3                                             1
  subtype4                                             2
  subtype5                                             3
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  2
  subtype2                              0                                  1
  subtype3                              1                                  0
  subtype4                              0                                  0
  subtype5                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             2
  subtype2                            1                             9
  subtype3                            0                             1
  subtype4                            0                             8
  subtype5                            1                             3
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             0
  subtype3                                             2
  subtype4                                             2
  subtype5                                             1
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            2
  subtype3                            4
  subtype4                            1
  subtype5                            3
D7V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                1        7        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        25       29       18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       95       61       59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        3        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6        7        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             2        9        1
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        2
  MUCINOUS (COLLOID) CARCINOMA                              0        2        4
                                                    clus
vv                                                   subtype4 subtype5
  LUNG ACINAR ADENOCARCINOMA                                6        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        21       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       75       30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             2        3
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1
  LUNG PAPILLARY ADENOCARCINOMA                             8        3
  LUNG SIGNET RING ADENOCARCINOMA                           0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        1
  MUCINOUS (COLLOID) CARCINOMA                              1        3
[1] 12  5
[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 88  4  1  6
  subtype2 76  4  0  6
  subtype3 59  2  2  3
  subtype4 83  3  0  5
  subtype5 38  0  1  5
D7V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       88       76       59       83       38
  R1        4        4        2        3        0
  R2        1        0        2        0        1
  RX        6        6        3        5        5
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        14
  subtype2                                0     2                        11
  subtype3                                0     1                         4
  subtype4                                0     2                        16
  subtype5                                0     0                         7
          vv
clus       WHITE
  subtype1    99
  subtype2    95
  subtype3    70
  subtype4    79
  subtype5    45
D7V14, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        2        1        2        0
  BLACK OR AFRICAN AMERICAN              14       11        4       16        7
  WHITE                                  99       95       70       79       45
[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"
D7V15, binary
          cls
clus         0   1
  subtype1   1 102
  subtype2   1  94
  subtype3   2  59
  subtype4   2  79
  subtype5   1  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  102
  subtype2    1   94
  subtype3    2   59
  subtype4    2   79
  subtype5    1   49
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        1        2        2        1
  NOT HISPANIC OR LATINO      102       94       59       79       49
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 51 25
  subtype2 73 35
  subtype3 57 40
  subtype4 30 17
  subtype5 37 14
  subtype6 16 33
  subtype7 56 19
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      76      108       97       47       51       49       75 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      25       35       40       17       14       33       19 
$subtype1
TCGA-38-7271 TCGA-49-4501 TCGA-50-5935 TCGA-50-6597 TCGA-55-7725 TCGA-55-7914 
       26.30        46.72        21.47        41.69        14.53         6.15 
TCGA-55-8090 TCGA-55-8207 TCGA-67-6217 TCGA-73-4662 TCGA-97-8172 TCGA-L9-A443 
       19.66        32.12        13.87        82.68        17.92         6.35 
TCGA-05-4249 TCGA-05-4425 TCGA-05-5423 TCGA-05-5715 TCGA-38-4626 TCGA-44-2659 
       50.07        21.99         4.96         2.04       120.79        44.94 
TCGA-44-2666 TCGA-44-3919 TCGA-44-A47A TCGA-49-4487 TCGA-49-4512 TCGA-49-6744 
        3.19        33.73        15.32        28.11        29.75        55.33 
TCGA-50-5944 TCGA-50-8457 TCGA-53-7626 TCGA-55-6971 TCGA-55-6986 TCGA-55-6987 
       57.53        36.99        30.54        46.03       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7574 TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 
       31.30        20.02        32.71        15.19        15.65        29.19 
TCGA-55-8299 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-67-3770 TCGA-67-3772 
       15.42        19.99        17.95        42.38        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-75-6212 TCGA-78-7143 TCGA-78-7158 
       14.04         5.72         4.64        49.84       163.10         5.88 
TCGA-78-7539 TCGA-78-8648 TCGA-86-7714 TCGA-86-8668 TCGA-86-8671 TCGA-86-A456 
       26.01        39.75        20.55        13.91        27.58        29.46 
TCGA-86-A4P7 TCGA-91-8496 TCGA-93-7347 TCGA-93-7348 TCGA-95-8039 TCGA-97-7546 
       13.64        16.60        22.45        17.46        27.29        42.25 
TCGA-97-7547 TCGA-97-7938 TCGA-97-8171 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 
       64.60         0.59        18.67        16.41        21.44        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4T6 
       18.67        24.56        21.63        14.30        14.53        58.85 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A7XG TCGA-O1-A52J 
       74.33         0.13        20.28        59.11 

$subtype2
TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 TCGA-44-2662 TCGA-44-7661 TCGA-49-6745 
       20.05        26.01        28.41        42.08        18.31        17.16 
TCGA-49-6761 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-8205 TCGA-73-4658 
       11.64        48.62         5.79         7.79        19.69        52.60 
TCGA-78-8660 TCGA-91-6836 TCGA-95-7948 TCGA-97-A4LX TCGA-L9-A444 TCGA-MP-A4TC 
       10.55        13.71        15.65        20.19        10.09         2.43 
TCGA-05-4250 TCGA-05-4398 TCGA-05-4426 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
        3.98        47.05        26.01        22.03         7.40         5.98 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2665 TCGA-44-2668 
       97.74        49.05        44.61        46.98        42.77        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-6777 TCGA-44-7662 
       37.15        38.24        34.06        26.56        32.45         7.17 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 
       12.66         8.55         9.44        28.57        35.54        14.07 
TCGA-49-6767 TCGA-49-AAR3 TCGA-50-5044 TCGA-50-5066 TCGA-50-5933 TCGA-50-5941 
       22.26        62.24        20.52        47.41        78.67        48.46 
TCGA-50-6590 TCGA-50-6594 TCGA-55-6712 TCGA-55-6980 TCGA-55-6981 TCGA-55-7281 
       42.35        12.16         5.62        69.34        45.34        28.67 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 
       22.03         3.91        15.39        18.64        17.65        19.82 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-A490 
       17.56        15.72         0.36        17.72        17.10         3.25 
TCGA-55-A493 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
        0.92        88.64        67.96        72.30        29.92        56.81 
TCGA-64-1679 TCGA-64-5815 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-A59K 
       81.80        28.47         6.64         5.42         4.41        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-75-5125 
        8.42         6.90        26.30        15.35         9.24        66.64 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7535 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       27.16         5.69        31.20        77.59        27.09        12.36 
TCGA-86-8073 TCGA-86-8279 TCGA-86-8673 TCGA-86-A4JF TCGA-93-A4JN TCGA-95-7039 
       24.33        31.20        28.34        24.23        23.61        41.82 
TCGA-95-7567 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 
       18.67         2.76        25.48        18.54        18.12        21.60 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TI TCGA-MP-A4TK 
       32.48        19.00         2.76        41.59        14.10        19.13 

$subtype3
TCGA-05-4382 TCGA-05-4402 TCGA-05-4434 TCGA-38-4630 TCGA-38-6178 TCGA-44-7670 
       19.96         8.02        15.02        35.28        14.73        29.00 
TCGA-49-AAR0 TCGA-55-1592 TCGA-55-7724 TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 
      156.66        23.05        23.18        21.44        19.73        16.93 
TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-80-5611 TCGA-93-A4JQ TCGA-95-7043 
       20.58        20.19        20.65        85.32        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-05-4389 TCGA-05-4397 
        2.86        15.68        24.30        27.19        45.01        24.03 
TCGA-05-4424 TCGA-35-5375 TCGA-38-4627 TCGA-44-5643 TCGA-44-6775 TCGA-44-6778 
       30.02         8.68        37.71        33.30        23.18        61.28 
TCGA-44-7660 TCGA-44-7669 TCGA-44-A4SU TCGA-49-4490 TCGA-49-6743 TCGA-49-AAQV 
       19.46        18.87        13.45        12.66        53.29        22.26 
TCGA-49-AARE TCGA-49-AARQ TCGA-50-5930 TCGA-50-5931 TCGA-50-5946 TCGA-50-6591 
       40.41       221.33         9.27        14.27        53.16         3.91 
TCGA-50-6595 TCGA-50-6673 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 
        6.21         0.72        35.21        30.58        14.30        42.51 
TCGA-55-6982 TCGA-55-7570 TCGA-55-7995 TCGA-55-8096 TCGA-55-8208 TCGA-55-8614 
       32.71        27.09        29.23        23.64        22.16        17.62 
TCGA-55-8620 TCGA-55-A48Z TCGA-62-8394 TCGA-64-5775 TCGA-67-3771 TCGA-69-7979 
       12.33        21.40         4.57         2.04        20.05        13.41 
TCGA-69-7980 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6214 TCGA-78-7147 
       13.51        50.33        11.18        43.82        36.66        19.27 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 TCGA-86-6851 
       38.50       238.29        10.55       232.18       110.50         5.88 
TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 
       34.39        32.78        19.89        35.24         4.08         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 TCGA-91-6829 TCGA-91-6830 
       22.82        31.04        21.47        11.61        41.36         1.97 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-A4JP TCGA-J2-A4AD 
       12.23        27.68         7.36         1.18        19.00        18.08 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-NJ-A4YQ 
       18.58        15.65        38.63        86.14        49.35        47.08 
TCGA-NJ-A55R 
       19.82 

$subtype4
TCGA-05-4384 TCGA-05-4396 TCGA-44-2655 TCGA-44-6776 TCGA-44-7671 TCGA-50-5932 
       14.01         9.96        43.53        86.01        29.23        40.60 
TCGA-55-A492 TCGA-73-7498 TCGA-78-7633 TCGA-91-7771 TCGA-97-A4M3 TCGA-J2-8194 
       19.59        39.09        50.24        16.18        17.75        23.80 
TCGA-05-4422 TCGA-35-3615 TCGA-49-4486 TCGA-49-4510 TCGA-49-AAR2 TCGA-55-6972 
       12.00         0.46        76.21        29.46        73.12        53.65 
TCGA-55-8085 TCGA-62-8395 TCGA-62-A46P TCGA-62-A46S TCGA-67-3774 TCGA-69-7763 
       29.72        39.98        19.53        54.35        12.66        22.68 
TCGA-69-7764 TCGA-69-8253 TCGA-73-4675 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 
       13.61        14.01        30.31         1.25        77.85        85.15 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7162 TCGA-78-7167 
      129.53        39.95       119.51        32.09       104.19        88.14 
TCGA-78-7537 TCGA-86-8674 TCGA-91-6849 TCGA-91-8497 TCGA-97-8174 TCGA-97-8179 
       53.33        26.50         1.15        14.27         5.39        14.30 
TCGA-97-A4M5 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A55O 
       20.84        24.36        73.91         1.64         0.43 

$subtype5
TCGA-44-8119 TCGA-55-8203 TCGA-91-A4BC TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4390 
        9.37        17.98         1.45         5.29        10.09        37.02 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 TCGA-44-5644 TCGA-44-6774 TCGA-44-7667 
       14.96        29.98        25.02        28.37        21.63        36.07 
TCGA-44-A479 TCGA-4B-A93V TCGA-50-5051 TCGA-50-7109 TCGA-53-7813 TCGA-55-1594 
       15.98         9.86        15.72        10.13        13.94        38.73 
TCGA-55-6642 TCGA-55-6969 TCGA-55-7815 TCGA-55-7910 TCGA-55-7913 TCGA-55-8094 
       80.52        40.73        25.41        34.19        18.44        17.79 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A494 TCGA-62-8402 TCGA-62-A470 
       13.74        20.28        14.66        15.81        49.25        39.25 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-69-7973 TCGA-73-4659 TCGA-78-7159 
       39.09        87.98        28.41         7.56        23.38        64.90 
TCGA-78-7161 TCGA-78-7536 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 
        9.57         8.02        93.11        31.13        38.04        37.74 
TCGA-86-8359 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 TCGA-95-A4VP 
       14.60        30.84         3.81        10.62        10.19        19.89 
TCGA-99-8032 TCGA-MP-A4TE TCGA-NJ-A4YF 
        1.45        29.46        71.05 

$subtype6
TCGA-05-4418 TCGA-05-5420 TCGA-38-4631 TCGA-49-6742 TCGA-78-7166 TCGA-93-8067 
        9.01        15.02        11.64        16.04         8.48         6.12 
TCGA-95-A4VK TCGA-MP-A4TA TCGA-05-4395 TCGA-05-4415 TCGA-05-5425 TCGA-44-6145 
       21.40        31.23         0.00         2.99        29.00        19.56 
TCGA-44-6779 TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-AAR9 
       16.44        13.64        32.84         8.81        55.89         8.55 
TCGA-50-5072 TCGA-50-5936 TCGA-50-5939 TCGA-50-6592 TCGA-53-7624 TCGA-55-1596 
        8.22         8.45        15.12        25.55        34.29        67.89 
TCGA-55-6970 TCGA-55-6975 TCGA-55-8089 TCGA-55-8092 TCGA-55-8505 TCGA-55-A48Y 
       15.25         3.88        23.08         5.06        14.47        20.71 
TCGA-62-8398 TCGA-62-A46O TCGA-62-A471 TCGA-64-5781 TCGA-69-8255 TCGA-73-4670 
       14.60        47.80        40.96        51.25         4.24         4.31 
TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7160 TCGA-78-7220 
      100.57        20.58        21.90        19.50        22.92        26.53 
TCGA-86-8672 TCGA-95-7944 TCGA-97-8176 TCGA-99-8033 TCGA-L9-A5IP TCGA-MP-A4T7 
        0.62        12.39        15.39        21.57         1.91         5.49 
TCGA-MP-A4TF 
       11.05 

$subtype7
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-49-AARN TCGA-55-7284 TCGA-55-7573 
       38.10        23.93        27.78        37.32         7.99        16.01 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-95-A4VN TCGA-97-A4M2 
       18.15        13.68        16.93        22.65        18.18        20.52 
TCGA-97-A4M7 TCGA-L9-A743 TCGA-05-4403 TCGA-05-4430 TCGA-05-4433 TCGA-05-5429 
       20.68        21.83        19.00        25.02        24.00         9.04 
TCGA-38-A44F TCGA-44-2657 TCGA-44-5645 TCGA-44-6148 TCGA-44-7659 TCGA-44-7672 
        4.37        44.42        28.01        23.15        22.72        23.64 
TCGA-44-A47G TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARR TCGA-50-5045 TCGA-50-5049 
       11.54        28.90       123.58       164.12        71.47       101.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5942 TCGA-50-6593 TCGA-50-8459 TCGA-50-8460 
       60.16        49.28        60.72        11.05        36.79        27.25 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-7728 TCGA-55-7907 TCGA-55-8512 
       92.81        24.99        40.54        23.15        11.28        19.96 
TCGA-55-8513 TCGA-55-8616 TCGA-62-A46R TCGA-62-A46Y TCGA-64-1680 TCGA-64-1681 
       26.01         1.58        56.71        13.61        37.02        38.37 
TCGA-64-5778 TCGA-67-4679 TCGA-69-7761 TCGA-69-7974 TCGA-69-8254 TCGA-69-8453 
       42.90        14.73         6.12         6.05        13.45        26.73 
TCGA-75-7025 TCGA-78-7540 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 TCGA-86-A4P8 
      108.66        39.35         4.57        32.65        23.05        26.47 
TCGA-91-6835 TCGA-91-A4BD TCGA-93-A4JO TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
        2.60        19.82         1.08        63.52        61.48        15.91 
TCGA-97-8552 TCGA-99-8025 TCGA-99-8028 TCGA-J2-A4AE TCGA-MP-A4SW TCGA-MP-A4T4 
       20.58        34.85        36.76        35.47        58.45        86.04 
TCGA-MP-A4TJ TCGA-NJ-A55A TCGA-S2-AA1A 
       11.15         0.49        16.87 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.13     0.36     0.72     0.43     1.45     0.00     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  163.10    97.74   238.29   129.53    93.11   100.57   164.12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   21.55    21.06    21.40    29.23    20.28    15.25    23.93 
[1] "0.1 - 163.1 (21.5)" "0.4 - 97.7 (21.1)"  "0.7 - 238.3 (21.4)"
[4] "0.4 - 129.5 (29.2)" "1.4 - 93.1 (20.3)"  "0.0 - 100.6 (15.2)"
[7] "0.5 - 164.1 (23.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       30       22        0         6         7          9
  subtype2       1       16       35        0        10        23         18
  subtype3       3       25       27        1        14         7         11
  subtype4       0       15       16        0         4         5          3
  subtype5       0       11       15        0         6         5         12
  subtype6       0        7        7        0         3        12         12
  subtype7       1       27       17        0         7        12          8
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        3
  subtype2          3        5
  subtype3          2        6
  subtype4          2        2
  subtype5          1        2
  subtype6          2        6
  subtype7          0        2
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           0        1        3        0        0        0        1
  STAGE IA         30       16       25       15       11        7       27
  STAGE IB         22       35       27       16       15        7       17
  STAGE II          0        0        1        0        0        0        0
  STAGE IIA         6       10       14        4        6        3        7
  STAGE IIB         7       23        7        5        5       12       12
  STAGE IIIA        9       18       11        3       12       12        8
  STAGE IIIB        1        3        2        2        1        2        0
  STAGE IV          3        5        6        2        2        6        2
[1] 9 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 36 36  4  3
  subtype2 24 69 13  5
  subtype3 39 51  3  3
  subtype4 17 24  4  3
  subtype5 12 35  5  1
  subtype6  8 29  8  3
  subtype7 33 33 10  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       36       24       39       17       12        8       33
  T2       36       69       51       24       35       29       33
  T3        4       13        3        4        5        8       10
  T4        3        5        3        3        1        3        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 57 12     9
  subtype2 66 25    19
  subtype3 60 23    12
  subtype4 37  8     2
  subtype5 37  3    12
  subtype6 22 12    14
  subtype7 52 13     8
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0          57       66       60       37       37       22       52
  N1          12       25       23        8        3       12       13
  N2+N3        9       19       12        2       12       14        8
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 52  3
  subtype2 79  4
  subtype3 55  6
  subtype4 38  2
  subtype5 38  2
  subtype6 37  6
  subtype7 47  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    3
  subtype2   79    4
  subtype3   55    6
  subtype4   38    2
  subtype5   38    2
  subtype6   37    6
  subtype7   47    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       52       79       55       38       38       37       47
  1        3        4        6        2        2        6        2
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 63 16
  subtype2 59 53
  subtype3 52 45
  subtype4 16 32
  subtype5 24 29
  subtype6 19 30
  subtype7 44 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   16
  subtype2   59   53
  subtype3   52   45
  subtype4   16   32
  subtype5   24   29
  subtype6   19   30
  subtype7   44   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       63       59       52       16       24       19       44
  MALE         16       53       45       32       29       30       33
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1 68  4
  subtype2 92 11
  subtype3 75 15
  subtype4 38  3
  subtype5 43  6
  subtype6 34 11
  subtype7 58 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    4
  subtype2   92   11
  subtype3   75   15
  subtype4   38    3
  subtype5   43    6
  subtype6   34   11
  subtype7   58   11
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        68       92       75       38       43       34       58
  YES        4       11       15        3        6       11       11
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                16
  subtype2                          1                                19
  subtype3                          3                                15
  subtype4                          2                                19
  subtype5                          4                                10
  subtype6                          1                                12
  subtype7                          2                                16
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 45
  subtype2                                                 81
  subtype3                                                 71
  subtype4                                                 18
  subtype5                                                 37
  subtype6                                                 31
  subtype7                                                 37
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          1
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
  subtype5                                          0
  subtype6                                          0
  subtype7                                          3
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             6
  subtype2                                             3
  subtype3                                             2
  subtype4                                             1
  subtype5                                             1
  subtype6                                             0
  subtype7                                             6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              1                                  2
  subtype3                              1                                  0
  subtype4                              0                                  0
  subtype5                              0                                  0
  subtype6                              0                                  0
  subtype7                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             5
  subtype2                            0                             4
  subtype3                            0                             2
  subtype4                            0                             7
  subtype5                            0                             0
  subtype6                            0                             2
  subtype7                            2                             3
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               0
  subtype6                               0
  subtype7                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             1
  subtype3                                             2
  subtype4                                             0
  subtype5                                             0
  subtype6                                             1
  subtype7                                             1
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            0
  subtype4                            1
  subtype5                            1
  subtype6                            2
  subtype7                            6
D8V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        1        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        16       19       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       45       81       71
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                1        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6        3        2
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        2        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             5        4        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        2
  MUCINOUS (COLLOID) CARCINOMA                              0        0        0
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  LUNG ACINAR ADENOCARCINOMA                                2        4        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        19       10       12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       18       37       31
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        1        0
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             7        0        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        1
  MUCINOUS (COLLOID) CARCINOMA                              1        1        2
                                                    clus
vv                                                   subtype7
  LUNG ACINAR ADENOCARCINOMA                                2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       37
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6
  LUNG CLEAR CELL ADENOCARCINOMA                            0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0
  LUNG MUCINOUS ADENOCARCINOMA                              2
  LUNG PAPILLARY ADENOCARCINOMA                             3
  LUNG SIGNET RING ADENOCARCINOMA                           1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1
  MUCINOUS (COLLOID) CARCINOMA                              6
[1] 12  7
[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 55  4  0  2
  subtype2 77  2  2  3
  subtype3 58  3  2  9
  subtype4 28  0  0  3
  subtype5 38  1  0  2
  subtype6 35  3  0  2
  subtype7 53  0  0  4
D8V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       55       77       58       28       38       35       53
  R1        4        2        3        0        1        3        0
  R2        0        2        2        0        0        0        0
  RX        2        3        9        3        2        2        4
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         6
  subtype2                                1     3                         9
  subtype3                                0     1                        14
  subtype4                                0     0                         5
  subtype5                                0     0                         6
  subtype6                                0     2                         2
  subtype7                                0     0                        10
          vv
clus       WHITE
  subtype1    62
  subtype2    84
  subtype3    70
  subtype4    37
  subtype5    38
  subtype6    38
  subtype7    59
D8V14, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   2        3        1        0        0
  BLACK OR AFRICAN AMERICAN               6        9       14        5        6
  WHITE                                  62       84       70       37       38
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   2        0
  BLACK OR AFRICAN AMERICAN               2       10
  WHITE                                  38       59
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
          cls
clus        0  1
  subtype1  1 60
  subtype2  0 85
  subtype3  4 71
  subtype4  0 34
  subtype5  0 37
  subtype6  2 31
  subtype7  0 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   60
  subtype2    0   85
  subtype3    4   71
  subtype4    0   34
  subtype5    0   37
  subtype6    2   31
  subtype7    0   65
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        4        0        0        2
  NOT HISPANIC OR LATINO       60       85       71       34       37       31
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       65
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 121  61
  subtype2 142  75
  subtype3  56  46
subtype1 subtype2 subtype3 
     182      217      102 
subtype1 subtype2 subtype3 
      61       75       46 
$subtype1
TCGA-05-4384 TCGA-05-4427 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6776 
       14.01        26.01        26.30        43.53        38.10        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-6745 TCGA-49-AARN TCGA-50-5932 
       18.31        29.23        11.08        17.16        37.32        40.60 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8205 
       16.01        23.18        14.53         6.15        19.66        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 
       32.12        13.68        16.93        22.65        19.59        13.87 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-7771 TCGA-93-A4JQ 
       39.09         8.48        50.24        10.55        16.18        17.29 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        18.18        20.19        20.52 
TCGA-97-A4M3 TCGA-L9-A743 TCGA-05-4403 TCGA-05-4426 TCGA-05-5429 TCGA-35-3615 
       17.75        21.83        19.00        26.01         9.04         0.46 
TCGA-38-4626 TCGA-38-A44F TCGA-44-2657 TCGA-44-2666 TCGA-44-3398 TCGA-44-3919 
      120.79         4.37        44.42         3.19        38.24        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6777 TCGA-44-7659 
       26.56        28.01        19.56        23.15        32.45        22.72 
TCGA-44-7672 TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
       23.64         9.44        11.54        76.21        28.11        12.66 
TCGA-49-4505 TCGA-49-4510 TCGA-49-6744 TCGA-49-AARR TCGA-50-5045 TCGA-50-5051 
       14.07        29.46        55.33       164.12        71.47        15.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       60.16        49.28         8.45        48.46        60.72        57.53 
TCGA-50-8457 TCGA-50-8460 TCGA-53-7626 TCGA-55-6712 TCGA-55-6970 TCGA-55-6972 
       36.99        27.25        30.54         5.62        15.25        53.65 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 
       24.99       107.21        31.30        28.67        20.02        22.03 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-8097 TCGA-55-8206 TCGA-55-8510 
        3.91        18.64        17.65        15.65        29.19        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       19.96        26.01        19.99        17.95        39.98        42.38 
TCGA-62-8399 TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 
       88.64        72.30        13.61        29.92        37.02        38.37 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       42.90        28.47        20.05        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        5.72         4.64         6.12        22.68        13.61         5.42 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4676 TCGA-75-5125 TCGA-75-5146 
       14.01        13.45        26.73         9.24        66.64        77.85 
TCGA-75-6206 TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 
       85.15        49.84       163.10        27.16        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
       39.95       119.51        19.50        32.09         5.88        22.92 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-8655 TCGA-86-6562 
      104.19        88.14        53.33        39.35        77.59        12.36 
TCGA-86-7714 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-A4P8 TCGA-91-6835 
       20.55        32.65        23.05        13.91        26.47         2.60 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JO 
        1.15        16.60        14.27        19.82        22.45         1.08 
TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
       18.67        27.29        19.89        42.25        63.52        61.48 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 
        0.59         5.39        18.12        15.39        14.30        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R 
       21.44        19.76        20.84        24.56        36.76        21.63 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SY TCGA-MP-A4T7 
       35.47        32.48        14.30        14.53        49.35         5.49 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O 
       24.36        11.15        19.13        74.33         0.49         0.43 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

$subtype2
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 
       19.96         9.96         8.02         9.01        15.02        15.02 
TCGA-38-4630 TCGA-38-4631 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-7670 
       35.28        11.64        42.08        23.93        27.78        29.00 
TCGA-44-8119 TCGA-49-4501 TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
        9.37        46.72       156.66        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 TCGA-55-8203 TCGA-55-8511 TCGA-55-A491 
       48.62         7.79         7.99        17.98        18.15        20.58 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC 
       20.19        20.65        82.68        85.32        13.71         1.45 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-97-8172 TCGA-J2-8194 TCGA-L9-A444 
        6.12        16.54         2.86        17.92        23.80        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       27.19         5.29        31.23         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
        0.00        24.03        47.05         2.99        29.98        12.00 
TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       30.02        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       22.03         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-3396 TCGA-44-3918 
       49.05        44.61        46.98        44.94        37.15        34.06 
TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A 
       33.30        28.37        19.46        12.66        15.98        15.32 
TCGA-44-A4SS TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       13.64        28.57        35.54        32.84         8.81        55.89 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ 
       53.29        22.26        73.12         8.55        40.41       221.33 
TCGA-4B-A93V TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5946 
        9.86       101.72        47.41         9.27        14.27        53.16 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       42.35        25.55         0.72        34.29        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6981 
       38.73        67.89        30.58        42.51        40.73        45.34 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       70.26        27.09        23.15        25.41        11.28        34.19 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        5.06        17.79        23.64        22.16        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8615 
       14.47         0.36        13.74        20.28        17.10        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
        1.58        12.33        21.40         3.25         0.92        15.81 
TCGA-62-8394 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
        4.57        14.60        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 
       67.96        39.25        40.96        39.09        87.98        28.41 
TCGA-67-3771 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       20.05         6.64         7.56         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-7499 TCGA-73-A9RS 
       13.51         4.24        19.43        23.38        50.33        11.18 
TCGA-75-5147 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7159 
       43.82         5.69        19.27        21.90        38.50        64.90 
TCGA-78-7161 TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 
        9.57        26.53         8.02        26.01        10.55       232.18 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        93.11        27.09         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       38.04        32.78        19.89        35.24        37.74         4.57 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 
       31.20        21.47        14.60        11.61        30.84        28.34 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       29.46         3.81        10.62         1.97        10.19        12.23 
TCGA-91-8499 TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-97-7547 TCGA-97-7941 
        1.18        19.00        41.82        12.39        64.60        15.91 
TCGA-97-8171 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
       18.67        18.67        34.85        21.57        18.08        19.00 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       58.45        86.04        29.46        73.91        71.05        47.08 
TCGA-NJ-A55R 
       19.82 

$subtype3
TCGA-05-4405 TCGA-38-4629 TCGA-38-6178 TCGA-49-6742 TCGA-49-6761 TCGA-55-6978 
       20.05        28.41        14.73        16.04        11.64         5.79 
TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 TCGA-73-4658 TCGA-97-A4M7 TCGA-J2-8192 
       21.44        19.73        16.93        52.60        20.68        24.30 
TCGA-L9-A443 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4417 TCGA-05-4425 
        6.35         2.43        10.09        50.07        14.96        21.99 
TCGA-38-4627 TCGA-44-2665 TCGA-44-2668 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 
       37.71        42.77        25.02        23.77        21.63        23.18 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8120 
       61.28        16.44         7.17        36.07        18.87         8.55 
TCGA-44-A4SU TCGA-49-4512 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO 
       13.45        29.75        22.26        62.24        28.90       123.58 
TCGA-50-5044 TCGA-50-5072 TCGA-50-5933 TCGA-50-5939 TCGA-50-6591 TCGA-50-6593 
       20.52         8.22        78.67        15.12         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-55-6543 TCGA-55-6642 
       12.16         6.21        10.13        36.79        14.30        80.52 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7574 
       46.03        69.34        32.71        92.81        40.54        32.71 
TCGA-55-7816 TCGA-55-8299 TCGA-55-8614 TCGA-55-A48Y TCGA-62-8402 TCGA-64-1676 
       15.39        15.42        17.62        20.71        49.25        56.81 
TCGA-64-1679 TCGA-64-5775 TCGA-64-5781 TCGA-67-3772 TCGA-71-6725 TCGA-71-8520 
       81.80         2.04        51.25        18.84         8.42         6.90 
TCGA-73-4675 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7163 TCGA-78-7535 
       30.31        36.66       108.66       100.57       238.29        31.20 
TCGA-78-8648 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       39.75         4.08        24.33         0.79        22.82        31.04 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6829 
       27.58         0.62        26.50        24.23        13.64        41.36 
TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JN TCGA-95-8494 TCGA-97-7554 
       27.68         7.36        17.46        23.61         2.76        25.48 
TCGA-97-7937 TCGA-97-8177 TCGA-97-8547 TCGA-99-8032 TCGA-MP-A4T2 TCGA-MP-A4T6 
       18.54        16.41        21.60         1.45        37.35        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
       41.59        11.05        14.10         0.13         1.64        20.28 

subtype1 subtype2 subtype3 
    0.43     0.00     0.13 
subtype1 subtype2 subtype3 
  164.12   232.18   238.29 
subtype1 subtype2 subtype3 
  21.535   21.900   21.615 
[1] "0.4 - 164.1 (21.5)" "0.0 - 232.2 (21.9)" "0.1 - 238.3 (21.6)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       67       40        0        18        24         22
  subtype2       4       51       66        0        20        32         27
  subtype3       0       15       33        1        12        14         24
          vv
clus       STAGE IIIB STAGE IV
  subtype1          2        8
  subtype2          7       12
  subtype3          2        4
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         67       51       15
  STAGE IB         40       66       33
  STAGE II          0        0        1
  STAGE IIA        18       20       12
  STAGE IIB        24       32       14
  STAGE IIIA       22       27       24
  STAGE IIIB        2        7        2
  STAGE IV          8       12        4
[1] 9 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  80  85  15   7
  subtype2  65 123  23   8
  subtype3  25  66   9   4
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       80       65       25
  T2       85      123       66
  T3       15       23        9
  T4        7        8        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1 120  38    23
  subtype2 148  37    31
  subtype3  62  20    22
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         120      148       62
  N1          38       37       20
  N2+N3       23       31       22
[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"
D9V6, binary
          cls
clus         0   1
  subtype1 127   8
  subtype2 152  12
  subtype3  67   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127    8
  subtype2  152   12
  subtype3   67    3
   clus
vv  subtype1 subtype2 subtype3
  0      127      152       67
  1        8       12        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"
D9V7, binary
          cls
clus         0   1
  subtype1 106  81
  subtype2 112 109
  subtype3  56  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106   81
  subtype2  112  109
  subtype3   56   49
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      106      112       56
  MALE         81      109       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"
D9V8, binary
          cls
clus         0   1
  subtype1 154  19
  subtype2 164  29
  subtype3  89  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  154   19
  subtype2  164   29
  subtype3   89   12
     clus
vv    subtype1 subtype2 subtype3
  NO       154      164       89
  YES       19       29       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          9                                47
  subtype2                          8                                48
  subtype3                          1                                11
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 97
  subtype2                                                145
  subtype3                                                 78
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          4
  subtype2                                          0
  subtype3                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            12
  subtype2                                             4
  subtype3                                             3
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              2                                  0
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             8
  subtype2                            1                             8
  subtype3                            0                             7
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             2
  subtype2                                             3
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            5
  subtype2                            2
  subtype3                            3
D9V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                9        8        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        47       48       11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       97      145       78
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                4        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            12        4        3
  LUNG CLEAR CELL ADENOCARCINOMA                            0        2        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             8        8        7
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        3        0
  MUCINOUS (COLLOID) CARCINOMA                              5        2        3
[1] 12  3
[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 121   4   1  10
  subtype2 157   5   3   9
  subtype3  63   4   0   7
D9V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      121      157       63
  R1        4        5        4
  R2        1        3        0
  RX       10        9        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        18   150
  subtype2     6                        25   155
  subtype3     2                         9    82
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        6        2
  BLACK OR AFRICAN AMERICAN       18       25        9
  WHITE                          150      155       82
[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"
D9V15, binary
          cls
clus         0   1
  subtype1   1 140
  subtype2   5 161
  subtype3   1  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  140
  subtype2    5  161
  subtype3    1   80
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        1
  NOT HISPANIC OR LATINO      140      161       80
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 49 22
  subtype2 26 12
  subtype3 90 53
  subtype4 78 49
  subtype5 59 35
  subtype6 17 11
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      71       38      143      127       94       28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      22       12       53       49       35       11 
$subtype1
TCGA-05-4384 TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F TCGA-49-AARN TCGA-50-5932 
       14.01        86.01        29.23        11.08        37.32        40.60 
TCGA-55-1595 TCGA-55-7573 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-7498 
       48.62        16.01        20.58        19.59        13.87        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-93-A4JQ TCGA-95-A4VK TCGA-97-A4LX 
        8.48        50.24        10.55        17.29        21.40        20.19 
TCGA-97-A4M3 TCGA-35-3615 TCGA-44-2656 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       17.75         0.46        46.98        38.24        33.73        26.56 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B TCGA-49-4486 
       32.45        22.72        23.64        15.32         9.44        76.21 
TCGA-50-5045 TCGA-50-5942 TCGA-50-5944 TCGA-50-8460 TCGA-55-6970 TCGA-55-6972 
       71.47        60.72        57.53        27.25        15.25        53.65 
TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7727 TCGA-55-7911 TCGA-62-8397 
      107.21        31.30        28.67         3.91        17.65        42.38 
TCGA-62-A472 TCGA-64-5815 TCGA-67-6215 TCGA-69-7763 TCGA-69-7765 TCGA-69-8253 
       29.92        28.47         5.72        22.68         5.42        14.01 
TCGA-75-5146 TCGA-75-6206 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 
       77.85        85.15        20.58       129.53        39.95        32.09 
TCGA-78-7537 TCGA-86-7714 TCGA-91-8496 TCGA-93-7347 TCGA-95-8039 TCGA-95-A4VP 
       53.33        20.55        16.60        22.45        27.29        19.89 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M0 TCGA-99-7458 TCGA-J2-A4AG 
        5.39        15.39        14.30        21.44        24.56        32.48 
TCGA-L4-A4E6 TCGA-MP-A4T7 TCGA-NJ-A4YG TCGA-NJ-A55O TCGA-O1-A52J 
       14.30         5.49        74.33         0.43        59.11 

$subtype2
TCGA-49-4501 TCGA-50-5935 TCGA-55-8203 TCGA-73-4662 TCGA-MP-A4TD TCGA-05-4390 
       46.72        21.47        17.98        82.68        10.09        37.02 
TCGA-05-4417 TCGA-05-5423 TCGA-05-5715 TCGA-38-4628 TCGA-49-4514 TCGA-50-5051 
       14.96         4.96         2.04        49.05        55.89        15.72 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6642 TCGA-55-7910 TCGA-55-7913 TCGA-55-8615 
       13.94        35.21        80.52        34.19        18.44        14.66 
TCGA-55-A494 TCGA-62-8394 TCGA-64-1678 TCGA-67-3772 TCGA-69-7760 TCGA-69-7973 
       15.81         4.57        39.09        18.84         6.64         7.56 
TCGA-69-A59K TCGA-73-4659 TCGA-78-7159 TCGA-78-7161 TCGA-80-5608 TCGA-86-6562 
       19.43        23.38        64.90         9.57        93.11        12.36 
TCGA-86-7701 TCGA-86-7954 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-97-A4M6 
       31.13        19.89        30.84         3.81        10.62        18.67 
TCGA-99-8032 TCGA-MP-A4SW 
        1.45        58.45 

$subtype3
TCGA-05-4396 TCGA-05-4405 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        9.96        20.05        15.02        28.41        35.28        11.64 
TCGA-44-2662 TCGA-49-6761 TCGA-55-6978 TCGA-55-6979 TCGA-55-8511 TCGA-64-1677 
       42.08        11.64         5.79         7.79        18.15        20.65 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-J2-8194 
       13.71         1.45         6.12        16.54         2.86        23.80 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4395 TCGA-05-4397 
       10.09        27.19         5.29        31.23         0.00        24.03 
TCGA-05-4422 TCGA-05-4425 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 TCGA-35-5375 
       12.00        21.99        29.00        22.03         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-44-2659 TCGA-44-2668 TCGA-44-3918 
       97.74       120.79        44.61        44.94        25.02        34.06 
TCGA-44-5643 TCGA-44-6774 TCGA-44-6775 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 
       33.30        21.63        23.18         7.17        12.66         8.55 
TCGA-44-A4SS TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
       13.64        28.57        35.54        32.84         8.81        29.75 
TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5066 
       22.26        62.24         8.55       221.33         9.86        47.41 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-6590 TCGA-50-6591 
        9.27        78.67        15.12        48.46        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 TCGA-55-6971 TCGA-55-6980 
       25.55        12.16        10.13        34.29        46.03        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       45.34        32.71        22.03        25.41        18.64        11.28 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       29.23        29.72        23.08        15.42        17.56        15.72 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG 
        0.36        17.72         1.58        20.71        21.40        19.99 
TCGA-62-8395 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       39.98        14.60        47.80        19.53        54.35        67.96 
TCGA-62-A471 TCGA-64-1676 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-69-7974 
       40.96        56.81        51.25        14.04        12.66         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4675 
        4.41        13.41        13.51         4.24         8.42        30.31 
TCGA-73-A9RS TCGA-75-7027 TCGA-78-7145 TCGA-78-7155 TCGA-78-7535 TCGA-78-7536 
       11.18       100.57        27.16        38.50        31.20         8.02 
TCGA-78-7539 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-7713 TCGA-86-7953 
       26.01        77.59       110.50        27.09        38.04        32.78 
TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 TCGA-86-8672 
       37.74        24.33        22.82        31.20        14.60         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-91-6847 TCGA-95-7039 
       28.34        26.50        29.46        24.23        27.68        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8177 
       18.67        12.39        25.48        18.54        18.67        16.41 
TCGA-97-8547 TCGA-99-8025 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A8F4 TCGA-MN-A4N4 
       21.60        34.85        21.57        19.00        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YP 
        2.76        11.05        73.91        71.05         1.64 

$subtype4
TCGA-05-4434 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-7661 TCGA-49-6745 
       15.02        26.30        38.10        23.93        18.31        17.16 
TCGA-50-6597 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       41.69        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        32.12        13.68        16.93        22.65 
TCGA-91-7771 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 
       16.18        15.68        15.65        18.18        17.92        20.52 
TCGA-L9-A743 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4403 TCGA-05-4426 TCGA-05-4433 
       21.83         2.43         3.98        19.00        26.01        24.00 
TCGA-05-5429 TCGA-35-4122 TCGA-38-A44F TCGA-44-2657 TCGA-44-2666 TCGA-44-5645 
        9.04         7.40         4.37        44.42         3.19        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6779 TCGA-44-A47G TCGA-49-4487 TCGA-49-4505 
       19.56        23.15        16.44        11.54        28.11        14.07 
TCGA-49-4510 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 
       29.46        55.33        22.26       164.12        20.52        60.16 
TCGA-50-5068 TCGA-50-5936 TCGA-50-6593 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 
       49.28         8.45        11.05         6.21        36.99        36.79 
TCGA-53-7626 TCGA-55-6712 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-7283 
       30.54         5.62        92.81        24.99        40.54        20.02 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7816 TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 
       32.71        23.15        15.39        15.19        15.65        29.19 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-62-A46R TCGA-62-A46Y TCGA-64-1680 
       19.96        26.01        17.62        56.71        13.61        37.02 
TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-4679 TCGA-69-7761 TCGA-69-7764 
       38.37        42.90        20.05        14.73         6.12        13.61 
TCGA-69-8254 TCGA-69-8453 TCGA-73-4676 TCGA-75-5125 TCGA-75-7025 TCGA-78-7143 
       13.45        26.73         9.24        66.64       108.66       163.10 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
       19.27       119.51        19.50         5.88        22.92       104.19 
TCGA-78-7167 TCGA-78-7540 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 TCGA-86-8671 
       88.14        39.35         4.57        32.65        23.05        27.58 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JN 
       26.47         2.60         1.15        14.27        19.82        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        1.08        19.00         2.76        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8552 TCGA-97-A4M1 
       61.48         0.59        15.91        18.12        20.58        19.76 
TCGA-97-A4M5 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L9-A50W TCGA-MP-A4T4 
       20.84        36.76        21.63        35.47        14.53        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A55A 
       41.59        24.36        14.10        11.15        19.13         0.49 
TCGA-S2-AA1A 
       16.87 

$subtype5
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-44-6147 TCGA-44-7670 
       19.96         8.02         9.01        26.01        27.78        29.00 
TCGA-44-8119 TCGA-49-6742 TCGA-49-AAR0 TCGA-55-1592 TCGA-55-7284 TCGA-55-A4DF 
        9.37        16.04       156.66        23.05         7.99        20.19 
TCGA-80-5611 TCGA-05-4389 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
       85.32        45.01        47.05         2.99        29.98        30.02 
TCGA-05-4430 TCGA-05-4432 TCGA-44-3396 TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 
       25.02        25.02        37.15        28.37        23.77        61.28 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-A479 TCGA-49-4490 TCGA-49-6743 
       19.46        36.07        18.87        15.98        12.66        53.29 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-50-5049 TCGA-50-5072 
       73.12        28.90        40.41       123.58       101.72         8.22 
TCGA-50-5931 TCGA-50-5946 TCGA-50-6673 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       14.27        53.16         0.72        38.73        67.89        30.58 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6987 TCGA-55-7570 TCGA-55-7994 TCGA-55-8092 
       42.51        40.73        70.26        27.09        19.82         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8208 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       17.79        23.64        22.16        14.47        13.74        20.28 
TCGA-55-8514 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8399 
       17.10        12.33         3.25         0.92        17.95        88.64 
TCGA-62-A470 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 
       39.25        81.80        87.98         2.04        28.41        20.05 
TCGA-73-7499 TCGA-75-5147 TCGA-75-6214 TCGA-78-7146 TCGA-78-7150 TCGA-78-7220 
       50.33        43.82        36.66         5.69        21.90        26.53 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-86-6851 TCGA-86-7711 TCGA-86-7955 
       10.55       232.18        39.75         5.88        34.39        35.24 
TCGA-86-8055 TCGA-86-8358 TCGA-86-8585 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
        4.08        21.47        11.61        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-J2-A4AD TCGA-L9-A5IP TCGA-L9-A7SV 
       12.23         7.36         1.18        18.08         1.91        18.58 
TCGA-MP-A4SV TCGA-MP-A4TE TCGA-NJ-A4YQ TCGA-NJ-A55R 
       86.14        29.46        47.08        19.82 

$subtype6
TCGA-38-6178 TCGA-44-2655 TCGA-55-8091 TCGA-73-4658 TCGA-97-A4M7 TCGA-J2-8192 
       14.73        43.53        19.73        52.60        20.68        24.30 
TCGA-L9-A443 TCGA-05-4249 TCGA-38-4627 TCGA-44-2665 TCGA-44-A4SU TCGA-55-6543 
        6.35        50.07        37.71        42.77        13.45        14.30 
TCGA-62-8402 TCGA-62-A46V TCGA-67-6216 TCGA-71-8520 TCGA-75-6212 TCGA-78-7163 
       49.25        72.30         4.64         6.90        49.84       238.29 
TCGA-86-8074 TCGA-86-8278 TCGA-86-8668 TCGA-86-A4P7 TCGA-93-7348 TCGA-MP-A4SY 
        0.79        31.04        13.91        13.64        17.46        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-NJ-A4YI TCGA-NJ-A7XG 
       37.35        58.85         0.13        20.28 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.43     1.45     0.00     0.49     0.72     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  129.53    93.11   221.33   164.12   232.18   238.29 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.640   18.755   22.030   20.050   23.705   22.490 
[1] "0.4 - 129.5 (23.6)" "1.4 - 93.1 (18.8)"  "0.0 - 221.3 (22.0)"
[4] "0.5 - 164.1 (20.1)" "0.7 - 232.2 (23.7)" "0.1 - 238.3 (22.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       27       19        0         4         8          9
  subtype2       0       11       10        0         4         6          4
  subtype3       3       26       48        0        12        22         22
  subtype4       1       38       30        1        15        18         15
  subtype5       1       22       25        0        12        11         17
  subtype6       0        9        7        0         3         5          6
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        2
  subtype2          2        1
  subtype3          4        7
  subtype4          2        9
  subtype5          2        5
  subtype6          0        0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        0        3        1        1        0
  STAGE IA         27       11       26       38       22        9
  STAGE IB         19       10       48       30       25        7
  STAGE II          0        0        0        1        0        0
  STAGE IIA         4        4       12       15       12        3
  STAGE IIB         8        6       22       18       11        5
  STAGE IIIA        9        4       22       15       17        6
  STAGE IIIB        1        2        4        2        2        0
  STAGE IV          2        1        7        9        5        0
[1] 9 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 31 33  4  4
  subtype2 11 22  4  2
  subtype3 34 90 16  4
  subtype4 50 61 13  5
  subtype5 32 51 10  3
  subtype6 12 17  0  1
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       31       11       34       50       32       12
  T2       33       22       90       61       51       17
  T3        4        4       16       13       10        0
  T4        4        2        4        5        3        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 50 13     6
  subtype2 28  5     5
  subtype3 97 23    24
  subtype4 80 29    17
  subtype5 59 16    19
  subtype6 16  9     5
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          50       28       97       80       59       16
  N1          13        5       23       29       16        9
  N2+N3        6        5       24       17       19        5
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1  50   2
  subtype2  33   1
  subtype3 102   7
  subtype4  80   8
  subtype5  59   5
  subtype6  22   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    2
  subtype2   33    1
  subtype3  102    7
  subtype4   80    8
  subtype5   59    5
  subtype6   22    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       50       33      102       80       59       22
  1        2        1        7        8        5        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 36 36
  subtype2 25 14
  subtype3 73 72
  subtype4 79 52
  subtype5 38 58
  subtype6 23  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   36
  subtype2   25   14
  subtype3   73   72
  subtype4   79   52
  subtype5   38   58
  subtype6   23    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       36       25       73       79       38       23
  MALE         36       14       72       52       58        7
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1  59  10
  subtype2  33   3
  subtype3 108  20
  subtype4 104  12
  subtype5  75  14
  subtype6  28   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   10
  subtype2   33    3
  subtype3  108   20
  subtype4  104   12
  subtype5   75   14
  subtype6   28    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        59       33      108      104       75       28
  YES       10        3       20       12       14        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          6                                19
  subtype2                          1                                11
  subtype3                          2                                28
  subtype4                          6                                28
  subtype5                          3                                17
  subtype6                          0                                 3
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 37
  subtype2                                                 24
  subtype3                                                101
  subtype4                                                 68
  subtype5                                                 67
  subtype6                                                 23
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          0
  subtype4                                          3
  subtype5                                          0
  subtype6                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             4
  subtype2                                             2
  subtype3                                             3
  subtype4                                             8
  subtype5                                             2
  subtype6                                             0
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  0
  subtype2                              0                                  0
  subtype3                              0                                  1
  subtype4                              0                                  0
  subtype5                              1                                  0
  subtype6                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             4
  subtype2                            0                             1
  subtype3                            0                             9
  subtype4                            2                             6
  subtype5                            0                             2
  subtype6                            0                             1
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               1
  subtype5                               0
  subtype6                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             0
  subtype3                                             1
  subtype4                                             2
  subtype5                                             2
  subtype6                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            1
  subtype2                            0
  subtype3                            0
  subtype4                            7
  subtype5                            2
  subtype6                            0
D10V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        1        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        19       11       28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       37       24      101
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             4        2        3
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             4        1        9
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        1
  MUCINOUS (COLLOID) CARCINOMA                              1        0        0
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  LUNG ACINAR ADENOCARCINOMA                                6        3        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        28       17        3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       68       67       23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             8        2        0
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             6        2        1
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        2        0
  MUCINOUS (COLLOID) CARCINOMA                              7        2        0
[1] 12  6
[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 41  1  0  4
  subtype2 29  1  0  2
  subtype3 97  5  0  7
  subtype4 84  3  3  8
  subtype5 65  2  1  5
  subtype6 25  1  0  0
D10V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       41       29       97       84       65       25
  R1        1        1        5        3        2        1
  R2        0        0        0        3        1        0
  RX        4        2        7        8        5        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    59
  subtype2     0                         3    30
  subtype3     4                        16   108
  subtype4     1                        11   105
  subtype5     1                        15    61
  subtype6     1                         1    24
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        4        1        1
  BLACK OR AFRICAN AMERICAN        6        3       16       11       15
  WHITE                           59       30      108      105       61
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        1
  WHITE                           24
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
          cls
clus         0   1
  subtype1   0  52
  subtype2   1  26
  subtype3   3 113
  subtype4   1 101
  subtype5   2  66
  subtype6   0  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   52
  subtype2    1   26
  subtype3    3  113
  subtype4    1  101
  subtype5    2   66
  subtype6    0   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        3        1        2        0
  NOT HISPANIC OR LATINO       52       26      113      101       66       23
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 46 12
  subtype2 54 34
  subtype3 43 49
  subtype4 28 14
  subtype5 45 25
  subtype6 55 21
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      58       88       92       42       70       76 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      12       34       49       14       25       21 
$subtype1
TCGA-05-4384 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-50-5935 
       14.01        23.93        27.78        86.01        29.23        21.47 
TCGA-50-6597 TCGA-55-7284 TCGA-55-7573 TCGA-55-8619 TCGA-55-8621 TCGA-67-6217 
       41.69         7.99        16.01        13.68        16.93        13.87 
TCGA-73-7498 TCGA-78-7633 TCGA-97-8172 TCGA-05-5423 TCGA-05-5429 TCGA-38-A44F 
       39.09        50.24        17.92         4.96         9.04         4.37 
TCGA-44-5645 TCGA-44-6148 TCGA-44-7659 TCGA-49-AARR TCGA-50-5942 TCGA-50-8457 
       28.01        23.15        22.72       164.12        60.72        36.99 
TCGA-50-8460 TCGA-55-7283 TCGA-55-7728 TCGA-55-8087 TCGA-55-8206 TCGA-55-8512 
       27.25        20.02        23.15        15.19        29.19        19.96 
TCGA-55-8513 TCGA-55-8616 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46Y TCGA-69-8253 
       26.01         1.58        39.98        42.38        13.61        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-75-5146 TCGA-75-6206 TCGA-75-7025 TCGA-78-7156 
       13.45        26.73        77.85        85.15       108.66        32.09 
TCGA-78-7540 TCGA-86-8056 TCGA-91-8496 TCGA-91-8497 TCGA-95-8039 TCGA-97-7546 
       39.35         4.57        16.60        14.27        27.29        42.25 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M1 TCGA-L9-A50W 
       63.52        15.91         5.39        20.58        19.76        14.53 
TCGA-MP-A4TH TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       24.36         0.49         0.43        16.87 

$subtype2
TCGA-05-4396 TCGA-38-4631 TCGA-44-8119 TCGA-50-5932 TCGA-55-8203 TCGA-78-7166 
        9.96        11.64         9.37        40.60        17.98         8.48 
TCGA-91-6836 TCGA-95-7043 TCGA-95-7562 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-05-4390 
       13.71        16.54         2.86        27.19         5.29        37.02 
TCGA-05-4415 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-44-5644 TCGA-44-7660 
        2.99        22.03         2.04         8.68        28.37        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5931 TCGA-50-5946 
       36.07        18.87        73.12         9.86        14.27        53.16 
TCGA-53-7813 TCGA-55-5899 TCGA-55-6968 TCGA-55-6972 TCGA-55-7570 TCGA-55-7910 
       13.94        30.58        42.51        53.65        27.09        34.19 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8094 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       18.44        19.82        17.79         0.36        13.74        20.28 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A490 TCGA-55-A494 TCGA-62-8394 
       17.10        14.66        12.33         3.25        15.81         4.57 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A471 
       14.60        49.25        47.80        19.53        54.35        40.96 
TCGA-64-5774 TCGA-64-5779 TCGA-67-6215 TCGA-69-7973 TCGA-69-8255 TCGA-69-A59K 
       87.98        28.41         5.72         7.56         4.24        19.43 
TCGA-73-A9RS TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
       11.18       129.53        38.50        64.90         9.57        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 
       31.20         8.02        26.01       232.18       110.50        93.11 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8358 TCGA-86-8359 
       12.36        38.04        35.24        37.74        21.47        14.60 
TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6831 TCGA-91-6840 
       30.84        28.34        26.50         3.81        10.19        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-97-8171 TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MP-A4TE 
       27.68         1.18        18.67        19.00        18.58        29.46 
TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A55R 
       11.05        73.91        71.05        19.82 

$subtype3
TCGA-05-4405 TCGA-05-4427 TCGA-05-5420 TCGA-38-7271 TCGA-44-7661 TCGA-44-7670 
       20.05        26.01        15.02        26.30        18.31        29.00 
TCGA-49-6742 TCGA-49-6745 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-91-7771 
       16.04        17.16        23.18        21.44         6.15        16.18 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4433 TCGA-05-5425 TCGA-38-4632 TCGA-44-5643 
       30.02        21.99        24.00        29.00        44.61        33.30 
TCGA-44-6145 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7672 
       19.56        32.45        61.28        16.44         7.17        23.64 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       28.11        12.66        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5051 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 
       22.26        20.52        15.72         8.22         9.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 
        8.45        15.12        48.46        57.53        42.35        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
       11.05        12.16         6.21        10.13        34.29        30.54 
TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
        5.62        31.30        28.67        32.71        22.03         3.91 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-64-1679 
       25.41        15.39        18.64        11.28        17.65        81.80 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5815 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 
       38.37         2.04        28.47         4.64         6.64         5.42 
TCGA-71-6725 TCGA-73-4676 TCGA-75-5125 TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 
        8.42         9.24        66.64        49.84       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        5.69        19.27        20.58        21.90        39.95        19.50 
TCGA-78-7160 TCGA-78-7220 TCGA-78-7542 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       22.92        26.53        10.55        31.13        34.39        20.55 
TCGA-91-6828 TCGA-91-6835 TCGA-95-7567 TCGA-97-7547 TCGA-97-7553 TCGA-97-7937 
       10.62         2.60        18.67        64.60        61.48        18.54 
TCGA-97-7938 TCGA-99-7458 
        0.59        24.56 

$subtype4
TCGA-38-6178 TCGA-55-8091 TCGA-73-4658 TCGA-91-A4BC TCGA-J2-8192 TCGA-MP-A4TD 
       14.73        19.73        52.60         1.45        24.30        10.09 
TCGA-05-4417 TCGA-44-6144 TCGA-44-6774 TCGA-44-A479 TCGA-44-A4SU TCGA-49-AAR9 
       14.96        23.77        21.63        15.98        13.45         8.55 
TCGA-50-6591 TCGA-50-8459 TCGA-55-6543 TCGA-55-6642 TCGA-55-6983 TCGA-55-8505 
        3.91        36.79        14.30        80.52        92.81        14.47 
TCGA-55-8614 TCGA-55-A48Y TCGA-62-A46V TCGA-71-8520 TCGA-75-7027 TCGA-78-7163 
       17.62        20.71        72.30         6.90       100.57       238.29 
TCGA-78-7537 TCGA-78-8648 TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 TCGA-86-8668 
       53.33        39.75         4.08         0.79        31.04        13.91 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6848 TCGA-93-7348 TCGA-97-7554 TCGA-97-8177 
        0.62        41.36         7.36        17.46        25.48        16.41 
TCGA-99-8032 TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
        1.45        37.35        58.85         0.13         1.64        20.28 

$subtype5
TCGA-44-A47F TCGA-49-AAR0 TCGA-49-AARN TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       11.08       156.66        37.32        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-78-8660 TCGA-93-A4JQ TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX 
       20.19        10.55        17.29        21.40        18.18        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.52        17.75        20.68         6.35        10.09        21.83 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-44-6775 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       31.23         2.43        23.18         9.44        11.54        13.64 
TCGA-49-AAQV TCGA-49-AARE TCGA-53-A4EZ TCGA-55-A48Z TCGA-55-A493 TCGA-55-A4DG 
       22.26        40.41        35.21        21.40         0.92        19.99 
TCGA-55-A57B TCGA-62-8399 TCGA-62-A46R TCGA-62-A46U TCGA-62-A470 TCGA-62-A472 
       17.95        88.64        56.71        67.96        39.25        29.92 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-A4BD TCGA-93-A4JN 
       29.46        24.23        13.64        26.47        19.82        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-A4VP TCGA-97-8176 TCGA-97-A4M0 TCGA-97-A4M5 
        1.08        19.00        19.89        15.39        21.44        20.84 
TCGA-97-A4M6 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       18.67        21.63        18.08        35.47        32.48        14.30 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        1.91        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TI TCGA-MP-A4TJ 
       49.35        86.04         5.49        41.59        14.10        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YQ TCGA-O1-A52J 
       19.13        74.33        47.08        59.11 

$subtype6
TCGA-49-6761 TCGA-55-6978 TCGA-55-6979 TCGA-55-8090 TCGA-55-8204 TCGA-55-8205 
       11.64         5.79         7.79        19.66        16.93        19.69 
TCGA-55-8511 TCGA-80-5611 TCGA-95-7947 TCGA-95-7948 TCGA-J2-8194 TCGA-44-8117 
       18.15        85.32        15.68        15.65        23.80        12.66 
TCGA-44-8120 TCGA-49-4488 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ 
        8.55        28.57        62.24        28.90       123.58       221.33 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-6673 
       71.47       101.72        60.16        47.41        49.28         0.72 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        15.25        46.03        69.34        45.34        32.71 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-8085 TCGA-55-8089 
       24.99        40.54       107.21        70.26        29.72        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        5.06        23.64        22.16        15.42        17.56        15.72 
TCGA-55-8510 TCGA-64-5778 TCGA-64-5781 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       17.72        42.90        51.25         6.05         4.41        13.41 
TCGA-69-7980 TCGA-73-7499 TCGA-75-5147 TCGA-75-6214 TCGA-78-8655 TCGA-83-5908 
       13.51        50.33        43.82        36.66        77.59        27.09 
TCGA-86-6851 TCGA-86-7953 TCGA-86-7954 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
        5.88        32.78        19.89        24.33        22.82        32.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8671 TCGA-91-6830 TCGA-91-6849 
       31.20        23.05        11.61        27.58         1.97         1.15 
TCGA-93-7347 TCGA-95-7039 TCGA-95-7944 TCGA-95-8494 TCGA-97-8175 TCGA-97-8179 
       22.45        41.82        12.39         2.76        18.12        14.30 
TCGA-97-8547 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       21.60        34.85        36.76        21.57 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.43     0.36     0.59     0.13     0.92     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  164.12   232.18   163.10   238.29   156.66   221.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.095   19.445   21.945   17.540   20.630   23.360 
[1] "0.4 - 164.1 (22.1)" "0.4 - 232.2 (19.4)" "0.6 - 163.1 (21.9)"
[4] "0.1 - 238.3 (17.5)" "0.9 - 156.7 (20.6)" "0.7 - 221.3 (23.4)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       21       15        0         5         9          5
  subtype2       1       15       28        0        16        11          8
  subtype3       0       18       21        0         9        14         25
  subtype4       0        7       14        0         5         7         10
  subtype5       0       31       11        1         6         9          7
  subtype6       3       20       25        0         8        10          9
          vv
clus       STAGE IIIB STAGE IV
  subtype1          0        2
  subtype2          5        5
  subtype3          2        7
  subtype4          0        1
  subtype5          1        4
  subtype6          0        1
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        1        0        0        0        3
  STAGE IA         21       15       18        7       31       20
  STAGE IB         15       28       21       14       11       25
  STAGE II          0        0        0        0        1        0
  STAGE IIA         5       16        9        5        6        8
  STAGE IIB         9       11       14        7        9       10
  STAGE IIIA        5        8       25       10        7        9
  STAGE IIIB        0        5        2        0        1        0
  STAGE IV          2        5        7        1        4        1
[1] 9 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 26 21 10  2
  subtype2 22 54  9  5
  subtype3 26 54  9  7
  subtype4 11 28  4  1
  subtype5 37 28  4  0
  subtype6 26 46  4  0
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       26       22       26       11       37       26
  T2       21       54       54       28       28       46
  T3       10        9        9        4        4        4
  T4        2        5        7        1        0        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 44  7     4
  subtype2 62 16    11
  subtype3 48 23    24
  subtype4 28  7     9
  subtype5 46 15     8
  subtype6 53 13     9
D11V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          44       62       48       28       46       53
  N1           7       16       23        7       15       13
  N2+N3        4       11       24        9        8        9
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus        0  1
  subtype1 34  2
  subtype2 62  5
  subtype3 66  6
  subtype4 28  1
  subtype5 42  4
  subtype6 48  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    2
  subtype2   62    5
  subtype3   66    6
  subtype4   28    1
  subtype5   42    4
  subtype6   48    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       34       62       66       28       42       48
  1        2        5        6        1        4        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1 34 25
  subtype2 37 53
  subtype3 53 44
  subtype4 22 22
  subtype5 38 32
  subtype6 50 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   25
  subtype2   37   53
  subtype3   53   44
  subtype4   22   22
  subtype5   38   32
  subtype6   50   27
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       34       37       53       22       38       50
  MALE         25       53       44       22       32       27
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1 48  6
  subtype2 73 11
  subtype3 73 17
  subtype4 40  2
  subtype5 60  8
  subtype6 63 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    6
  subtype2   73   11
  subtype3   73   17
  subtype4   40    2
  subtype5   60    8
  subtype6   63   11
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        48       73       73       40       60       63
  YES        6       11       17        2        8       11
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          4                                15
  subtype2                          3                                19
  subtype3                          1                                21
  subtype4                          0                                 4
  subtype5                          6                                14
  subtype6                          2                                13
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 22
  subtype2                                                 59
  subtype3                                                 62
  subtype4                                                 32
  subtype5                                                 45
  subtype6                                                 48
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          0
  subtype4                                          2
  subtype5                                          0
  subtype6                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             6
  subtype2                                             2
  subtype3                                             4
  subtype4                                             1
  subtype5                                             0
  subtype6                                             6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              0                                  0
  subtype3                              1                                  2
  subtype4                              0                                  0
  subtype5                              0                                  0
  subtype6                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             2
  subtype2                            0                             5
  subtype3                            0                             4
  subtype4                            0                             3
  subtype5                            0                             3
  subtype6                            0                             5
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               1
  subtype6                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             1
  subtype3                                             0
  subtype4                                             0
  subtype5                                             1
  subtype6                                             3
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            5
  subtype2                            1
  subtype3                            2
  subtype4                            2
  subtype5                            0
  subtype6                            0
D11V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4        3        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        15       19       21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       22       59       62
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6        2        4
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             2        5        4
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        0
  MUCINOUS (COLLOID) CARCINOMA                              5        1        2
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  LUNG ACINAR ADENOCARCINOMA                                0        6        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         4       14       13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       32       45       48
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        0        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             3        3        5
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        3
  MUCINOUS (COLLOID) CARCINOMA                              2        0        0
[1] 12  6
[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 34  0  0  3
  subtype2 66  1  0  3
  subtype3 56  6  1  2
  subtype4 30  1  0  2
  subtype5 47  1  0 11
  subtype6 48  1  0  1
D11V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       34       66       56       30       47       48
  R1        0        1        6        1        1        1
  R2        0        0        1        0        0        0
  RX        3        3        2        2       11        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         7    45
  subtype2     1                        14    64
  subtype3     1                         7    74
  subtype4     1                         3    34
  subtype5     2                         9    54
  subtype6     0                        10    62
D11V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        1        1        2
  BLACK OR AFRICAN AMERICAN        7       14        7        3        9
  WHITE                           45       64       74       34       54
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN       10
  WHITE                           62
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
          cls
clus        0  1
  subtype1  0 48
  subtype2  1 68
  subtype3  3 56
  subtype4  0 33
  subtype5  2 59
  subtype6  0 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   48
  subtype2    1   68
  subtype3    3   56
  subtype4    0   33
  subtype5    2   59
  subtype6    0   62
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        3        0        2        0
  NOT HISPANIC OR LATINO       48       68       56       33       59       62
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1  77  24
  subtype2 145  89
  subtype3  49  42
subtype1 subtype2 subtype3 
     101      234       91 
subtype1 subtype2 subtype3 
      24       89       42 
$subtype1
TCGA-05-4384 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-A47F TCGA-50-5932 
       14.01        23.93        27.78        86.01        11.08        40.60 
TCGA-55-7284 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 
        7.99        13.68        16.93        22.65        19.59        13.87 
TCGA-73-7498 TCGA-78-7633 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       39.09        50.24        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-L9-A743 TCGA-05-4433 TCGA-05-5429 TCGA-38-A44F 
       20.52        17.75        21.83        24.00         9.04         4.37 
TCGA-44-5645 TCGA-44-A47B TCGA-44-A47G TCGA-49-AAQV TCGA-49-AARR TCGA-50-8457 
       28.01         9.44        11.54        22.26       164.12        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-55-6972 TCGA-55-6984 TCGA-55-7727 TCGA-55-7728 
       36.79        27.25        53.65        24.99         3.91        23.15 
TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8206 TCGA-55-8512 TCGA-55-8513 
       17.65        29.72        15.19        29.19        19.96        26.01 
TCGA-55-8616 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-A46S TCGA-62-A46Y 
        1.58        19.99        39.98        42.38        54.35        13.61 
TCGA-62-A472 TCGA-64-5778 TCGA-67-6215 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
       29.92        42.90         5.72        13.45        26.73        19.43 
TCGA-75-5146 TCGA-75-6206 TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7167 
       77.85        85.15       129.53        39.95        32.09        88.14 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 
       53.33        26.01        39.35         4.57        32.65        23.05 
TCGA-86-8669 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-8496 TCGA-91-8497 
       30.84        29.46        24.23        26.47        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-8039 
       19.82        22.45        23.61         1.08        19.00        27.29 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7941 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M0 
       19.89        63.52        15.91         5.39        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       19.76        20.84        21.63        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 
       14.53         5.49        41.59        24.36        11.15        73.91 
TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J TCGA-S2-AA1A 
       74.33         0.49         0.43        59.11        16.87 

$subtype2
TCGA-05-4396 TCGA-05-5420 TCGA-38-4631 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 
        9.96        15.02        11.64        29.00         9.37        16.04 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-55-6978 TCGA-55-6979 
       11.64       156.66        37.32        21.47         5.79         7.79 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 
       19.66        19.73        17.98        16.93        19.69        18.15 
TCGA-55-A491 TCGA-55-A4DF TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       20.58        20.19         8.48        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       16.18         1.45        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-J2-8194 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       15.65        23.80        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4390 TCGA-05-4415 TCGA-05-4424 TCGA-05-5423 
        2.43        10.09        37.02         2.99        30.02         4.96 
TCGA-05-5425 TCGA-05-5715 TCGA-35-5375 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       29.00         2.04         8.68        33.30        28.37        23.77 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       23.15        23.18        61.28        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS TCGA-49-4490 
       18.87        12.66         8.55        15.98        13.64        12.66 
TCGA-49-4514 TCGA-49-6743 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       55.89        53.29        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       40.41       123.58       221.33         9.86        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6673 
       14.27        53.16        42.35         3.91        25.55         0.72 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 
       10.13        34.29        13.94        35.21        30.58        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        15.25        46.03        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7910 
       92.81        40.54       107.21        70.26        27.09        34.19 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       18.44        19.82        23.08         5.06        17.79        23.64 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       13.74        20.28        17.72        17.10        17.62        14.66 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       17.95         4.57        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-5774 
       56.71        67.96        39.25        40.96        81.80        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        2.04        28.41        51.25         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-73-7499 TCGA-73-A9RS 
       13.41        13.51        14.01         4.24        50.33        11.18 
TCGA-75-5147 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
       43.82        36.66       108.66       100.57         5.69        20.58 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 
       21.90        19.50        38.50        64.90         9.57        26.53 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
        8.02        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       38.04        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
       24.33        22.82        31.04        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
       11.61        27.58         0.62        28.34        26.50         3.81 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
       10.62        41.36         1.97        10.19        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
        7.36         1.15         1.18        41.82        18.67        12.39 
TCGA-95-8494 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
        2.76        18.67        18.12        15.39        14.30        21.60 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       18.67        34.85        36.76         1.45        21.57        18.08 
TCGA-L4-A4E5 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       19.00         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.14        58.45        49.35        86.04        29.46        11.05 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55R 
       14.10        19.13        71.05         1.64        47.08        19.82 

$subtype3
TCGA-05-4405 TCGA-05-4427 TCGA-38-6178 TCGA-38-7271 TCGA-44-7661 TCGA-44-7671 
       20.05        26.01        14.73        26.30        18.31        29.23 
TCGA-49-6745 TCGA-50-6597 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 
       17.16        41.69        16.01        23.18        21.44         6.15 
TCGA-73-4658 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-05-4417 TCGA-05-4425 
       52.60        20.68        24.30         6.35        14.96        21.99 
TCGA-05-5428 TCGA-38-4632 TCGA-44-6145 TCGA-44-6774 TCGA-44-6777 TCGA-44-6779 
       22.03        44.61        19.56        21.63        32.45        16.44 
TCGA-44-7659 TCGA-44-7672 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4512 
       22.72        23.64        13.45        28.11        28.57        29.75 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
       55.33        22.26        20.52        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       48.46        60.72        57.53        11.05        12.16         6.21 
TCGA-53-7626 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 
       30.54        14.30        80.52         5.62        31.30        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       20.02        32.71        22.03        25.41        15.39        18.64 
TCGA-55-7907 TCGA-62-8402 TCGA-62-A46V TCGA-64-1681 TCGA-64-5815 TCGA-67-6216 
       11.28        49.25        72.30        38.37        28.47         4.64 
TCGA-69-7760 TCGA-69-7765 TCGA-71-6725 TCGA-71-8520 TCGA-73-4676 TCGA-75-5125 
        6.64         5.42         8.42         6.90         9.24        66.64 
TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7160 TCGA-78-7163 
       49.84       163.10        27.16        19.27        22.92       238.29 
TCGA-78-7535 TCGA-86-7714 TCGA-86-8074 TCGA-86-8668 TCGA-86-A4P7 TCGA-91-6835 
       31.20        20.55         0.79        13.91        13.64         2.60 
TCGA-93-7348 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       17.46        42.25        64.60        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-8177 TCGA-99-7458 TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-NJ-A4YI 
        0.59        16.41        24.56        37.35        58.85         0.13 
TCGA-NJ-A7XG 
       20.28 

subtype1 subtype2 subtype3 
    0.43     0.36     0.13 
subtype1 subtype2 subtype3 
  164.12   232.18   238.29 
subtype1 subtype2 subtype3 
  22.450   19.675   22.030 
[1] "0.4 - 164.1 (22.4)" "0.4 - 232.2 (19.7)" "0.1 - 238.3 (22.0)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       35       25        1        10        15          9
  subtype2       4       52       64        0        30        36         36
  subtype3       0       25       25        0         9         9         19
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        6
  subtype2          5        9
  subtype3          2        5
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         35       52       25
  STAGE IB         25       64       25
  STAGE II          1        0        0
  STAGE IIA        10       30        9
  STAGE IIB        15       36        9
  STAGE IIIA        9       36       19
  STAGE IIIB        1        5        2
  STAGE IV          6        9        5
[1] 9 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  44  43  13   3
  subtype2  71 139  22   5
  subtype3  33  49   5   7
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       44       71       33
  T2       43      139       49
  T3       13       22        5
  T4        3        5        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1  77  13     8
  subtype2 150  47    39
  subtype3  54  21    18
D12V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          77      150       54
  N1          13       47       21
  N2+N3        8       39       18
[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  67   6
  subtype2 154   9
  subtype3  59   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    6
  subtype2  154    9
  subtype3   59    4
   clus
vv  subtype1 subtype2 subtype3
  0       67      154       59
  1        6        9        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus         0   1
  subtype1  53  51
  subtype2 114 124
  subtype3  67  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   51
  subtype2  114  124
  subtype3   67   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       53      114       67
  MALE         51      124       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus         0   1
  subtype1  92   6
  subtype2 187  36
  subtype3  78  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    6
  subtype2  187   36
  subtype3   78   13
     clus
vv    subtype1 subtype2 subtype3
  NO        92      187       78
  YES        6       36       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                27
  subtype2                          9                                40
  subtype3                          2                                19
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 44
  subtype2                                                164
  subtype3                                                 60
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             7
  subtype2                                             7
  subtype3                                             5
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              1                                  0
  subtype3                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             9
  subtype2                            1                             9
  subtype3                            0                             4
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             4
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            6
  subtype2                            3
  subtype3                            1
D12V10, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        9        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        27       40       19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       44      164       60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             7        7        5
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              1        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             9        9        4
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        4        0
  MUCINOUS (COLLOID) CARCINOMA                              6        3        1
[1] 12  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  66   0   0   8
  subtype2 157   4   1  12
  subtype3  58   6   0   2
D12V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       66      157       58
  R1        0        4        6
  R2        0        1        0
  RX        8       12        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     2                         9    83
  subtype2     1                        34   176
  subtype3     2                         7    74
D12V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        9       34        7
  WHITE                           83      176       74
[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  84
  subtype2   6 177
  subtype3   0  65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   84
  subtype2    6  177
  subtype3    0   65
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        6        0
  NOT HISPANIC OR LATINO       84      177       65
[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"
