[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/15084450/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/15111023/LUAD-TP.mergedcluster.txt"

nPatients in clinical file=521, in cluster file=519, common to both=518
[1]  12 518
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
 5  9 12  6 
 1  2  3  4 
 5  9 12  6 
[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 
 69 228  78 140 
  1   2   3   4 
 69 228  78 140 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
145 148 164 
  1   2   3 
145 148 164 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
44 73 64 
 1  2  3 
44 73 64 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
40 33 45 31 32 
 1  2  3  4  5 
40 33 45 31 32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
167 197 150 
  1   2   3 
167 197 150 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
 79 112  97  48  52  49  77 
  1   2   3   4   5   6   7 
 79 112  97  48  52  49  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
190 227  95 
  1   2   3 
190 227  95 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 72 198 142 100 
  1   2   3   4 
 72 198 142 100 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
146 197  93 
  1   2   3 
146 197  93 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
103 247  86 
  1   2   3 
103 247  86 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 518 columns.

[1] "Batch" "23"   
[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=147,	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=324,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 518 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
170 279  47  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
170 279  47  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
170 279  47  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
170 279  47  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
333  97  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  333    97    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
333  97  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  333    97    76 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=95, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, 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  4  0
  subtype2  7  2
  subtype3 10  2
  subtype4  4  2
subtype1 subtype2 subtype3 subtype4 
       4        9       12        6 
subtype1 subtype2 subtype3 subtype4 
       0        2        2        2 
$subtype1
TCGA-35-4123 TCGA-44-2665 TCGA-44-3919 TCGA-55-1595 
        5.98        42.77         6.25        48.62 

$subtype2
TCGA-05-4249 TCGA-05-4250 TCGA-35-4122 TCGA-44-2656 TCGA-44-2662 TCGA-44-2668 
       50.07         3.98         7.40        46.98        42.08        25.02 
TCGA-44-3398 TCGA-44-3918 TCGA-64-1676 
       38.24        34.06        56.81 

$subtype3
TCGA-35-3615 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
        0.46        43.53        13.15        44.94        24.36         3.19 
TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       26.56        37.02         1.02        18.84        14.04        12.66 

$subtype4
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-64-1677 TCGA-64-1678 TCGA-67-3771 
       23.05        38.73        45.21        20.65        39.09        20.05 

subtype1 subtype2 subtype3 subtype4 
    5.98     3.98     0.46    20.05 
subtype1 subtype2 subtype3 subtype4 
   48.62    56.81    44.94    45.21 
subtype1 subtype2 subtype3 subtype4 
   24.51    38.24    16.44    30.89 
[1] "6.0 - 48.6 (24.5)"  "4.0 - 56.8 (38.2)"  "0.5 - 44.9 (16.4)" 
[4] "20.1 - 45.2 (30.9)"
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IV
  subtype1        3        0         0         1          0        1
  subtype2        4        4         0         0          1        0
  subtype3        3        7         0         1          0        1
  subtype4        2        0         1         1          2        0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          3        4        3        2
  STAGE IB          0        4        7        0
  STAGE IIA         0        0        0        1
  STAGE IIB         1        0        1        1
  STAGE IIIA        0        1        0        2
  STAGE IV          1        0        1        0
[1] 6 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
  subtype1  3  2  0
  subtype2  4  4  1
  subtype3  4  8  0
  subtype4  1  5  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        4        4        1
  T2        2        4        8        5
  T3        0        1        0        0
[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"
          vv
clus       N0 N1 N2+N3
  subtype1  3  1     1
  subtype2  8  1     0
  subtype3  9  1     1
  subtype4  3  1     2
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0           3        8        9        3
  N1           1        1        1        1
  N2+N3        1        0        1        2
[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"
D1V6, binary
          cls
clus        0  1
  subtype1  4  1
  subtype2  9  0
  subtype3 11  1
  subtype4  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    9    0
  subtype3   11    1
  subtype4    6    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        4        9       11        6
  1        1        0        1        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 3 6
  subtype3 9 3
  subtype4 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    3    6
  subtype3    9    3
  subtype4    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        3        9        3
  MALE          2        6        3        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype4 
       1        1        1 
character(0)
          vv
clus       LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                                 0
  subtype2                                 0
  subtype3                                 1
  subtype4                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                  4
  subtype2                                                  9
  subtype3                                                 11
  subtype4                                                  6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA
  subtype1                              1
  subtype2                              0
  subtype3                              0
  subtype4                              0
D1V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         0        0        1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        4        9       11
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
                                                    clus
vv                                                   subtype4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus        0  1
  subtype1  0  5
  subtype2  0  9
  subtype3  1 11
  subtype4  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    5
  subtype2    0    9
  subtype3    1   11
  subtype4    0    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        0        1        0
  YES        5        9       11        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        9        6        3 
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype3" "subtype4" "subtype2" "subtype4" "subtype4" "subtype3"
D1V12, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        6        6        5 
 [1] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype4"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
          vv
clus       R0 R2 RX
  subtype1  3  0  1
  subtype2  7  1  0
  subtype3 10  0  1
  subtype4  6  0  0
D1V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        3        7       10        6
  R2        0        1        0        0
  RX        1        0        1        0
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     3
  subtype2     0                         0     7
  subtype3     0                         0    12
  subtype4     1                         1     4
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                            3        7       12        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
          cls
clus        0  1
  subtype1  0  4
  subtype2  0  7
  subtype3  1 11
  subtype4  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype2    0    7
  subtype3    1   11
  subtype4    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        0        1        0
  NOT HISPANIC OR LATINO        4        7       11        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  9  2
  subtype3  5  2
subtype1 subtype2 subtype3 
      13       11        7 
subtype1 subtype2 subtype3 
       2        2        2 
$subtype1
TCGA-35-3615 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        0.46        43.53        46.98        13.15        44.94        24.36 
TCGA-44-2666 TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        3.19        26.56        37.02         1.02        18.84        14.04 
TCGA-67-3774 
       12.66 

$subtype2
TCGA-05-4249 TCGA-05-4250 TCGA-35-4122 TCGA-35-4123 TCGA-44-2662 TCGA-44-2665 
       50.07         3.98         7.40         5.98        42.08        42.77 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-64-1676 
       25.02        38.24        34.06         6.25        56.81 

$subtype3
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-64-1677 TCGA-64-1678 
       23.05        38.73        48.62        45.21        20.65        39.09 
TCGA-67-3771 
       20.05 

subtype1 subtype2 subtype3 
    0.46     3.98    20.05 
subtype1 subtype2 subtype3 
   46.98    56.81    48.62 
subtype1 subtype2 subtype3 
   18.84    34.06    38.73 
[1] "0.5 - 47.0 (18.8)"  "4.0 - 56.8 (34.1)"  "20.1 - 48.6 (38.7)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IV
  subtype1        3        8         0         1          0        2
  subtype2        6        3         0         1          1        0
  subtype3        3        0         1         1          2        0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          3        6        3
  STAGE IB          8        3        0
  STAGE IIA         0        0        1
  STAGE IIB         1        1        1
  STAGE IIIA        0        1        2
  STAGE IV          2        0        0
[1] 6 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, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       2        1 
character(0)
          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
D2V9, 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"
D2V10, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  0 11
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    0   11
  subtype3    0    7
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        0
  YES       13       11        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"
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  47  18
  subtype2 161  56
  subtype3  44  31
  subtype4  85  49
subtype1 subtype2 subtype3 subtype4 
      65      217       75      134 
subtype1 subtype2 subtype3 subtype4 
      18       56       31       49 
$subtype1
TCGA-05-4389 TCGA-05-4390 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-35-5375 
       45.01        37.02        14.96        30.02        25.02         8.68 
TCGA-44-3917 TCGA-44-6774 TCGA-44-6778 TCGA-44-8119 TCGA-44-A47F TCGA-4B-A93V 
       38.89        21.63        61.28         3.25        11.08         9.86 
TCGA-50-5051 TCGA-50-5932 TCGA-50-5935 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ 
       15.72        40.60        21.47        10.13        13.94         9.21 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6970 TCGA-55-6972 TCGA-55-7903 TCGA-55-8085 
        2.86        42.51        15.25        48.49        18.64        29.72 
TCGA-55-8203 TCGA-55-8615 TCGA-55-8616 TCGA-55-A494 TCGA-62-8395 TCGA-62-A46P 
       17.98         0.49         1.58        15.81        39.98        19.53 
TCGA-62-A46S TCGA-62-A470 TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       54.35        39.25        20.65        87.98         2.04        28.41 
TCGA-67-3771 TCGA-69-7764 TCGA-69-7973 TCGA-73-4675 TCGA-78-7149 TCGA-78-7159 
       20.05        13.61         7.56         1.32        35.93        64.90 
TCGA-78-7167 TCGA-78-7536 TCGA-86-7701 TCGA-86-8054 TCGA-86-A4D0 TCGA-91-6828 
       88.14         8.02        31.13        24.49         3.81        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-8067 TCGA-95-7948 TCGA-95-A4VP 
       10.19        12.23         1.18         6.12        15.65        19.89 
TCGA-97-8171 TCGA-97-8179 TCGA-99-8032 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 
       18.67        14.30         1.45         3.81         0.20         2.76 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A7XG 
       29.46        11.05        71.05         0.13         9.70 

$subtype2
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 TCGA-05-4426 
       50.07        14.01         9.96        19.00        12.00        26.01 
TCGA-05-4430 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        15.02        15.02         9.04         2.04         0.46 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       97.74       120.79        37.71        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        13.15        24.36        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 
       25.02        37.15        38.24        34.06        26.56        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        27.78        23.15        23.18        63.72 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
       14.60        12.03        17.59        23.64        15.98        15.32 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 
       11.54        13.64        76.21        28.11        35.54        32.84 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 
       12.13        29.26        17.16        11.64        22.26       153.04 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       62.24        28.90       164.12        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 
       60.16        31.04        49.28        15.12        29.03        42.35 
TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        6.21         0.72        25.61         7.59        27.25        30.54 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 
       32.65        40.73         3.88         5.49         2.20        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       60.03        24.99       107.21        70.26         0.59         1.15 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
        0.13         3.12        23.18         1.28         0.79         1.78 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8097 
       17.65         6.15        15.19         3.29        19.66        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.08         1.51        22.16        15.42         1.45         0.95 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.10         4.80         1.61        16.93        22.65        20.71 
TCGA-55-A492 TCGA-55-A57B TCGA-62-A46U TCGA-62-A46Y TCGA-64-1680 TCGA-64-5781 
       19.59        17.95        67.96        13.61        37.02        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        14.04        12.66         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
        6.12        22.68         5.42         2.30        14.01        13.45 
TCGA-69-8453 TCGA-73-4658 TCGA-73-4659 TCGA-73-4677 TCGA-73-7498 TCGA-78-7152 
       26.73        52.60        23.38         1.25        39.09        39.52 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       24.99        32.09         5.88        22.29       104.19       223.96 
TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        8.48        53.33        39.35        32.68        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       10.55        27.09        20.55         4.57        24.33        16.08 
TCGA-86-8278 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       15.65         1.15        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 
       17.62        13.64        26.47         1.97         2.60         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7944 
        4.18        23.61         1.08        19.00        17.29        12.39 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        31.69        64.60        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       16.41        20.58        20.19        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8194 
       20.84        20.68        24.56        36.76        21.63        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 TCGA-MP-A4SY TCGA-MP-A4T9 
       35.47        16.44        14.30        17.46        49.35        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       31.23         2.43        10.09        14.66        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91        62.60         1.64         0.26         0.43        19.82 
TCGA-S2-AA1A 
       16.87 

$subtype3
TCGA-05-4250 TCGA-05-4382 TCGA-05-4395 TCGA-05-4415 TCGA-05-4418 TCGA-05-4433 
        3.98        19.96         0.00         2.99         9.01        24.00 
TCGA-05-5425 TCGA-35-4122 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-44-5643 
       29.00         7.40        49.05        35.28        11.64        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       28.37        23.77        16.44        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-A47B TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       29.00         9.44         8.81        29.46        55.89        14.63 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 
       63.95         8.55        40.41         8.22        14.27         8.45 
TCGA-50-6592 TCGA-53-7624 TCGA-55-1594 TCGA-55-1595 TCGA-55-6971 TCGA-55-7284 
       25.55        34.29        38.73        48.62         0.82         7.99 
TCGA-55-7570 TCGA-55-7726 TCGA-55-7907 TCGA-55-7995 TCGA-55-8091 TCGA-55-8092 
        0.20         1.28         0.53         0.16        19.73         5.06 
TCGA-55-8094 TCGA-55-8302 TCGA-55-8508 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF 
        0.13         0.76         0.49         1.58         0.92        20.19 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1678 TCGA-69-7760 
       14.60        49.25        72.30        40.96        39.09         6.64 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4666 TCGA-73-4670 TCGA-73-A9RS TCGA-78-7146 
       12.56         4.24        26.30         4.31        11.18         5.69 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7220 TCGA-86-7713 TCGA-86-7953 TCGA-86-8669 
       20.58        21.90        26.53        13.87        19.43        30.84 
TCGA-91-7771 TCGA-95-7567 TCGA-97-A4M6 TCGA-99-8033 TCGA-L9-A5IP TCGA-MN-A4N4 
       16.18        18.67        18.67         5.59         1.91        38.63 
TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-NJ-A4YQ 
       86.14         5.49        29.13 

$subtype4
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4420 TCGA-05-4425 
       24.03        47.05         8.02        20.05        29.98        21.99 
TCGA-05-4427 TCGA-05-5423 TCGA-05-5428 TCGA-35-4123 TCGA-38-4629 TCGA-38-4632 
       26.01         4.96        22.03         5.98        28.41        44.61 
TCGA-38-6178 TCGA-44-2659 TCGA-44-3919 TCGA-44-6777 TCGA-44-7662 TCGA-44-8117 
       14.73        44.94         6.25        32.45         7.17        12.66 
TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
        8.55        13.45        28.57        12.66        46.72        14.07 
TCGA-49-4512 TCGA-49-6767 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-50-5930 
       29.75        22.26        37.32       123.58       211.82         9.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
       78.67        18.64        25.12        22.55         3.91        11.05 
TCGA-50-6594 TCGA-50-6597 TCGA-55-1592 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 
       12.16        41.69        23.05        45.21         0.07         0.79 
TCGA-55-6979 TCGA-55-6981 TCGA-55-6985 TCGA-55-7576 TCGA-55-7727 TCGA-55-7910 
        7.79        45.34        40.54         1.32         1.12         6.48 
TCGA-55-7994 TCGA-55-8096 TCGA-55-8207 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
       19.82        23.64         2.17         0.36         0.26        17.72 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 
        0.30         6.64        17.62         2.17        21.40        20.58 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R 
       19.99         4.57        42.38        88.64        47.80        56.71 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
       29.92        56.81        55.43        38.37        42.90         1.02 
TCGA-67-6217 TCGA-69-7974 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
       13.87         6.05         2.93         7.04         2.01        29.98 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       15.35         5.39        23.51       163.10        27.16        19.27 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 
       19.50        38.50         7.07        31.20        10.75        10.55 
TCGA-78-8640 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7954 
      214.62       110.50        12.36         5.88        34.39        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
       16.70         4.08         0.79        15.75        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-91-6829 TCGA-91-6836 
       21.47        14.60        13.91        14.96        41.36        13.71 
TCGA-91-6847 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 
       27.68         1.12         1.22         2.86        15.68        27.29 
TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-8025 
        2.76        25.48         5.95        21.60        21.44        34.85 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 
       24.30        18.08        19.00        14.53        12.59        11.87 
TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 
       27.19        58.45        37.35        86.04        58.85         5.29 
TCGA-MP-A4TK TCGA-O1-A52J 
       19.13        59.11 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.10     0.00     0.07 
subtype1 subtype2 subtype3 subtype4 
   88.14   223.96    86.14   214.62 
subtype1 subtype2 subtype3 subtype4 
  15.720   18.180   16.440   19.385 
[1] "0.1 - 88.1 (15.7)"  "0.1 - 224.0 (18.2)" "0.0 - 86.1 (16.4)" 
[4] "0.1 - 214.6 (19.4)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       21       17        0         4         7         13
  subtype2       2       75       63        1        20        28         27
  subtype3       1       15       18        0         7        17         11
  subtype4       2       24       42        0        20        21         21
          vv
clus       STAGE IIIB STAGE IV
  subtype1          2        5
  subtype2          3        8
  subtype3          2        7
  subtype4          4        6
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        2        1        2
  STAGE IA         21       75       15       24
  STAGE IB         17       63       18       42
  STAGE II          0        1        0        0
  STAGE IIA         4       20        7       20
  STAGE IIB         7       28       17       21
  STAGE IIIA       13       27       11       21
  STAGE IIIB        2        3        2        4
  STAGE IV          5        8        7        6
[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  24  36   5   4
  subtype2  90 112  16   9
  subtype3  19  45  11   2
  subtype4  37  85  14   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       24       90       19       37
  T2       36      112       45       85
  T3        5       16       11       14
  T4        4        9        2        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1  48   8    12
  subtype2 154  40    27
  subtype3  49  16    12
  subtype4  81  32    25
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          48      154       49       81
  N1           8       40       16       32
  N2+N3       12       27       12       25
[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  51   5
  subtype2 156   7
  subtype3  51   7
  subtype4  90   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    5
  subtype2  156    7
  subtype3   51    7
  subtype4   90    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       51      156       51       90
  1        5        7        7        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  28  41
  subtype2 128 100
  subtype3  35  43
  subtype4  84  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   41
  subtype2  128  100
  subtype3   35   43
  subtype4   84   56
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28      128       35       84
  MALE         41      100       43       56
[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, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          6                                14
  subtype2                          7                                50
  subtype3                          2                                14
  subtype4                          4                                29
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 41
  subtype2                                                132
  subtype3                                                 54
  subtype4                                                 92
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          3
  subtype3                                          0
  subtype4                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             1
  subtype2                                            11
  subtype3                                             1
  subtype4                                             6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              1                                  1
  subtype3                              1                                  0
  subtype4                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             7
  subtype2                            2                            10
  subtype3                            0                             2
  subtype4                            0                             4
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
  subtype4                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             3
  subtype3                                             1
  subtype4                                             1
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            7
  subtype3                            3
  subtype4                            0
D3V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        7        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        14       50       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       41      132       54
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        3        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1       11        1
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        2        0
  LUNG PAPILLARY ADENOCARCINOMA                             7       10        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        3        1
  MUCINOUS (COLLOID) CARCINOMA                              0        7        3
                                                    clus
vv                                                   subtype4
  LUNG ACINAR ADENOCARCINOMA                                4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6
  LUNG CLEAR CELL ADENOCARCINOMA                            0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2
  LUNG MUCINOUS ADENOCARCINOMA                              0
  LUNG PAPILLARY ADENOCARCINOMA                             4
  LUNG SIGNET RING ADENOCARCINOMA                           0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1
  MUCINOUS (COLLOID) CARCINOMA                              0
[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"
D3V10, binary
          cls
clus         0   1
  subtype1   5  64
  subtype2   6 222
  subtype3   5  73
  subtype4   5 135
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   64
  subtype2    6  222
  subtype3    5   73
  subtype4    5  135
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         5        6        5        5
  YES       64      222       73      135
[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"
D3V11, continuous
D3V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  43   2   0   5
  subtype2 146   3   2  12
  subtype3  55   2   1   3
  subtype4  99   5   1   6
D3V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       43      146       55       99
  R1        2        3        2        5
  R2        0        2        1        1
  RX        5       12        3        6
[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                                0     2                         5
  subtype2                                0     2                        20
  subtype3                                0     1                        10
  subtype4                                1     2                        16
          vv
clus       WHITE
  subtype1    53
  subtype2   180
  subtype3    55
  subtype4   101
D3V14, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   2        2        1        2
  BLACK OR AFRICAN AMERICAN               5       20       10       16
  WHITE                                  53      180       55      101
[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  51
  subtype2   2 177
  subtype3   3  55
  subtype4   1  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   51
  subtype2    2  177
  subtype3    3   55
  subtype4    1   99
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        3        1
  NOT HISPANIC OR LATINO       51      177       55       99
[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 104  33
  subtype2  88  53
  subtype3 109  47
subtype1 subtype2 subtype3 
     137      141      156 
subtype1 subtype2 subtype3 
      33       53       47 
$subtype1
TCGA-05-4384 TCGA-05-5423 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2665 
       14.01         4.96        26.30         4.37        46.98        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        3.19        25.02        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7661 TCGA-44-A479 
       23.15        21.63        23.18        32.45        12.03        15.98 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4512 TCGA-49-6744 TCGA-49-6767 
       11.54        13.64        28.11        29.75        29.26        22.26 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 
       22.26        62.24        28.90       123.58       164.12        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5942 
       71.47        70.55        60.16        31.04        49.28        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       25.12        42.35         6.21        25.61         7.59        27.25 
TCGA-53-7626 TCGA-55-6543 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       30.54         0.07         0.82         5.49         7.79         2.20 
TCGA-55-6984 TCGA-55-6987 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
       24.99        70.26         0.13         3.12        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
        1.28         0.79         1.45        15.19         3.29        19.73 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65         1.51        22.16        15.42         1.45 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.72         0.10         4.80         1.61        16.93        22.65 
TCGA-62-8397 TCGA-64-5781 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-8254 
       42.38        51.25         4.64        13.87         6.12        13.45 
TCGA-69-8453 TCGA-73-7498 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-8648 
       26.73        39.09        22.29       104.19       223.96        39.75 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 
       20.55        19.43        16.08        23.05        13.91        27.58 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 
       13.64        26.47         1.97         2.60         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JQ 
       14.27        19.82         9.76         4.18         1.08        17.29 
TCGA-95-7944 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
       12.39        31.69        64.60        63.52        43.79         0.72 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
        5.39        16.41        20.58        20.19        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R 
       20.84        18.67        24.56        36.76         5.59        21.63 
TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 
       24.30        16.44        14.30        14.53        17.46        11.87 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI 
       37.35        86.04         5.49        41.59        14.66        14.10 
TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       11.15        29.13         0.26         0.43        16.87 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4424 TCGA-05-5420 TCGA-05-5425 TCGA-35-5375 
       37.02         2.99        30.02        15.02        29.00         8.68 
TCGA-38-4631 TCGA-44-5643 TCGA-44-6144 TCGA-44-6776 TCGA-44-6778 TCGA-44-7660 
       11.64        33.30        23.77        63.72        61.28        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-8120 
       36.07        18.87        29.00        17.59         3.25         8.55 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4490 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       11.08        13.45        12.66        55.89        14.63        12.13 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-4B-A93V 
      153.04        63.95         8.55        40.41       211.82         9.86 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5936 
       15.72         8.22         9.27        14.27        21.47         8.45 
TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6673 TCGA-50-7109 
       15.12        22.55         3.91        25.55         0.72        10.13 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       34.29         9.21         2.86        32.65        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-7570 TCGA-55-7910 TCGA-55-7995 
       15.25        48.49         3.88         0.20         6.48         0.16 
TCGA-55-8085 TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8614 
       29.72         0.13         0.95         0.26         0.49        17.62 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
        0.49         2.17        20.71        21.40         1.58        19.59 
TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       20.19        17.95         4.57        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 
       47.80        54.35        39.25        40.96        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 
       87.98        42.90        28.41        13.61         7.56         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 
       12.56        14.01         4.24        23.51        11.18        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 
        5.69        20.58        35.93        21.90        19.50        38.50 
TCGA-78-7156 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7633 TCGA-78-8640 
       32.09         8.48        26.53         8.02        32.68       214.62 
TCGA-78-8662 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
      110.50        34.39        13.87        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8674 
        4.08        15.75        21.47         1.15        30.84        13.32 
TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        3.81        41.36        10.19        12.23        27.68         7.36 
TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-A4JP TCGA-95-7043 TCGA-95-7947 
       16.18         1.18         1.45        19.00         1.22        15.68 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-8171 TCGA-97-8176 TCGA-97-A4M3 TCGA-99-8032 
       21.40        19.89        18.67        15.39        17.75         1.45 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4TA 
       18.08        19.00         3.81         1.91        12.59        31.23 
TCGA-MP-A4TF TCGA-NJ-A55R TCGA-O1-A52J 
       11.05        19.82        59.11 

$subtype3
TCGA-05-4396 TCGA-05-4405 TCGA-05-4417 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 
        9.96        20.05        14.96        21.99        26.01        24.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-38-4632 TCGA-38-6178 TCGA-44-3917 
       22.03         9.04         2.04        44.61        14.73        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5644 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 
       34.06        26.56        28.37        16.44        14.60         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 TCGA-49-6745 
       23.64        12.66        15.32         9.44        28.57        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-6593 
       11.64        37.32        40.60        78.67        18.64        11.05 
TCGA-50-6594 TCGA-50-6597 TCGA-53-7813 TCGA-55-6712 TCGA-55-6981 TCGA-55-6982 
       12.16        41.69        13.94         0.79        45.34        32.71 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       60.03        40.54       107.21         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        7.99         1.32         1.12         1.78        18.64         0.53 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8203 
       17.65         6.15        19.82        19.66         5.06        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 TCGA-55-8514 
        1.08         2.17         0.76         0.36         0.30         6.64 
TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
        1.58        20.58         0.92        15.81        19.99        39.98 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 
       19.53        56.71        67.96        72.30        13.61        29.92 
TCGA-64-5775 TCGA-64-5815 TCGA-67-6215 TCGA-69-7760 TCGA-69-7763 TCGA-69-7765 
        2.04        28.47         5.72         6.64        22.68         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
        6.05         2.30         7.04         2.01         0.10        52.60 
TCGA-73-4676 TCGA-78-7143 TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 TCGA-78-7158 
        5.39       163.10        19.27        39.52        24.99         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
       64.90         7.07        88.14        31.20        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
       39.35        10.55        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8278 
        5.88        31.13         4.57        24.33         0.79        15.65 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF 
       15.85        14.60         0.62        14.96        13.32        17.62 
TCGA-91-6828 TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7562 
       10.62        13.71         6.12        23.61         1.12         2.86 
TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7554 
       18.67        15.65        27.29         2.76        18.18        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
        5.95         0.59        17.92        18.12        14.30        21.60 
TCGA-97-A4M0 TCGA-97-A4M7 TCGA-99-8025 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L9-A444 
       21.44        20.68        34.85        23.80        35.47         0.20 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TK 
       58.85         5.29         2.43        10.09        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        62.60         0.13         1.64         9.70 

subtype1 subtype2 subtype3 
    0.07     0.13     0.10 
subtype1 subtype2 subtype3 
  223.96   214.62   163.10 
subtype1 subtype2 subtype3 
  18.670   17.620   16.145 
[1] "0.1 - 224.0 (18.7)" "0.1 - 214.6 (17.6)" "0.1 - 163.1 (16.1)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       57       34        1        16        17         12
  subtype2       4       36       36        0        17        15         26
  subtype3       0       27       55        0        15        31         26
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        5
  subtype2          4       10
  subtype3          4        6
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         57       36       27
  STAGE IB         34       36       55
  STAGE II          1        0        0
  STAGE IIA        16       17       15
  STAGE IIB        17       15       31
  STAGE IIIA       12       26       26
  STAGE IIIB        1        4        4
  STAGE IV          5       10        6
[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 68 62 10  3
  subtype2 48 83 11  5
  subtype3 38 98 20  8
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       68       48       38
  T2       62       83       98
  T3       10       11       20
  T4        3        5        8
[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 101  25    12
  subtype2  92  24    30
  subtype3 105  34    24
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         101       92      105
  N1          25       24       34
  N2+N3       12       30       24
[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  84   4
  subtype2  98  10
  subtype3 112   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84    4
  subtype2   98   10
  subtype3  112    5
   clus
vv  subtype1 subtype2 subtype3
  0       84       98      112
  1        4       10        5
[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 97 48
  subtype2 59 89
  subtype3 87 77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97   48
  subtype2   59   89
  subtype3   87   77
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       97       59       87
  MALE         48       89       77
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                23
  subtype2                          8                                29
  subtype3                          6                                40
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 88
  subtype2                                                 92
  subtype3                                                 99
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          4
  subtype2                                          0
  subtype3                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             8
  subtype2                                             3
  subtype3                                             8
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              1                                  0
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             7
  subtype2                            0                             9
  subtype3                            0                             6
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             3
  subtype3                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            6
  subtype2                            3
  subtype3                            1
D4V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        8        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        23       29       40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       88       92       99
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                4        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             8        3        8
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             7        9        6
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        3        2
  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"
D4V10, binary
          cls
clus         0   1
  subtype1   6 139
  subtype2   9 139
  subtype3   3 161
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  139
  subtype2    9  139
  subtype3    3  161
     clus
vv    subtype1 subtype2 subtype3
  NO         6        9        3
  YES      139      139      161
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  87   2   1   9
  subtype2  94   4   0   6
  subtype3 112   4   0   8
D4V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       87       94      112
  R1        2        4        4
  R2        1        0        0
  RX        9        6        8
[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   114
  subtype2     2                        19   114
  subtype3     4                        12   124
D4V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        4
  BLACK OR AFRICAN AMERICAN       18       19       12
  WHITE                          114      114      124
[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   2 118
  subtype2   5 108
  subtype3   0 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  118
  subtype2    5  108
  subtype3    0  115
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        0
  NOT HISPANIC OR LATINO      118      108      115
[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 28 15
  subtype2 43 22
  subtype3 34 26
subtype1 subtype2 subtype3 
      43       65       60 
subtype1 subtype2 subtype3 
      15       22       26 
$subtype1
TCGA-05-4249 TCGA-05-4384 TCGA-05-4426 TCGA-35-3615 TCGA-38-4626 TCGA-44-2657 
       50.07        14.01        26.01         0.46       120.79        13.15 
TCGA-44-7659 TCGA-44-7671 TCGA-49-4486 TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 
       14.60        17.59        76.21        29.46        14.63        29.26 
TCGA-50-5051 TCGA-50-5932 TCGA-53-7626 TCGA-55-6970 TCGA-64-1680 TCGA-69-7761 
       15.72        40.60        30.54        15.25        37.02         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-73-4659 TCGA-73-4676 TCGA-73-7498 TCGA-78-7143 
       22.68        13.61        23.38         5.39        39.09       163.10 
TCGA-78-7147 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
       19.27        32.09         5.88         7.07       104.19        88.14 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-86-7713 TCGA-91-6849 TCGA-91-7771 
       53.33        10.75        32.68        13.87         1.15        16.18 
TCGA-95-7947 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       15.68        31.69        43.79         5.95         0.59         0.72 
TCGA-99-7458 
       24.56 

$subtype2
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 
        9.96        47.05         8.02        20.05        14.96        12.00 
TCGA-05-4430 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-38-6178 TCGA-44-2656 
       25.02        15.02         4.96         9.04        14.73        46.98 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3919 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 
       24.36        42.77         6.25        12.59         9.93        27.78 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-49-4488 TCGA-49-4501 TCGA-49-4505 
       23.18        63.72        32.45        28.57        46.72        14.07 
TCGA-49-4512 TCGA-49-6745 TCGA-49-6767 TCGA-50-5049 TCGA-50-5068 TCGA-50-5936 
       29.75        17.16        22.26        70.55        49.28         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 
       18.64        29.03        25.12        11.05        41.69         0.72 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-6979 TCGA-55-6981 
       23.05        38.73        45.21         0.79         7.79        45.34 
TCGA-55-6982 TCGA-55-7573 TCGA-55-7911 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
       32.71         0.13        17.65        55.43        38.37        42.90 
TCGA-64-5781 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-71-6725 
       51.25         5.72         4.64        13.87         6.64         2.01 
TCGA-73-4675 TCGA-78-7145 TCGA-78-7535 TCGA-86-6562 TCGA-86-6851 TCGA-91-6828 
        1.32        27.16        31.20        12.36         5.88        10.62 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-95-7039 TCGA-95-7948 
       41.36         2.60        12.23         1.12        15.65 

$subtype3
TCGA-05-4418 TCGA-05-4420 TCGA-05-5715 TCGA-38-4627 TCGA-44-3396 TCGA-44-4112 
        9.01        29.98         2.04        37.71        37.15        26.56 
TCGA-44-6145 TCGA-44-6774 TCGA-44-6779 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 
       10.78        21.63        16.44         7.17        29.00        23.64 
TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6761 
       28.11        35.54        32.84         8.81        55.89        11.64 
TCGA-50-5044 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-6595 
       20.52         8.22        14.27        78.67        15.12         6.21 
TCGA-50-7109 TCGA-53-7813 TCGA-55-6543 TCGA-55-6971 TCGA-55-6978 TCGA-55-7574 
       10.13        13.94         0.07         0.82         5.49         3.12 
TCGA-55-7728 TCGA-55-7815 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
        0.79         1.78        56.81        20.65        39.09        87.98 
TCGA-67-3771 TCGA-69-7765 TCGA-73-4658 TCGA-73-7499 TCGA-78-7148 TCGA-78-7149 
       20.05         5.42        52.60        23.51        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
       21.90        39.52        24.99        19.50        38.50        64.90 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
       22.29       223.96         8.48         8.02        39.35        10.55 
TCGA-91-6847 TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-97-7552 TCGA-97-7554 
       27.68         4.18         1.22        18.67        63.52        25.48 

subtype1 subtype2 subtype3 
    0.46     0.13     0.07 
subtype1 subtype2 subtype3 
  163.10    70.55   223.96 
subtype1 subtype2 subtype3 
  19.270   17.650   20.615 
[1] "0.5 - 163.1 (19.3)" "0.1 - 70.5 (17.6)"  "0.1 - 224.0 (20.6)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       12        9         6         7          6          1
  subtype2       1       17       20         5        12         14          2
  subtype3       0       12       23         4         6         13          4
          vv
clus       STAGE IV
  subtype1        3
  subtype2        2
  subtype3        2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        1        0
  STAGE IA         12       17       12
  STAGE IB          9       20       23
  STAGE IIA         6        5        4
  STAGE IIB         7       12        6
  STAGE IIIA        6       14       13
  STAGE IIIB        1        2        4
  STAGE IV          3        2        2
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 12 27  2  3
  subtype2 20 43  7  3
  subtype3 16 38  4  6
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       12       20       16
  T2       27       43       38
  T3        2        7        4
  T4        3        3        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 27  9     7
  subtype2 40 15    14
  subtype3 39 10    14
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          27       40       39
  N1           9       15       10
  N2+N3        7       14       14
[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"
D5V6, binary
          cls
clus        0  1
  subtype1 30  3
  subtype2 57  2
  subtype3 50  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    3
  subtype2   57    2
  subtype3   50    1
   clus
vv  subtype1 subtype2 subtype3
  0       30       57       50
  1        3        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 20 24
  subtype2 48 25
  subtype3 37 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   24
  subtype2   48   25
  subtype3   37   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       48       37
  MALE         24       25       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          3                                15
  subtype2                          2                                14
  subtype3                          0                                14
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 17
  subtype2                                                 51
  subtype3                                                 43
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          3
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             5
  subtype2                                             2
  subtype3                                             1
          vv
clus       LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  subtype1                                  1                            0
  subtype2                                  1                            1
  subtype3                                  0                            0
          vv
clus       LUNG PAPILLARY ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
  subtype1                             2                            1
  subtype2                             1                            1
  subtype3                             2                            1
D5V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                3        2        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        15       14       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       17       51       43
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        0        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             5        2        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             2        1        2
  MUCINOUS (COLLOID) CARCINOMA                              1        1        1
[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"
D5V10, binary
          cls
clus        0  1
  subtype1  3 41
  subtype2  3 70
  subtype3  7 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   41
  subtype2    3   70
  subtype3    7   57
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        7
  YES       41       70       57
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 30  3  0  1
  subtype2 47  3  1  4
  subtype3 42  2  0  0
D5V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       30       47       42
  R1        3        3        2
  R2        0        1        0
  RX        1        4        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    36
  subtype2     2                         1    52
  subtype3     0                         2    53
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           36       52       53
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
          cls
clus        0  1
  subtype1  0 28
  subtype2  1 42
  subtype3  1 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   28
  subtype2    1   42
  subtype3    1   36
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        1
  NOT HISPANIC OR LATINO       28       42       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 25 13
  subtype2 20 11
  subtype3 23 18
  subtype4 14 14
  subtype5 23  7
subtype1 subtype2 subtype3 subtype4 subtype5 
      38       31       41       28       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
      13       11       18       14        7 
$subtype1
TCGA-05-4249 TCGA-05-4402 TCGA-05-4405 TCGA-05-4430 TCGA-05-5423 TCGA-44-2656 
       50.07         8.02        20.05        25.02         4.96        46.98 
TCGA-44-2661 TCGA-44-3919 TCGA-44-5645 TCGA-44-6147 TCGA-44-6776 TCGA-49-4488 
       24.36         6.25        12.59        27.78        63.72        28.57 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
       46.72        14.07        29.75        29.03        25.12        41.69 
TCGA-50-6673 TCGA-55-1592 TCGA-55-6981 TCGA-55-7573 TCGA-55-7815 TCGA-55-7911 
        0.72        23.05        45.34         0.13         1.78        17.65 
TCGA-64-1680 TCGA-64-1681 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 
       37.02        38.37         5.72         4.64        13.87         2.01 
TCGA-73-4675 TCGA-78-7143 TCGA-78-7147 TCGA-86-6562 TCGA-91-6828 TCGA-91-6835 
        1.32       163.10        19.27        12.36        10.62         2.60 
TCGA-91-6840 TCGA-95-7948 
       12.23        15.65 

$subtype2
TCGA-05-4384 TCGA-05-4396 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-35-3615 
       14.01         9.96        14.96        29.98        12.00         0.46 
TCGA-44-7671 TCGA-49-4486 TCGA-49-4494 TCGA-49-4510 TCGA-50-5051 TCGA-55-6543 
       17.59        76.21        35.54        29.46        15.72         0.07 
TCGA-55-6971 TCGA-64-5774 TCGA-67-3771 TCGA-69-7763 TCGA-73-7498 TCGA-78-7148 
        0.82        87.98        20.05        22.68        39.09        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
       35.93        39.52        24.99        32.09        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7633 
      104.19       223.96        88.14         8.02        53.33        32.68 
TCGA-86-7713 
       13.87 

$subtype3
TCGA-05-4398 TCGA-05-5715 TCGA-38-4627 TCGA-38-6178 TCGA-44-2665 TCGA-44-4112 
       47.05         2.04        37.71        14.73        42.77        26.56 
TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-49-4487 TCGA-49-6745 TCGA-49-6761 
       10.78        23.18        32.45        28.11        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 
       22.26        20.52        70.55        49.28        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-6593 TCGA-55-1594 TCGA-55-1596 
        8.45        15.12        18.64        11.05        38.73        45.21 
TCGA-55-6712 TCGA-55-6978 TCGA-55-6979 TCGA-55-6982 TCGA-64-1676 TCGA-64-1679 
        0.79         5.49         7.79        32.71        56.81        55.43 
TCGA-64-5778 TCGA-69-7760 TCGA-78-7145 TCGA-78-7155 TCGA-78-7535 TCGA-86-6851 
       42.90         6.64        27.16        38.50        31.20         5.88 
TCGA-91-6829 TCGA-91-6847 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
       41.36        27.68         1.12         1.22        18.67 

$subtype4
TCGA-05-4418 TCGA-05-5429 TCGA-44-3396 TCGA-44-6146 TCGA-44-6774 TCGA-44-6779 
        9.01         9.04        37.15         9.93        21.63        16.44 
TCGA-44-7662 TCGA-44-7670 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-50-5072 
        7.17        29.00        32.84         8.81        55.89         8.22 
TCGA-50-6595 TCGA-50-7109 TCGA-53-7813 TCGA-55-7728 TCGA-64-1677 TCGA-64-1678 
        6.21        10.13        13.94         0.79        20.65        39.09 
TCGA-64-5781 TCGA-69-7761 TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7166 
       51.25         6.12        21.90        19.50        64.90         8.48 
TCGA-78-7540 TCGA-78-7542 TCGA-95-7947 TCGA-97-7552 
       39.35        10.55        15.68        63.52 

$subtype5
TCGA-05-4426 TCGA-05-5420 TCGA-38-4626 TCGA-44-2657 TCGA-44-7659 TCGA-44-7672 
       26.01        15.02       120.79        13.15        14.60        23.64 
TCGA-49-6742 TCGA-49-6744 TCGA-50-5932 TCGA-53-7626 TCGA-55-6970 TCGA-55-7574 
       14.63        29.26        40.60        30.54        15.25         3.12 
TCGA-69-7764 TCGA-69-7765 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 TCGA-73-7499 
       13.61         5.42        52.60        23.38         5.39        23.51 
TCGA-78-7158 TCGA-78-7539 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 TCGA-97-7546 
        5.88        10.75         1.15        16.18         4.18        31.69 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-99-7458 
       43.79        25.48         5.95         0.59         0.72        24.56 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.07     0.79     0.79     0.59 
subtype1 subtype2 subtype3 subtype4 subtype5 
  163.10   223.96    78.67    64.90   120.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.460   22.680   23.180   16.060   15.135 
[1] "0.1 - 163.1 (18.5)" "0.1 - 224.0 (22.7)" "0.8 - 78.7 (23.2)" 
[4] "0.8 - 64.9 (16.1)"  "0.6 - 120.8 (15.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       16       12         3         3          3          0
  subtype2       0        7       12         1         3          5          2
  subtype3       0        5       14         4         9          9          3
  subtype4       0        4        8         2         6         10          1
  subtype5       0        9        6         5         4          6          1
          vv
clus       STAGE IV
  subtype1        2
  subtype2        3
  subtype3        1
  subtype4        0
  subtype5        1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        0        0        0
  STAGE IA         16        7        5        4        9
  STAGE IB         12       12       14        8        6
  STAGE IIA         3        1        4        2        5
  STAGE IIB         3        3        9        6        4
  STAGE IIIA        3        5        9       10        6
  STAGE IIIB        0        2        3        1        1
  STAGE IV          2        3        1        0        1
[1] 8 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 17 22  1  0
  subtype2  6 21  2  4
  subtype3  9 29  3  4
  subtype4  6 18  6  1
  subtype5 10 18  1  3
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       17        6        9        6       10
  T2       22       21       29       18       18
  T3        1        2        3        6        1
  T4        0        4        4        1        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 27  7     3
  subtype2 23  4     6
  subtype3 22 11    11
  subtype4 15  6     9
  subtype5 19  6     6
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          27       23       22       15       19
  N1           7        4       11        6        6
  N2+N3        3        6       11        9        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"
D6V6, binary
          cls
clus        0  1
  subtype1 31  2
  subtype2 28  3
  subtype3 32  1
  subtype4 26  0
  subtype5 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    2
  subtype2   28    3
  subtype3   32    1
  subtype4   26    0
  subtype5   20    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       31       28       32       26       20
  1        2        3        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 30 10
  subtype2 11 22
  subtype3 27 18
  subtype4 16 15
  subtype5 21 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   10
  subtype2   11   22
  subtype3   27   18
  subtype4   16   15
  subtype5   21   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       11       27       16       21
  MALE         10       22       18       15       11
[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"
D6V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        2        2        1        6 
[1] "subtype1" "subtype1" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
[8] "subtype5" "subtype5"
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          1                                 7
  subtype2                          0                                17
  subtype3                          1                                 8
  subtype4                          1                                 4
  subtype5                          2                                 7
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 29
  subtype2                                                 13
  subtype3                                                 33
  subtype4                                                 20
  subtype5                                                 16
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          1
  subtype3                                          0
  subtype4                                          2
  subtype5                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             1
  subtype2                                             1
  subtype3                                             2
  subtype4                                             1
  subtype5                                             3
          vv
clus       LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  subtype1                                  1                            0
  subtype2                                  0                            0
  subtype3                                  0                            0
  subtype4                                  0                            1
  subtype5                                  1                            0
          vv
clus       LUNG PAPILLARY ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
  subtype1                             1                            0
  subtype2                             1                            0
  subtype3                             0                            1
  subtype4                             1                            1
  subtype5                             2                            1
D6V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                1        0        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         7       17        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       29       13       33
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        1        2
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        1        0
  MUCINOUS (COLLOID) CARCINOMA                              0        0        1
                                                    clus
vv                                                   subtype4 subtype5
  LUNG ACINAR ADENOCARCINOMA                                1        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         4        7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       20       16
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        3
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        2
  MUCINOUS (COLLOID) CARCINOMA                              1        1
[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"
D6V10, binary
          cls
clus        0  1
  subtype1  2 38
  subtype2  2 31
  subtype3  3 42
  subtype4  4 27
  subtype5  2 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   38
  subtype2    2   31
  subtype3    3   42
  subtype4    4   27
  subtype5    2   30
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        2        3        4        2
  YES       38       31       42       27       30
[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"
D6V11, continuous
D6V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 30  1  1  3
  subtype2 28  1  0  1
  subtype3 22  2  0  1
  subtype4 19  1  0  0
  subtype5 20  3  0  0
D6V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       30       28       22       19       20
  R1        1        1        2        1        3
  R2        1        0        0        0        0
  RX        3        1        1        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    30
  subtype2     0                         3    22
  subtype3     1                         0    38
  subtype4     0                         0    25
  subtype5     0                         2    26
D6V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        0        0
  BLACK OR AFRICAN AMERICAN        1        3        0        0        2
  WHITE                           30       22       38       25       26
[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"
D6V15, binary
          cls
clus        0  1
  subtype1  0 27
  subtype2  0 11
  subtype3  1 28
  subtype4  1 16
  subtype5  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   27
  subtype2    0   11
  subtype3    1   28
  subtype4    1   16
  subtype5    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        1        1        0
  NOT HISPANIC OR LATINO       27       11       28       16       24
[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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 123  34
  subtype2 114  75
  subtype3 100  44
subtype1 subtype2 subtype3 
     157      189      144 
subtype1 subtype2 subtype3 
      34       75       44 
$subtype1
TCGA-05-4249 TCGA-05-4403 TCGA-05-4405 TCGA-05-4430 TCGA-05-5423 TCGA-35-3615 
       50.07        19.00        20.05        25.02         4.96         0.46 
TCGA-38-4626 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
      120.79        26.30         4.37        43.53        13.15        44.94 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3398 TCGA-44-3919 TCGA-44-5645 TCGA-44-6147 
       24.36         3.19        38.24         6.25        12.59        27.78 
TCGA-44-6148 TCGA-44-7659 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-49-4501 
       23.15        14.60         8.55        15.32        11.54        46.72 
TCGA-49-4512 TCGA-49-6744 TCGA-49-AARN TCGA-49-AARR TCGA-50-5045 TCGA-50-5055 
       29.75        29.26        37.32       164.12        71.47        60.16 
TCGA-50-5068 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 
       49.28        21.47        18.64        29.03        25.12        11.05 
TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
       41.69         0.72        25.61         7.59        27.25        30.54 
TCGA-55-6543 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7283 
        0.07        24.99        40.54       107.21         1.74         1.15 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
        7.99         0.13         3.12        23.18         1.28         1.12 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8206 
        6.15        15.19        19.66        19.73        15.65         1.51 
TCGA-55-8207 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 
        2.17        17.72         0.10         4.80         6.64         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 
        1.61        16.93        22.65        19.99        17.95        42.38 
TCGA-62-A46R TCGA-62-A46Y TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
       56.71        13.61        37.02        38.37        42.90         1.02 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        12.66         5.72         4.64        13.87 
TCGA-69-7763 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 
       22.68         6.05        14.01        13.45        26.73         2.01 
TCGA-73-4662 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7147 
       29.98         1.32         1.25        39.09       163.10        19.27 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7540 TCGA-86-7714 TCGA-86-8056 
        5.88       104.19       223.96        39.35        20.55         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 TCGA-86-A456 
       24.33        16.08        23.05        13.91        27.58        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BD 
       13.64        26.47         2.60         1.15        16.60        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7947 
        9.76         4.18        23.61         1.08        19.00        15.68 
TCGA-95-8039 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       27.29        18.18        31.69        64.60        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4LX 
        0.59         0.72        17.92        16.41        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG 
       24.56        34.85        36.76        21.63        35.47        16.44 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4SW TCGA-MP-A4T6 
       14.30         3.81        14.53        17.46        58.45        58.85 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       14.66        11.15        62.60         0.26         9.70        59.11 
TCGA-S2-AA1A 
       16.87 

$subtype2
TCGA-05-4250 TCGA-05-4382 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        3.98        19.96         0.00        24.03        47.05         8.02 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4434 
        2.99         9.01        21.99        26.01        26.01        15.02 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       22.03         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
       46.98        42.08        42.77        25.02        37.15        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       26.56        33.30        21.63        23.18        32.45        16.44 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
       19.46        12.03         7.17        29.00        23.64        12.66 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.64        13.45        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       32.84         8.81        12.13        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       22.26        62.24        28.90         8.55        40.41       123.58 
TCGA-49-AARQ TCGA-50-5044 TCGA-50-5049 TCGA-50-5066 TCGA-50-5931 TCGA-50-5933 
      211.82        20.52        70.55        31.04        14.27        78.67 
TCGA-50-5939 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 
       15.12        22.55        42.35         3.91        25.55        12.16 
TCGA-50-6595 TCGA-53-7624 TCGA-55-1595 TCGA-55-6712 TCGA-55-6968 TCGA-55-6975 
        6.21        34.29        48.62         0.79        42.51         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 
        5.49         7.79         2.20        45.34        32.71         0.59 
TCGA-55-7576 TCGA-55-7726 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
        1.32         1.28         1.45        18.64         0.53        17.65 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
       19.82         3.29        23.64         1.08        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 TCGA-55-8614 TCGA-55-A48Z 
        1.45         0.76         0.36         0.30        17.62        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-62-8394 TCGA-62-A46U TCGA-62-A46V 
        1.58        20.58         0.92         4.57        67.96        72.30 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5775 TCGA-64-5781 
       29.92        56.81        20.65        55.43         2.04        51.25 
TCGA-64-5815 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       28.47         6.64         5.42         2.30         2.93        12.56 
TCGA-69-A59K TCGA-71-8520 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        7.04         0.10        52.60        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7155 TCGA-78-7535 
        5.39        23.51        27.16         5.69        38.50        31.20 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       10.55        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
       12.36         5.88        34.39        19.43        16.70         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8672 
        0.79        15.75        15.65        15.85         1.15         0.62 
TCGA-86-8673 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
       14.96        17.62        41.36        13.71        27.68         7.36 
TCGA-91-8499 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
        1.18        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 
       15.65         2.76        25.48         5.95        18.12        21.60 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A5IP 
        5.59        24.30        18.08        19.00         0.20         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       12.59        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
       49.35        86.04        41.59         2.43        11.05        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       19.13         0.13        29.13 

$subtype3
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4417 TCGA-05-4420 
       14.01        45.01        37.02         9.96        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       12.00        30.02        25.02        24.00        15.02        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-44-5644 TCGA-44-6145 TCGA-44-6146 TCGA-44-6776 
        9.04         2.04        28.37        10.78         9.93        63.72 
TCGA-44-6778 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-8119 TCGA-44-A479 
       61.28        36.07        18.87        17.59         3.25        15.98 
TCGA-44-A47B TCGA-49-4486 TCGA-49-4487 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
        9.44        76.21        28.11        29.46        55.89        14.63 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5051 TCGA-50-5072 TCGA-50-5930 
      153.04        63.95         9.86        15.72         8.22         9.27 
TCGA-50-5932 TCGA-50-5936 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       40.60         8.45        10.13        13.94         9.21        23.05 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 
       38.73        45.21         2.86        32.65        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6987 TCGA-55-7570 TCGA-55-7728 
        0.82        48.49        60.03        70.26         0.20         0.79 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8092 TCGA-55-8094 
        1.78         6.48         0.16        29.72         5.06         0.13 
TCGA-55-8203 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-8620 
       17.98         0.95         0.26         0.49         0.49         2.17 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 
       20.71        19.59        15.81        20.19        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 
       88.64        49.25        47.80        19.53        54.35        39.25 
TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-69-7761 
       40.96        39.09        87.98        28.41        20.05         6.12 
TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 TCGA-73-4659 TCGA-73-A9RS TCGA-78-7148 
       13.61         7.56         4.24        23.38        11.18        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       35.93        21.90        39.52        24.99        19.50        32.09 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       64.90        22.29         7.07         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-86-7701 
        8.02        53.33        10.75        32.68       214.62        31.13 
TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 
       13.87        19.89        24.49        21.47        14.60        30.84 
TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       13.32         3.81        10.62         1.97        10.19        12.23 
TCGA-91-7771 TCGA-91-8497 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-A4VK 
       16.18        14.27         1.45         6.12         1.22        21.40 
TCGA-95-A4VP TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M3 
       19.89        18.67         5.39        15.39        14.30        17.75 
TCGA-99-8032 TCGA-J2-8194 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD 
        1.45        23.80         5.49         5.29        31.23        10.09 
TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       29.46        73.91        71.05         1.64         0.43        19.82 

subtype1 subtype2 subtype3 
    0.07     0.00     0.13 
subtype1 subtype2 subtype3 
  223.96   211.82   214.62 
subtype1 subtype2 subtype3 
  18.840   17.620   18.325 
[1] "0.1 - 224.0 (18.8)" "0.0 - 211.8 (17.6)" "0.1 - 214.6 (18.3)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       2       63       47        0        14        15         19
  subtype2       3       33       54        1        21        35         29
  subtype3       0       37       39        0        16        22         25
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        5
  subtype2          7       14
  subtype3          3        8
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        3        0
  STAGE IA         63       33       37
  STAGE IB         47       54       39
  STAGE II          0        1        0
  STAGE IIA        14       21       16
  STAGE IIB        15       35       22
  STAGE IIIA       19       29       25
  STAGE IIIB        1        7        3
  STAGE IV          5       14        8
[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  77  72  13   4
  subtype2  49 117  19  10
  subtype3  42  88  15   5
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       77       49       42
  T2       72      117       88
  T3       13       19       15
  T4        4       10        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1 119  25    17
  subtype2 113  47    33
  subtype3  98  24    26
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         119      113       98
  N1          25       47       24
  N2+N3       17       33       26
[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"
D7V6, binary
          cls
clus         0   1
  subtype1 109   5
  subtype2 129  12
  subtype3 107   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109    5
  subtype2  129   12
  subtype3  107    8
   clus
vv  subtype1 subtype2 subtype3
  0      109      129      107
  1        5       12        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1 112  55
  subtype2 113  84
  subtype3  51  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  112   55
  subtype2  113   84
  subtype3   51   99
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      112      113       51
  MALE         55       84       99
[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"
D7V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          7                                35
  subtype2                          3                                34
  subtype3                          9                                38
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 90
  subtype2                                                146
  subtype3                                                 82
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          5
  subtype2                                          0
  subtype3                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            14
  subtype2                                             3
  subtype3                                             2
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              2                                  2
  subtype3                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             8
  subtype2                            0                             4
  subtype3                            1                            11
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             3
  subtype3                                             1
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            4
  subtype2                            0
  subtype3                            6
D7V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                7        3        9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        35       34       38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       90      146       82
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                5        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            14        3        2
  LUNG CLEAR CELL ADENOCARCINOMA                            0        2        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        2        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             8        4       11
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        3        1
  MUCINOUS (COLLOID) CARCINOMA                              4        0        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"
D7V10, binary
          cls
clus         0   1
  subtype1   6 161
  subtype2   8 189
  subtype3   7 143
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  161
  subtype2    8  189
  subtype3    7  143
     clus
vv    subtype1 subtype2 subtype3
  NO         6        8        7
  YES      161      189      143
[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"
D7V11, continuous
D7V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 112   3   1  11
  subtype2 127   6   3   8
  subtype3 103   3   0   6
D7V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      112      127      103
  R1        3        6        3
  R2        1        3        0
  RX       11        8        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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        18
  subtype2                                1     2                        19
  subtype3                                0     3                        14
          vv
clus       WHITE
  subtype1   131
  subtype2   148
  subtype3   108
D7V14, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   3        2        3
  BLACK OR AFRICAN AMERICAN              18       19       14
  WHITE                                 131      148      108
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
          cls
clus         0   1
  subtype1   1 136
  subtype2   4 147
  subtype3   2  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  136
  subtype2    4  147
  subtype3    2   98
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        2
  NOT HISPANIC OR LATINO      136      147       98
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 55 20
  subtype2 80 27
  subtype3 58 35
  subtype4 32 13
  subtype5 37 12
  subtype6 19 29
  subtype7 56 17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      75      107       93       45       49       48       73 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      20       27       35       13       12       29       17 
$subtype1
TCGA-05-4249 TCGA-05-4425 TCGA-05-5423 TCGA-05-5715 TCGA-38-4626 TCGA-38-7271 
       50.07        21.99         4.96         2.04       120.79        26.30 
TCGA-44-2659 TCGA-44-2666 TCGA-44-3919 TCGA-44-A47A TCGA-49-4487 TCGA-49-4501 
       44.94         3.19         6.25        15.32        28.11        46.72 
TCGA-49-4512 TCGA-49-6744 TCGA-50-5935 TCGA-50-5944 TCGA-50-6597 TCGA-50-8457 
       29.75        29.26        21.47        25.12        41.69        25.61 
TCGA-53-7626 TCGA-55-6971 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 
       30.54         0.82       107.21        70.26         1.74         1.15 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 
        3.12         1.28         6.15        15.19        19.66        15.65 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 
        1.51         2.17        15.42        19.99        17.95        42.38 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1.02        18.84        14.04         5.72         4.64        13.87 
TCGA-73-4662 TCGA-78-7143 TCGA-78-7158 TCGA-78-7539 TCGA-78-8648 TCGA-86-7714 
       29.98       163.10         5.88        10.75        39.75        20.55 
TCGA-86-8668 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-8496 TCGA-93-7347 
       13.91        27.58        13.32        13.64        16.60         9.76 
TCGA-93-7348 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7938 TCGA-97-8171 
        4.18        27.29        31.69        64.60         0.59        18.67 
TCGA-97-8172 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       17.92        16.41        21.44        19.76        18.67        24.56 
TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-MP-A4T6 TCGA-NJ-A4YG 
       21.63        14.30         3.81        14.53        58.85        62.60 
TCGA-NJ-A4YI TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13         9.70        59.11 

$subtype2
TCGA-05-4250 TCGA-05-4398 TCGA-05-4405 TCGA-05-4426 TCGA-05-4427 TCGA-05-5428 
        3.98        47.05        20.05        26.01        26.01        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 
        7.40         5.98        97.74        49.05        28.41        44.61 
TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       46.98        42.08        42.77        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-4112 TCGA-44-6777 TCGA-44-7661 TCGA-44-7662 TCGA-44-8117 
       34.06        26.56        32.45        12.03         7.17        12.66 
TCGA-44-8120 TCGA-44-A47B TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-6745 
        8.55         9.44        28.57        35.54        14.07        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-50-5044 TCGA-50-5066 TCGA-50-5933 
       11.64        22.26        62.24        20.52        31.04        78.67 
TCGA-50-5941 TCGA-50-6590 TCGA-50-6594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6978 
       18.64        42.35        12.16        48.62         0.79         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 
        7.79         2.20        45.34         0.59         1.32         1.12 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8205 TCGA-55-8301 
        1.45        18.64        17.65        19.82         1.08         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-A490 TCGA-55-A493 
        0.76         0.36        17.72         6.64         1.58         0.92 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       88.64        67.96        72.30        29.92        56.81        55.43 
TCGA-64-5815 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-A59K TCGA-71-6725 
       28.47         6.64         5.42         2.30         7.04         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-78-7145 
        0.10        52.60        26.30        15.35         5.39        27.16 
TCGA-78-7146 TCGA-78-7535 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
        5.69        31.20        77.59        10.55        27.09        12.36 
TCGA-86-8073 TCGA-86-8279 TCGA-86-8673 TCGA-86-A4JF TCGA-91-6836 TCGA-93-A4JN 
       24.33        15.85        14.96        17.62        13.71        23.61 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 
        1.12        18.67        15.65         2.76        25.48         5.95 
TCGA-97-8175 TCGA-97-8547 TCGA-97-A4LX TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 
       18.12        21.60        20.19        16.44        19.00         0.20 
TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        2.76        41.59         2.43        14.10        19.13 

$subtype3
TCGA-05-4382 TCGA-05-4389 TCGA-05-4397 TCGA-05-4402 TCGA-05-4424 TCGA-05-4434 
       19.96        45.01        24.03         8.02        30.02        15.02 
TCGA-35-5375 TCGA-38-4627 TCGA-38-4630 TCGA-38-6178 TCGA-44-5643 TCGA-44-6775 
        8.68        37.71        35.28        14.73        33.30        23.18 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7669 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4490 
       61.28        19.46        18.87        29.00        13.45        12.66 
TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARQ TCGA-50-5930 
       12.13        22.26       153.04        40.41       211.82         9.27 
TCGA-50-5931 TCGA-50-5946 TCGA-50-6591 TCGA-50-6595 TCGA-50-6673 TCGA-53-A4EZ 
       14.27        22.55         3.91         6.21         0.72         9.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6982 TCGA-55-7570 
       23.05         2.86         0.07        42.51        32.71         0.20 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7995 TCGA-55-8091 TCGA-55-8096 TCGA-55-8208 
       23.18         1.28         0.16        19.73        23.64        22.16 
TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF TCGA-62-8394 
       17.62         2.17        21.40        20.58        20.19         4.57 
TCGA-64-1677 TCGA-64-5775 TCGA-67-3771 TCGA-69-7979 TCGA-69-7980 TCGA-73-7499 
       20.65         2.04        20.05         2.93        12.56        23.51 
TCGA-73-A9RS TCGA-78-7147 TCGA-78-7155 TCGA-78-7163 TCGA-78-7542 TCGA-78-8640 
       11.18        19.27        38.50       223.96        10.55       214.62 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
      110.50         5.88        34.39        19.43        19.89        16.70 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 
        4.08         0.79        15.75        15.65        21.47         1.15 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
       41.36         1.97        12.23        27.68         7.36         1.18 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-J2-8192 
       19.00        17.29         1.22         2.86        15.68        24.30 
TCGA-J2-A4AD TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
       18.08        12.59        11.87        27.19        38.63        86.14 
TCGA-MP-A4SY TCGA-NJ-A4YQ TCGA-NJ-A55R 
       49.35        29.13        19.82 

$subtype4
TCGA-05-4384 TCGA-05-4396 TCGA-05-4422 TCGA-35-3615 TCGA-44-2655 TCGA-44-6776 
       14.01         9.96        12.00         0.46        43.53        63.72 
TCGA-44-7671 TCGA-49-4486 TCGA-49-4510 TCGA-49-AAR2 TCGA-50-5932 TCGA-55-6972 
       17.59        76.21        29.46        63.95        40.60        48.49 
TCGA-55-8085 TCGA-55-A492 TCGA-62-8395 TCGA-62-A46P TCGA-62-A46S TCGA-67-3774 
       29.72        19.59        39.98        19.53        54.35        12.66 
TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 
       22.68        13.61        14.01         1.32         1.25        39.09 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7162 TCGA-78-7167 
       35.93        39.52        24.99        32.09       104.19        88.14 
TCGA-78-7537 TCGA-78-7633 TCGA-86-8674 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
       53.33        32.68        13.32         1.15        16.18        14.27 
TCGA-97-8174 TCGA-97-8179 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-J2-8194 TCGA-MP-A4TH 
        5.39        14.30        17.75        20.84        23.80        14.66 
TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A55O 
       73.91         1.64         0.43 

$subtype5
TCGA-05-4390 TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 TCGA-44-5644 TCGA-44-6774 
       37.02        14.96        29.98        25.02        28.37        21.63 
TCGA-44-7667 TCGA-44-8119 TCGA-44-A479 TCGA-4B-A93V TCGA-50-5051 TCGA-50-7109 
       36.07         3.25        15.98         9.86        15.72        10.13 
TCGA-53-7813 TCGA-55-1594 TCGA-55-6642 TCGA-55-6969 TCGA-55-7815 TCGA-55-7910 
       13.94        38.73        32.65        40.73         1.78         6.48 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A494 
        0.13        17.98         0.26         0.49         0.49        15.81 
TCGA-62-8402 TCGA-62-A470 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-69-7973 
       49.25        39.25        39.09        87.98        28.41         7.56 
TCGA-73-4659 TCGA-78-7159 TCGA-78-7161 TCGA-78-7536 TCGA-86-7701 TCGA-86-7713 
       23.38        64.90         7.07         8.02        31.13        13.87 
TCGA-86-8054 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 
       24.49        14.60        30.84         3.81        10.62        10.19 
TCGA-91-A4BC TCGA-95-A4VP TCGA-99-8032 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE 
        1.45        19.89         1.45         5.29        10.09        29.46 
TCGA-NJ-A4YF 
       71.05 

$subtype6
TCGA-05-4395 TCGA-05-4415 TCGA-05-4418 TCGA-05-5420 TCGA-05-5425 TCGA-38-4631 
        0.00         2.99         9.01        15.02        29.00        11.64 
TCGA-44-6145 TCGA-44-6779 TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       10.78        16.44        13.64        32.84         8.81        55.89 
TCGA-49-6742 TCGA-49-AAR9 TCGA-50-5072 TCGA-50-5936 TCGA-50-5939 TCGA-50-6592 
       14.63         8.55         8.22         8.45        15.12        25.55 
TCGA-53-7624 TCGA-55-1596 TCGA-55-6970 TCGA-55-6975 TCGA-55-8089 TCGA-55-8092 
       34.29        45.21        15.25         3.88         3.29         5.06 
TCGA-55-8505 TCGA-55-A48Y TCGA-62-8398 TCGA-62-A46O TCGA-62-A471 TCGA-64-5781 
        0.95        20.71        14.60        47.80        40.96        51.25 
TCGA-69-8255 TCGA-73-4670 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7160 
        4.24         4.31        20.58        21.90        19.50        22.29 
TCGA-78-7166 TCGA-78-7220 TCGA-86-8672 TCGA-93-8067 TCGA-95-7944 TCGA-95-A4VK 
        8.48        26.53         0.62         6.12        12.39        21.40 
TCGA-97-8176 TCGA-99-8033 TCGA-L9-A5IP TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TF 
       15.39         5.59         1.91         5.49        31.23        11.05 

$subtype7
TCGA-05-4403 TCGA-05-4430 TCGA-05-4433 TCGA-05-5429 TCGA-38-A44F TCGA-44-2657 
       19.00        25.02        24.00         9.04         4.37        13.15 
TCGA-44-2661 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-7659 
       24.36        12.59         9.93        27.78        23.15        14.60 
TCGA-44-7672 TCGA-44-A47G TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR 
       23.64        11.54        28.90        37.32       123.58       164.12 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5942 TCGA-50-6593 
       71.47        70.55        60.16        49.28        29.03        11.05 
TCGA-50-8459 TCGA-50-8460 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-7284 
        7.59        27.25        60.03        24.99        40.54         7.99 
TCGA-55-7573 TCGA-55-7728 TCGA-55-7907 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.13         0.79         0.53         0.30         0.10         4.80 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-62-A46R TCGA-62-A46Y 
        1.58         1.61        16.93        22.65        56.71        13.61 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-69-7761 TCGA-69-7974 TCGA-69-8254 
       37.02        38.37        42.90         6.12         6.05        13.45 
TCGA-69-8453 TCGA-78-7540 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 TCGA-86-A4P8 
       26.73        39.35         4.57        16.08        23.05        26.47 
TCGA-91-6835 TCGA-91-A4BD TCGA-93-A4JO TCGA-95-A4VN TCGA-97-7552 TCGA-97-7553 
        2.60        19.82         1.08        18.18        63.52        43.79 
TCGA-97-7941 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
        0.72        20.58        20.52        20.68        34.85        36.76 
TCGA-J2-A4AE TCGA-L9-A743 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TJ TCGA-NJ-A55A 
       35.47        17.46        58.45        86.04        11.15         0.26 
TCGA-S2-AA1A 
       16.87 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.13     0.10     0.07     0.43     0.13     0.00     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  163.10    97.74   223.96   104.19    87.98    55.89   164.12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   17.95    18.12    19.27    20.84    15.81    14.12    20.58 
[1] "0.1 - 163.1 (17.9)" "0.1 - 97.7 (18.1)"  "0.1 - 224.0 (19.3)"
[4] "0.4 - 104.2 (20.8)" "0.1 - 88.0 (15.8)"  "0.0 - 55.9 (14.1)" 
[7] "0.1 - 164.1 (20.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       30       22        0         8         6          9
  subtype2       1       16       35        0         9        24         18
  subtype3       3       26       27        1        14         7         11
  subtype4       0       17       15        0         4         5          3
  subtype5       0        9       16        0         7         5         12
  subtype6       0        7        7        0         2        13         12
  subtype7       1       28       18        0         7        12          8
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        3
  subtype2          3        6
  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       26       17        9        7       28
  STAGE IB         22       35       27       15       16        7       18
  STAGE II          0        0        1        0        0        0        0
  STAGE IIA         8        9       14        4        7        2        7
  STAGE IIB         6       24        7        5        5       13       12
  STAGE IIIA        9       18       11        3       12       12        8
  STAGE IIIB        1        3        2        2        1        2        0
  STAGE IV          3        6        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 11 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       11        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 36  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       36       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 37  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   37    2
  subtype6   37    6
  subtype7   47    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       52       79       55       38       37       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 23 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   23   29
  subtype6   19   30
  subtype7   44   33
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       63       59       52       16       23       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, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                16
  subtype2                          2                                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                                                 80
  subtype3                                                 71
  subtype4                                                 18
  subtype5                                                 36
  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
D8V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        2        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        16       19       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       45       80       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       36       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"
D8V10, binary
          cls
clus         0   1
  subtype1   2  77
  subtype2   4 108
  subtype3   2  95
  subtype4   0  48
  subtype5   4  48
  subtype6   4  45
  subtype7   5  72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   77
  subtype2    4  108
  subtype3    2   95
  subtype4    0   48
  subtype5    4   48
  subtype6    4   45
  subtype7    5   72
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         2        4        2        0        4        4        5
  YES       77      108       95       48       48       45       72
[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"
D8V11, continuous
D8V12, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 54  4  0  2
  subtype2 77  1  2  3
  subtype3 58  3  2  9
  subtype4 28  0  0  3
  subtype5 37  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       54       77       58       28       37       35       53
  R1        4        1        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                         5
  subtype6                                0     2                         2
  subtype7                                0     0                        10
          vv
clus       WHITE
  subtype1    62
  subtype2    84
  subtype3    70
  subtype4    37
  subtype5    38
  subtype6    38
  subtype7    58
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        5
  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       58
[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 36
  subtype6  2 31
  subtype7  0 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   60
  subtype2    0   85
  subtype3    4   71
  subtype4    0   34
  subtype5    0   36
  subtype6    2   31
  subtype7    0   64
                        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       36       31
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       64
[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 132  48
  subtype2 149  70
  subtype3  55  34
subtype1 subtype2 subtype3 
     180      219       89 
subtype1 subtype2 subtype3 
      48       70       34 
$subtype1
TCGA-05-4250 TCGA-05-4384 TCGA-05-4403 TCGA-05-4426 TCGA-05-5429 TCGA-35-3615 
        3.98        14.01        19.00        26.01         9.04         0.46 
TCGA-35-4122 TCGA-38-4626 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
        7.40       120.79        26.30         4.37        43.53        13.15 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       24.36         3.19        38.24         6.25        26.56        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
       10.78         9.93        23.15        63.72        32.45        14.60 
TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
       12.03        17.59        23.64         9.44        11.08        11.54 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4505 TCGA-49-4510 TCGA-49-6744 TCGA-49-6745 
       76.21        28.11        14.07        29.46        29.26        17.16 
TCGA-49-AARN TCGA-49-AARR TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
       37.32       164.12        71.47        15.72        60.16        49.28 
TCGA-50-5932 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-8457 
       40.60         8.45        18.64        29.03        25.12        25.61 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-6712 TCGA-55-6970 TCGA-55-6972 
       27.25        30.54        48.62         0.79        15.25        48.49 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 
       24.99       107.21         1.74         0.59         1.15         0.13 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 
        1.32        23.18         1.28         1.12        18.64        17.65 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        6.15        19.66        15.65         1.08         1.51         2.17 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.72         0.10         4.80         1.61        16.93        22.65 
TCGA-55-A492 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V 
       19.59        17.95        39.98        42.38        88.64        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5815 
       13.61        29.92        37.02        38.37        42.90        28.47 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1.02        14.04        12.66         5.72         4.64        13.87 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-8253 TCGA-69-8254 
        6.12        22.68        13.61         5.42        14.01        13.45 
TCGA-69-8453 TCGA-73-4662 TCGA-73-4676 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 
       26.73        29.98         5.39        39.09       163.10        27.16 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       20.58        35.93        39.52        24.99        19.50        32.09 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
       22.29       104.19         8.48        88.14        53.33        39.35 
TCGA-78-7633 TCGA-78-8655 TCGA-78-8660 TCGA-86-6562 TCGA-86-7714 TCGA-86-8076 
       32.68        77.59        10.55        12.36        20.55        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 
       15.65        23.05        13.91        26.47         2.60         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JO 
       16.18        16.60        14.27        19.82         9.76         1.08 
TCGA-93-A4JQ TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
       17.29        18.67        15.68        15.65        27.29        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       18.18        19.89        31.69        63.52        43.79         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 
        0.72         5.39        18.12        15.39        14.30        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       24.56        36.76        21.63        35.47        16.44        14.30 
TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A4TJ 
       14.53        17.46        49.35         5.49        14.66        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J TCGA-S2-AA1A 
       19.13        62.60         0.26         0.43        59.11        16.87 

$subtype2
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       19.96        45.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
       47.05         8.02         2.99        14.96         9.01        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4630 
        2.04         5.98         8.68        97.74        49.05        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-3396 
       11.64        44.61        46.98        44.94        42.08        37.15 
TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 
       34.06        33.30        28.37        19.46        36.07        29.00 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A4SS TCGA-49-4488 
       12.66         3.25        15.98        15.32        13.64        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       12.66        35.54        46.72        32.84         8.81        55.89 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 
       12.13        22.26       153.04        63.95        28.90         8.55 
TCGA-49-AARE TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 
       40.41       211.82         9.86        70.55        31.04         9.27 
TCGA-50-5931 TCGA-50-5935 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6597 
       14.27        21.47        22.55        42.35        25.55        41.69 
TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
        0.72        34.29        13.94         9.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6979 TCGA-55-6981 
       45.21         2.86        42.51        40.73         7.79        45.34 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
       70.26         7.99         0.20         0.79         1.78         0.53 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.48        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8208 TCGA-55-8301 
        5.06         0.13        23.64        17.98        22.16         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
        0.76         0.95         0.36         0.26         0.49         0.30 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
        6.64         0.49         1.58         2.17        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
        1.58        20.58         0.92        15.81        20.19         4.57 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
       67.96        39.25        40.96        20.65        39.09        87.98 
TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 
       28.41        20.05        18.84         6.64         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 
        2.30         2.93        12.56         4.24         7.04        23.38 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 
       23.51        11.18         5.69        19.27        21.90        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        5.88        64.90         7.07        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
       10.75        10.55       214.62       110.50        27.09         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        13.87        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       24.49         4.57        15.85        21.47        14.60         1.15 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 
       30.84        27.58        14.96        13.32         3.81        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 TCGA-91-A4BC 
        1.97        10.19        13.71        12.23         1.18         1.45 
TCGA-93-8067 TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
        6.12        19.00         1.12         1.22         2.86        12.39 
TCGA-97-7547 TCGA-97-8171 TCGA-97-8172 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8032 
       64.60        18.67        17.92        18.67        34.85         1.45 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A5IP 
        5.59        23.80        18.08        19.00         0.20         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       12.59        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A5C7 
       58.45        86.04         5.29        31.23        29.46        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R 
       71.05        29.13        19.82 

$subtype3
TCGA-05-4249 TCGA-05-4405 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-44-2665 
       50.07        20.05        37.71        28.41        14.73        42.77 
TCGA-44-2668 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
       25.02        23.77        27.78        21.63        23.18        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4512 
       16.44         7.17        18.87         8.55        13.45        29.75 
TCGA-49-6742 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AARO TCGA-50-5044 
       14.63        11.64        22.26        62.24       123.58        20.52 
TCGA-50-5072 TCGA-50-5933 TCGA-50-5939 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
        8.22        78.67        15.12         3.91        11.05        12.16 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 
        6.21        10.13         7.59         0.07        32.65         0.82 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7574 
        5.49         2.20        32.71        60.03        40.54         3.12 
TCGA-55-7726 TCGA-55-7816 TCGA-55-8091 TCGA-55-8299 TCGA-55-8614 TCGA-55-A4DG 
        1.28         1.45        19.73        15.42        17.62        19.99 
TCGA-64-1676 TCGA-64-1679 TCGA-64-5775 TCGA-64-5781 TCGA-71-6725 TCGA-71-8520 
       56.81        55.43         2.04        51.25         2.01         0.10 
TCGA-73-4658 TCGA-73-4675 TCGA-78-7163 TCGA-78-8648 TCGA-86-8055 TCGA-86-8073 
       52.60         1.32       223.96        39.75         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
        0.79        15.75         0.62        13.32        17.62        13.64 
TCGA-91-6829 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JN TCGA-95-8494 
       41.36        27.68         7.36         4.18        23.61         2.76 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 
       25.48         5.95        16.41        21.60        20.68        24.30 
TCGA-L9-A443 TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
        3.81        37.35        58.85        41.59         2.43        10.09 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
       11.05        14.10         0.13         1.64         9.70 

subtype1 subtype2 subtype3 
    0.10     0.00     0.07 
subtype1 subtype2 subtype3 
  164.12   214.62   223.96 
subtype1 subtype2 subtype3 
   18.41    19.00    16.41 
[1] "0.1 - 164.1 (18.4)" "0.0 - 214.6 (19.0)" "0.1 - 224.0 (16.4)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       72       40        0        19        25         22
  subtype2       4       46       70        0        22        34         30
  subtype3       0       16       30        1        10        12         21
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        9
  subtype2          8       13
  subtype3          2        3
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         72       46       16
  STAGE IB         40       70       30
  STAGE II          0        0        1
  STAGE IIA        19       22       10
  STAGE IIB        25       34       12
  STAGE IIIA       22       30       21
  STAGE IIIB        1        8        2
  STAGE IV          9       13        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  83  85  16   6
  subtype2  60 133  23   9
  subtype3  26  56   8   4
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       83       60       26
  T2       85      133       56
  T3       16       23        8
  T4        6        9        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 124  39    21
  subtype2 149  38    36
  subtype3  56  18    19
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         124      149       56
  N1          39       38       18
  N2+N3       21       36       19
[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 130   8
  subtype2 156  13
  subtype3  59   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  130    8
  subtype2  156   13
  subtype3   59    2
   clus
vv  subtype1 subtype2 subtype3
  0      130      156       59
  1        8       13        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1 108  82
  subtype2 116 111
  subtype3  49  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108   82
  subtype2  116  111
  subtype3   49   46
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      108      116       49
  MALE         82      111       46
[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, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                         10                                45
  subtype2                          8                                53
  subtype3                          1                                 8
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 99
  subtype2                                                147
  subtype3                                                 72
          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                              1                                  1
  subtype2                              1                                  0
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             8
  subtype2                            0                             9
  subtype3                            0                             6
          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
D9V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                               10        8        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        45       53        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       99      147       72
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                4        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            12        4        3
  LUNG CLEAR CELL ADENOCARCINOMA                            1        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             8        9        6
  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"
D9V10, binary
          cls
clus         0   1
  subtype1   7 183
  subtype2   9 218
  subtype3   4  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  183
  subtype2    9  218
  subtype3    4   91
     clus
vv    subtype1 subtype2 subtype3
  NO         7        9        4
  YES      183      218       91
[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"
D9V11, continuous
D9V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 122   2   2  10
  subtype2 162   7   2   9
  subtype3  55   3   0   7
D9V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      122      162       55
  R1        2        7        3
  R2        2        2        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     1                        18   152
  subtype2     5                        25   158
  subtype3     2                         8    76
D9V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        5        2
  BLACK OR AFRICAN AMERICAN       18       25        8
  WHITE                          152      158       76
[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   1 144
  subtype2   5 161
  subtype3   1  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  144
  subtype2    5  161
  subtype3    1   74
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        1
  NOT HISPANIC OR LATINO      144      161       74
[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  20
  subtype2 133  58
  subtype3  92  41
  subtype4  62  33
subtype1 subtype2 subtype3 subtype4 
      69      191      133       95 
subtype1 subtype2 subtype3 subtype4 
      20       58       41       33 
$subtype1
TCGA-05-4384 TCGA-35-3615 TCGA-44-2656 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       14.01         0.46        46.98        38.24         6.25        26.56 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B 
       63.72        32.45        14.60        17.59        23.64         9.44 
TCGA-44-A47F TCGA-49-4486 TCGA-49-AARN TCGA-50-5045 TCGA-50-5932 TCGA-50-5942 
       11.08        76.21        37.32        71.47        40.60        29.03 
TCGA-50-5944 TCGA-50-8460 TCGA-55-1595 TCGA-55-6970 TCGA-55-6972 TCGA-55-6986 
       25.12        27.25        48.62        15.25        48.49       107.21 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7573 TCGA-55-7727 TCGA-55-7911 TCGA-55-A491 
        1.74         0.59         0.13         1.12        17.65        20.58 
TCGA-55-A492 TCGA-62-8397 TCGA-62-A472 TCGA-64-5815 TCGA-67-6215 TCGA-67-6217 
       19.59        42.38        29.92        28.47         5.72        13.87 
TCGA-69-7763 TCGA-69-7765 TCGA-69-8253 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 
       22.68         5.42        14.01        39.09        20.58        35.93 
TCGA-78-7156 TCGA-78-7166 TCGA-78-7537 TCGA-78-7633 TCGA-78-8660 TCGA-86-7714 
       32.09         8.48        53.33        32.68        10.55        20.55 
TCGA-91-8496 TCGA-93-7347 TCGA-93-A4JQ TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP 
       16.60         9.76        17.29        27.29        21.40        19.89 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M3 
        5.39        15.39        14.30        20.19        21.44        17.75 
TCGA-99-7458 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TC 
       24.56        16.44        14.30        49.35         5.49         2.43 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-O1-A52J 
       19.13        62.60        59.11 

$subtype2
TCGA-05-4249 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4417 
       50.07        37.02         0.00         9.96        24.03        14.96 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       12.00        21.99        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
       22.03         2.04         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-44-2655 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
       14.73        43.53        44.94        42.08        42.77        25.02 
TCGA-44-3918 TCGA-44-5643 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A 
       34.06        33.30         7.17        12.66         8.55        15.32 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
       13.64        13.45        28.57        35.54        46.72        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AARQ 
        8.81        55.89        11.64        22.26        62.24       211.82 
TCGA-4B-A93V TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 
        9.86        15.72        31.04         9.27        78.67        21.47 
TCGA-50-5941 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-7109 
       18.64        42.35         3.91        25.55        12.16        10.13 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 
       34.29        13.94         9.21         0.07        32.65         0.82 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-7576 TCGA-55-7815 
        5.49         7.79        45.34        32.71         1.32         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
       18.64         0.53         6.48         0.16        29.72         3.29 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
       19.73        17.98        15.42         1.45         0.76         0.36 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       17.72         0.30         0.49         1.58        20.71        21.40 
TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P 
       15.81         4.57        39.98        14.60        49.25        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 
       54.35        67.96        72.30        40.96        56.81        20.65 
TCGA-64-1678 TCGA-64-5781 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
       39.09        51.25        18.84        14.04        12.66         4.64 
TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        6.64         7.56         6.05         2.30         2.93        12.56 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24         7.04         2.01         0.10        52.60        23.38 
TCGA-73-4662 TCGA-73-4675 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7155 TCGA-78-7159 
       29.98         1.32        11.18        27.16        38.50        64.90 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8655 
        7.07       223.96        31.20         8.02        10.75        77.59 
TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
      110.50        27.09        31.13        13.87        19.43        19.89 
TCGA-86-8054 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
       24.49        24.33         0.79        15.75        15.65        15.85 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       14.60        13.91        30.84         0.62        14.96        13.32 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6836 TCGA-91-6847 
        3.81        17.62        13.64        10.62        13.71        27.68 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        4.18         6.12         1.12         1.22         2.86        18.67 
TCGA-95-7944 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8547 TCGA-97-A4M6 
       12.39        25.48         5.95        18.67        21.60        18.67 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       20.68        34.85         1.45         5.59        24.30        23.80 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00         3.81         0.20        11.87        27.19         2.76 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TF 
       58.45        37.35        58.85         5.29        10.09        11.05 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
       73.91        71.05         0.13         1.64         9.70 

$subtype3
TCGA-05-4250 TCGA-05-4403 TCGA-05-4405 TCGA-05-4426 TCGA-05-4433 TCGA-05-5429 
        3.98        19.00        20.05        26.01        24.00         9.04 
TCGA-35-4122 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 
        7.40        26.30         4.37        13.15        24.36         3.19 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       12.59        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6779 TCGA-44-7661 TCGA-44-A47G TCGA-49-4487 TCGA-49-4505 
       23.18        16.44        12.03        11.54        28.11        14.07 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AARR 
       29.46        29.75        29.26        17.16        22.26       164.12 
TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5936 TCGA-50-6593 TCGA-50-6595 
       20.52        60.16        49.28         8.45        11.05         6.21 
TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-53-7626 TCGA-55-6712 TCGA-55-6980 
       41.69        25.61         7.59        30.54         0.79         2.20 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 
       60.03        24.99        40.54         1.15         7.99         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-7914 
       23.18         1.28         1.28         0.79         1.45         6.15 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       15.19        19.66        15.65         1.08         1.51         2.17 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        0.10         4.80        17.62         1.61        16.93        22.65 
TCGA-55-A4DG TCGA-62-A46R TCGA-62-A46Y TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
       19.99        56.71        13.61        37.02        38.37        42.90 
TCGA-67-3770 TCGA-69-7761 TCGA-69-7764 TCGA-69-8254 TCGA-69-8453 TCGA-73-4676 
        1.02         6.12        13.61        13.45        26.73         5.39 
TCGA-78-7143 TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 
      163.10        19.27        39.52        24.99        19.50         5.88 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7540 TCGA-86-6562 TCGA-86-8056 
       22.29       104.19        88.14        39.35        12.36         4.57 
TCGA-86-8076 TCGA-86-8280 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6835 
       16.08        23.05        27.58        13.32        26.47         2.60 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JN TCGA-93-A4JO 
        1.15        16.18        14.27        19.82        23.61         1.08 
TCGA-93-A4JP TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 
       19.00        15.68        15.65         2.76        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 
       64.60        63.52        43.79         0.59         0.72        17.92 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 
       18.12        16.41        20.58        19.76        20.52        20.84 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4T4 
       36.76        21.63        35.47        14.53        17.46        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A55A TCGA-NJ-A55O 
       41.59        14.66        14.10        11.15         0.26         0.43 
TCGA-S2-AA1A 
       16.87 

$subtype4
TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4418 
       19.96        45.01        47.05         8.02         2.99         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-44-3396 
       29.98        30.02        26.01        25.02        25.02        37.15 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       28.37        23.77        61.28        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 TCGA-49-4490 TCGA-49-6742 TCGA-49-6743 
       29.00         3.25        15.98        12.66        14.63        12.13 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
      153.04        63.95        28.90         8.55        40.41       123.58 
TCGA-50-5049 TCGA-50-5072 TCGA-50-5931 TCGA-50-5939 TCGA-50-5946 TCGA-50-6673 
       70.55         8.22        14.27        15.12        22.55         0.72 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 
       23.05        38.73        45.21         2.86        42.51        40.73 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       70.26         0.20        19.82         5.06         0.13        23.64 
TCGA-55-8208 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8620 
       22.16         0.95         0.26         0.49         6.64         2.17 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8399 TCGA-62-A46O 
        1.58         0.92        20.19        17.95        88.64        47.80 
TCGA-62-A470 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 
       39.25        55.43        87.98         2.04        28.41        20.05 
TCGA-73-7499 TCGA-78-7146 TCGA-78-7150 TCGA-78-7220 TCGA-78-7542 TCGA-78-8640 
       23.51         5.69        21.90        26.53        10.55       214.62 
TCGA-78-8648 TCGA-86-6851 TCGA-86-7711 TCGA-86-7955 TCGA-86-8055 TCGA-86-8358 
       39.75         5.88        34.39        16.70         4.08        21.47 
TCGA-86-8585 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 
        1.15        41.36         1.97        10.19        12.23         7.36 
TCGA-91-8499 TCGA-91-A4BC TCGA-J2-A4AD TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 
        1.18         1.45        18.08         1.91        12.59        38.63 
TCGA-MP-A4SV TCGA-MP-A4TA TCGA-MP-A4TE TCGA-NJ-A4YQ TCGA-NJ-A55R 
       86.14        31.23        29.46        29.13        19.82 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.00     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 
  107.21   223.96   164.12   214.62 
subtype1 subtype2 subtype3 subtype4 
   20.55    15.72    17.46    20.19 
[1] "0.1 - 107.2 (20.6)" "0.0 - 224.0 (15.7)" "0.1 - 164.1 (17.5)"
[4] "0.1 - 214.6 (20.2)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       29       16        0         3        10         10
  subtype2       3       39       61        0        20        30         30
  subtype3       1       42       36        1        16        19         16
  subtype4       1       24       27        0        12        12         17
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        3
  subtype2          6        9
  subtype3          2        8
  subtype4          2        5
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        3        1        1
  STAGE IA         29       39       42       24
  STAGE IB         16       61       36       27
  STAGE II          0        0        1        0
  STAGE IIA         3       20       16       12
  STAGE IIB        10       30       19       12
  STAGE IIIA       10       30       16       17
  STAGE IIIB        1        6        2        2
  STAGE IV          3        9        8        5
[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  31  33   4   4
  subtype2  50 120  19   8
  subtype3  55  67  14   4
  subtype4  33  54  10   3
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       31       50       55       33
  T2       33      120       67       54
  T3        4       19       14       10
  T4        4        8        4        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  48  14     7
  subtype2 128  36    32
  subtype3  89  29    18
  subtype4  64  16    19
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          48      128       89       64
  N1          14       36       29       16
  N2+N3        7       32       18       19
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1  50   2
  subtype2 144   9
  subtype3  89   7
  subtype4  62   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    2
  subtype2  144    9
  subtype3   89    7
  subtype4   62    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       50      144       89       62
  1        2        9        7        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  35  37
  subtype2 113  85
  subtype3  86  56
  subtype4  39  61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   37
  subtype2  113   85
  subtype3   86   56
  subtype4   39   61
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35      113       86       39
  MALE         37       85       56       61
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          6                                18
  subtype2                          4                                40
  subtype3                          6                                30
  subtype4                          3                                18
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 39
  subtype2                                                135
  subtype3                                                 73
  subtype4                                                 71
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          2
  subtype3                                          3
  subtype4                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             4
  subtype2                                             4
  subtype3                                            10
  subtype4                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  0
  subtype2                              0                                  2
  subtype3                              0                                  0
  subtype4                              1                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             4
  subtype2                            0                            10
  subtype3                            2                             7
  subtype4                            0                             2
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               1
  subtype4                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             1
  subtype3                                             2
  subtype4                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            8
  subtype4                            2
D10V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        4        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        18       40       30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       39      135       73
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        2        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             4        4       10
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        2        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        2
  LUNG PAPILLARY ADENOCARCINOMA                             4       10        7
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        2
  MUCINOUS (COLLOID) CARCINOMA                              0        0        8
                                                    clus
vv                                                   subtype4
  LUNG ACINAR ADENOCARCINOMA                                3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       71
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1
  LUNG CLEAR CELL ADENOCARCINOMA                            1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0
  LUNG MUCINOUS ADENOCARCINOMA                              0
  LUNG PAPILLARY ADENOCARCINOMA                             2
  LUNG SIGNET RING ADENOCARCINOMA                           0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2
  MUCINOUS (COLLOID) CARCINOMA                              2
[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"
D10V10, binary
          cls
clus         0   1
  subtype1   4  68
  subtype2   8 190
  subtype3   4 138
  subtype4   4  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   68
  subtype2    8  190
  subtype3    4  138
  subtype4    4   96
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         4        8        4        4
  YES       68      190      138       96
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  41   1   0   4
  subtype2 140   6   1   8
  subtype3  90   3   2   9
  subtype4  68   2   1   5
D10V13, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       41      140       90       68
  R1        1        6        3        2
  R2        0        1        2        1
  RX        4        8        9        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    58
  subtype2     4                        18   150
  subtype3     2                        11   114
  subtype4     1                        16    64
D10V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        4        2        1
  BLACK OR AFRICAN AMERICAN        6       18       11       16
  WHITE                           58      150      114       64
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
          cls
clus         0   1
  subtype1   0  52
  subtype2   3 149
  subtype3   2 108
  subtype4   2  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   52
  subtype2    3  149
  subtype3    2  108
  subtype4    2   70
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        3        2        2
  NOT HISPANIC OR LATINO       52      149      108       70
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1  90  47
  subtype2 138  52
  subtype3  59  28
subtype1 subtype2 subtype3 
     137      190       87 
subtype1 subtype2 subtype3 
      47       52       28 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 
       14.01         9.96        20.05        30.02        21.99        26.01 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-35-5375 TCGA-38-4632 TCGA-38-7271 
       24.00         4.96         9.04         8.68        44.61        26.30 
TCGA-38-A44F TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
        4.37        33.30        28.37        12.59        10.78         9.93 
TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       27.78        23.18        63.72        61.28        16.44        14.60 
TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-49-4487 
       12.03        18.87        29.00        17.59        23.64        28.11 
TCGA-49-4490 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       12.66        55.89        14.63        12.13        29.26        17.16 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
       20.52        15.72        60.16        49.28         9.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12        18.64        29.03        25.12 
TCGA-50-6593 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 
       11.05        41.69        10.13        25.61        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       30.54        13.94         0.79         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 
        7.99         0.13         3.12         1.32        23.18         1.12 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78        18.64         0.53         6.48        17.65         6.15 
TCGA-55-8206 TCGA-55-8512 TCGA-55-8621 TCGA-62-8397 TCGA-64-1681 TCGA-67-6215 
        1.51         0.10        16.93        42.38        38.37         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-8254 TCGA-69-8453 
        4.64        13.87         6.64         5.42        13.45        26.73 
TCGA-71-6725 TCGA-73-4676 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        2.01         5.39       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 
       20.58        35.93        39.52        19.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       22.29         7.07         8.48        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-86-6562 
       53.33        10.75        39.35        10.55        32.68        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-8056 TCGA-91-6828 TCGA-91-6829 
       31.13        34.39        20.55         4.57        10.62        41.36 
TCGA-91-6835 TCGA-91-6836 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-95-7567 
        2.60        13.71        16.18        16.60        14.27        18.67 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        43.79         5.95         0.59 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
       17.92         5.39        20.58        19.76        20.84        24.56 
TCGA-99-AA5R TCGA-L9-A50W TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-S2-AA1A 
       21.63        14.53         0.43         9.70        16.87 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
       37.02         2.99        15.02        29.00        22.03         2.04 
TCGA-44-7660 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       19.46        12.66         3.25        15.98         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4488 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       11.54        13.64        28.57        22.26       153.04        63.95 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5931 
        8.55        40.41        37.32       211.82         9.86        14.27 
TCGA-50-5946 TCGA-50-6673 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       22.55         0.72         9.21        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 
        0.82        48.49         7.79         2.20        45.34        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7728 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
      107.21        70.26         0.79        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8208 
        3.29        19.66         5.06         0.13        17.98        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.30         4.80         6.64         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       19.59         0.92        15.81        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        67.96        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-69-7973 
       40.96        29.92        87.98        42.90        28.41         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
        6.05         2.30         2.93        12.56        14.01         4.24 
TCGA-69-A59K TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7155 TCGA-78-7536 
        7.04        39.09        23.51        11.18        38.50         8.02 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
      214.62        77.59        10.55       110.50        27.09         5.88 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8076 
       13.87        19.43        19.89        16.70        24.49        16.08 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
       23.05        21.47        14.60         1.15        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 
       14.96        13.32        13.32         3.81        17.62        26.47 
TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8499 TCGA-91-A4BC 
        1.97        12.23        27.68         1.15         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       19.82         9.76        23.61         1.08        19.00        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.22         2.86        12.39        15.68        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       21.40        18.18        19.89         0.72        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       15.39        14.30        20.19        21.44        20.52        17.75 
TCGA-97-A4M6 TCGA-99-8025 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       18.67        34.85        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
       19.00        14.30         0.20         1.91        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       11.87        27.19         2.76        86.14        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-O1-A52J 
       71.05        29.13        19.82        59.11 

$subtype3
TCGA-05-4417 TCGA-38-4631 TCGA-38-6178 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 
       14.96        11.64        14.73        23.77        23.15        21.63 
TCGA-44-6777 TCGA-44-7662 TCGA-44-7667 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4512 
       32.45         7.17        36.07         8.55        13.45        29.75 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARR 
       11.64        22.26        62.24        28.90       123.58       164.12 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 TCGA-50-6590 
       71.47        70.55        31.04         8.22        78.67        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-8459 TCGA-55-5899 
        3.91        25.55        12.16         6.21         7.59         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6978 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
        0.07        32.65         5.49        32.71        60.03        40.54 
TCGA-55-7570 TCGA-55-7726 TCGA-55-7816 TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 
        0.20         1.28         1.45        19.73        23.64         1.08 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8614 TCGA-62-A46V TCGA-64-1679 TCGA-64-5775 
       15.42         0.95        17.62        72.30        55.43         2.04 
TCGA-64-5781 TCGA-64-5815 TCGA-71-8520 TCGA-73-4658 TCGA-78-7150 TCGA-78-7163 
       51.25        28.47         0.10        52.60        21.90       223.96 
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        15.75        15.65 
TCGA-86-8279 TCGA-86-8668 TCGA-86-8672 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6848 
       15.85        13.91         0.62        13.64        10.19         7.36 
TCGA-93-7348 TCGA-95-7039 TCGA-95-8494 TCGA-97-7554 TCGA-97-8177 TCGA-97-8547 
        4.18         1.12         2.76        25.48        16.41        21.60 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-L9-A443 
       20.68        36.76         1.45         5.59        24.30         3.81 
TCGA-MN-A4N4 TCGA-MP-A4SY TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TI TCGA-NJ-A4YG 
       38.63        49.35         2.43        10.09        14.10        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
        0.13         1.64         0.26 

subtype1 subtype2 subtype3 
    0.10     0.13     0.07 
subtype1 subtype2 subtype3 
  163.10   214.62   223.96 
subtype1 subtype2 subtype3 
   17.65    17.85    15.75 
[1] "0.1 - 163.1 (17.6)" "0.1 - 214.6 (17.9)" "0.1 - 224.0 (15.8)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       36       33        0        18        19         24
  subtype2       4       58       52        1        23        26         22
  subtype3       0       19       29        0         7        16         18
          vv
clus       STAGE IIIB STAGE IV
  subtype1          4       10
  subtype2          3        8
  subtype3          1        3
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         36       58       19
  STAGE IB         33       52       29
  STAGE II          0        1        0
  STAGE IIA        18       23        7
  STAGE IIB        19       26       16
  STAGE IIIA       24       22       18
  STAGE IIIB        4        3        1
  STAGE IV         10        8        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  48  73  14  11
  subtype2  76 100  18   2
  subtype3  23  58   8   2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       48       76       23
  T2       73      100       58
  T3       14       18        8
  T4       11        2        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        N0  N1 N2+N3
  subtype1  86  34    21
  subtype2 138  31    26
  subtype3  56  16    18
D11V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          86      138       56
  N1          34       31       16
  N2+N3       21       26       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"
D11V6, binary
          cls
clus         0   1
  subtype1  97   9
  subtype2 123   8
  subtype3  59   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97    9
  subtype2  123    8
  subtype3   59    2
   clus
vv  subtype1 subtype2 subtype3
  0       97      123       59
  1        9        8        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus         0   1
  subtype1  77  69
  subtype2 105  92
  subtype3  51  42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   69
  subtype2  105   92
  subtype3   51   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       77      105       51
  MALE         69       92       42
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          4                                38
  subtype2                         13                                39
  subtype3                          0                                 9
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 75
  subtype2                                                117
  subtype3                                                 74
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            11
  subtype2                                             7
  subtype3                                             1
          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                             7
  subtype2                            0                            11
  subtype3                            1                             4
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             5
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            4
  subtype2                            4
  subtype3                            2
D11V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4       13        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        38       39        9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       75      117       74
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            11        7        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             7       11        4
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        5        0
  MUCINOUS (COLLOID) CARCINOMA                              4        4        2
[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"
D11V10, binary
          cls
clus         0   1
  subtype1   9 137
  subtype2   3 194
  subtype3   6  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  137
  subtype2    3  194
  subtype3    6   87
     clus
vv    subtype1 subtype2 subtype3
  NO         9        3        6
  YES      137      194       87
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  83   5   1   4
  subtype2 139   2   0  15
  subtype3  57   2   0   3
D11V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       83      139       57
  R1        5        2        2
  R2        1        0        0
  RX        4       15        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     1                        15   110
  subtype2     3                        24   148
  subtype3     1                        10    74
D11V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        1
  BLACK OR AFRICAN AMERICAN       15       24       10
  WHITE                          110      148       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"
D11V15, binary
          cls
clus         0   1
  subtype1   4  91
  subtype2   2 159
  subtype3   0  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   91
  subtype2    2  159
  subtype3    0   74
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        0
  NOT HISPANIC OR LATINO       91      159       74
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1  79  20
  subtype2 156  77
  subtype3  52  30
subtype1 subtype2 subtype3 
      99      233       82 
subtype1 subtype2 subtype3 
      20       77       30 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4433 TCGA-05-5429 TCGA-38-A44F TCGA-44-5645 
       14.01         9.96        24.00         9.04         4.37        12.59 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        9.93        23.15        63.72         9.44        11.08        11.54 
TCGA-49-AAQV TCGA-49-AARR TCGA-50-5932 TCGA-50-5942 TCGA-50-8457 TCGA-50-8459 
       22.26       164.12        40.60        29.03        25.61         7.59 
TCGA-50-8460 TCGA-55-6972 TCGA-55-6983 TCGA-55-6984 TCGA-55-7284 TCGA-55-7727 
       27.25        48.49        60.03        24.99         7.99         1.12 
TCGA-55-7728 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8206 TCGA-55-8512 
        0.79        17.65        29.72        15.19         1.51         0.10 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
        4.80         1.58         1.61        16.93        22.65        19.59 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-A46S TCGA-62-A46Y 
       19.99        17.95        39.98        42.38        54.35        13.61 
TCGA-62-A472 TCGA-67-6215 TCGA-67-6217 TCGA-69-8254 TCGA-69-8453 TCGA-73-7498 
       29.92         5.72        13.87        13.45        26.73        39.09 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 
       35.93        39.52        32.09        88.14        53.33        10.75 
TCGA-78-7540 TCGA-78-7633 TCGA-86-8056 TCGA-86-8280 TCGA-86-A456 TCGA-86-A4JF 
       39.35        32.68         4.57        23.05        13.32        17.62 
TCGA-86-A4P8 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JN 
       26.47        16.18        16.60        14.27        19.82        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
        1.08        19.00        27.29        21.40        18.18        19.89 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4LX 
       63.52         0.72        17.92         5.39        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-AA5R 
       21.44        19.76        20.52        17.75        20.84        21.63 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4T7 
       35.47        16.44        14.30        14.53        17.46         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A55A 
       41.59        14.66        11.15        73.91        62.60         0.26 
TCGA-NJ-A55O TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        59.11        16.87 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4424 TCGA-05-4425 TCGA-05-5420 TCGA-05-5423 
       37.02         2.99        30.02        21.99        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-38-4631 TCGA-38-4632 
       29.00        22.03         2.04         8.68        11.64        44.61 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6778 
       33.30        28.37        23.77        10.78        27.78        61.28 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 
       19.46         7.17        36.07        18.87        29.00        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS TCGA-49-4488 TCGA-49-4490 
        3.25         8.55        15.98        13.64        28.57        12.66 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 
       55.89        14.63        12.13        11.64        22.26       153.04 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       63.95        62.24        28.90         8.55        40.41        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      123.58       211.82         9.86        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
       31.04        49.28         8.22         9.27        14.27        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
        8.45        15.12        18.64        22.55        42.35        25.55 
TCGA-50-6594 TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       12.16         0.72        34.29        13.94         9.21         2.86 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73        15.25         0.82         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7570 TCGA-55-7910 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.20         6.48        19.82         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8208 
        5.06         0.13        23.64        17.98         1.08        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.49        17.72         0.30         6.64        17.62         0.49 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
        2.17        20.71        21.40         1.58        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
       15.81        20.19         4.57        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 
       19.53        56.71        67.96        39.25        40.96        55.43 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-69-7973 
       87.98         2.04        42.90        28.41        51.25         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
        6.05         2.30         2.93        12.56        14.01         4.24 
TCGA-69-A59K TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7150 
        7.04         5.39        23.51        11.18         5.69        21.90 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7220 
       19.50        38.50        64.90        22.29         7.07        26.53 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        8.02        10.55       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        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 
       13.87        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 
       24.33        15.75        16.08        15.65        15.85        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60         1.15        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.32         3.81        10.62        41.36         1.97        10.19 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 
       13.71        12.23        27.68         7.36         1.15         1.18 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.45         9.76        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 TCGA-97-8171 
       18.67        12.39        15.68        15.65         2.76        18.67 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M6 TCGA-99-8025 
       18.12        15.39        14.30        21.60        18.67        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L4-A4E5 
       36.76         1.45         5.59        23.80        18.08        19.00 
TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
        0.20         1.91        12.59        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T8 
        2.76        86.14        58.45        49.35        86.04         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
       31.23         2.43        10.09        29.46        11.05        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55R 
       19.13        71.05         1.64        29.13        19.82 

$subtype3
TCGA-05-4405 TCGA-05-4417 TCGA-05-4427 TCGA-38-6178 TCGA-38-7271 TCGA-44-6774 
       20.05        14.96        26.01        14.73        26.30        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 
       23.18        32.45        16.44        14.60        12.03        17.59 
TCGA-44-7672 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 
       23.64        13.45        28.11        29.75        29.26        17.16 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5933 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 
       20.52        71.47        78.67        25.12         3.91        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-53-7626 TCGA-55-6543 TCGA-55-6642 
        6.21        41.69        10.13        30.54         0.07        32.65 
TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 
        0.79         1.74         0.59         1.15         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.32        23.18         1.28         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7914 TCGA-62-8402 TCGA-62-A46V TCGA-64-1681 TCGA-64-5815 
        0.53         6.15        49.25        72.30        38.37        28.47 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
        4.64         6.64         5.42         2.01         0.10        52.60 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7163 TCGA-78-7166 
      163.10        27.16        19.27        20.58       223.96         8.48 
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 
        4.18        31.69        64.60        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-L9-A443 
        0.59        16.41        20.68        24.56        24.30         3.81 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-NJ-A4YI TCGA-NJ-A7XG 
       37.35        58.85         0.13         9.70 

subtype1 subtype2 subtype3 
    0.10     0.13     0.07 
subtype1 subtype2 subtype3 
  164.12   214.62   223.96 
subtype1 subtype2 subtype3 
  19.000   15.850   17.375 
[1] "0.1 - 164.1 (19.0)" "0.1 - 214.6 (15.8)" "0.1 - 224.0 (17.4)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       35       22        1        10        16          9
  subtype2       4       54       68        0        30        37         39
  subtype3       0       24       24        0         8         8         16
          vv
clus       STAGE IIIB STAGE IV
  subtype1          2        6
  subtype2          4       11
  subtype3          2        4
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        4        0
  STAGE IA         35       54       24
  STAGE IB         22       68       24
  STAGE II          1        0        0
  STAGE IIA        10       30        8
  STAGE IIB        16       37        8
  STAGE IIIA        9       39       16
  STAGE IIIB        2        4        2
  STAGE IV          6       11        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  43  42  13   4
  subtype2  74 143  24   5
  subtype3  30  46   3   6
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       74       30
  T2       42      143       46
  T3       13       24        3
  T4        4        5        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1  75  15     8
  subtype2 155  46    43
  subtype3  50  20    14
D12V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          75      155       50
  N1          15       46       20
  N2+N3        8       43       14
[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  66   6
  subtype2 160  11
  subtype3  53   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    6
  subtype2  160   11
  subtype3   53    2
   clus
vv  subtype1 subtype2 subtype3
  0       66      160       53
  1        6       11        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus         0   1
  subtype1  52  51
  subtype2 119 128
  subtype3  62  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   51
  subtype2  119  128
  subtype3   62   24
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       52      119       62
  MALE         51      128       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                27
  subtype2                          9                                44
  subtype3                          3                                15
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 43
  subtype2                                                168
  subtype3                                                 55
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             6
  subtype2                                             8
  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                            2                             8
  subtype2                            0                            10
  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                            7
  subtype2                            3
  subtype3                            0
D12V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        9        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        27       44       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       43      168       55
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6        8        5
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             8       10        4
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        4        0
  MUCINOUS (COLLOID) CARCINOMA                              7        3        0
[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"
D12V10, binary
          cls
clus         0   1
  subtype1   1 102
  subtype2  11 236
  subtype3   6  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  102
  subtype2   11  236
  subtype3    6   80
     clus
vv    subtype1 subtype2 subtype3
  NO         1       11        6
  YES      102      236       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"
D12V11, continuous
D12V12, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  65   0   0   9
  subtype2 164   5   1  10
  subtype3  50   4   0   3
D12V13, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       65      164       50
  R1        0        5        4
  R2        0        1        0
  RX        9       10        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                         9    81
  subtype2     1                        34   181
  subtype3     2                         6    70
D12V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        9       34        6
  WHITE                           81      181       70
[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  82
  subtype2   5 182
  subtype3   1  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   82
  subtype2    5  182
  subtype3    1   60
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        5        1
  NOT HISPANIC OR LATINO       82      182       60
[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"
