[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTKICH-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/KICH-TP/11541404/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/11588615/KICH-TP.mergedcluster.txt"

nPatients in clinical file=96, in cluster file=66, common to both=66
[1]  8 66
[1] "CN_CNMF"
[1] 3
 1  2  3 
 5 47 14 
 1  2  3 
 5 47 14 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
18 35 13 
 1  2  3 
18 35 13 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
19 22 15 10 
 1  2  3  4 
19 22 15 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
19 16  7  6 10  4  4 
 1  2  3  4  5  6  7 
19 16  7  6 10  4  4 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
20 24 22 
 1  2  3 
20 24 22 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
18 11 12  6  5  5  9 
 1  2  3  4  5  6  7 
18 11 12  6  5  5  9 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2 
19 29 
 1  2 
19 29 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
10  6  5  8  4  6  5  4 
 1  2  3  4  5  6  7  8 
10  6  5  8  4  6  5  4 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "KARNOFSKYPERFORMANCESCORE"             
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 66 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
          NA         4311           NA         3322         4169         3127 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
        2752         3304         3010         2582         2991         2949 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
        2815           NA         1364         2633           NA         2024 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
          NA         2248         1815          876         1665         1897 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
        4622          708         1366          876         1437         1520 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
        3745         1553          953         3474          714         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
         775          788         1983         2211          108           18 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
          NA         2064           NA          712           76          341 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
        1125         2727          637         2304         2339           NA 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
        2279         2404         2820           NA         2445         2670 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        3141         2619         2368         1739         1873         1945 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 66 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
21 25 18  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   21    25    20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
21 25 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   21    25    20 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
40  3  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   40     5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   40     5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  4  0
  subtype2 39  2
  subtype3 14  0
subtype1 subtype2 subtype3 
       4       41       14 
subtype1 subtype2 subtype3 
       0        2        0 
$subtype1
TCGA-KL-8329 TCGA-KM-8440 TCGA-KN-8434 TCGA-KO-8407 
        2752         1366         1125         2820 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
        4311         3322         3127         1977         3010         2582 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
        2991         2949         1961         2633         2024         1986 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
        2248         1815          876         1665         1897         4622 
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
         708          876         1437         1520         1553          953 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
        3474          714         2674          775          788         1983 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8437 TCGA-KO-8403 
         108           18         2064          712         2304         2339 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
        2279         2404         1971         1997         2670 

$subtype3
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8433 
        4169         1364         3745         2211           76          341 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
        2727          637         3141         2619         2368         1739 
TCGA-KO-8416 TCGA-KO-8417 
        1873         1945 

subtype1 subtype2 subtype3 
    1125       18       76 
subtype1 subtype2 subtype3 
    2820     4622     4169 
subtype1 subtype2 subtype3 
    2059     1986     2078 
[1] "1125.0 - 2820.0 (2059.0)" "18.0 - 4622.0 (1986.0)"  
[3] "76.0 - 4169.0 (2078.0)"  
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       1        2         2        0
  subtype2      13       18        10        6
  subtype3       7        5         2        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          1       13        7
  STAGE II         2       18        5
  STAGE III        2       10        2
  STAGE IV         0        6        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       T1 T2 T3+T4
  subtype1  1  2     2
  subtype2 13 18    16
  subtype3  7  5     2
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           1       13        7
  T2           2       18        5
  T3+T4        2       16        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"
          vv
clus       N0 N1+N2
  subtype1  2     0
  subtype2 30     5
  subtype3  8     0
D1V5, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2       35        8 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3"
       clus
vv      subtype2 subtype3
  N0          30        8
  N1+N2        5        0
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  3  0  1
  subtype2 23  2  7
  subtype3  8  0  1
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        3       23        8
  M1        0        2        0
  MX        1        7        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"
D1V7, binary
          cls
clus        0  1
  subtype1  3  2
  subtype2 18 29
  subtype3  6  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2   18   29
  subtype3    6    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3       18        6
  MALE          2       29        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"
D1V8, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       1        7        3 
 [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype3" "subtype3"
D1V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype2 subtype3 
       9        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[8] "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1     3
  subtype2     1                         2    42
  subtype3     0                         1    13
D1V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        1        2        1
  WHITE                            3       42       13
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
          cls
clus        0  1
  subtype1  0  3
  subtype2  2 20
  subtype3  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    2   20
  subtype3    2    9
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        2
  NOT HISPANIC OR LATINO        3       20        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16  0
  subtype2 29  2
  subtype3 12  0
subtype1 subtype2 subtype3 
      16       31       12 
subtype1 subtype2 subtype3 
       0        2        0 
$subtype1
TCGA-KL-8327 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8419 
        4169         2248         1665         1520         3745          714 
TCGA-KN-8425 TCGA-KN-8434 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 
        2211         1125         2339         2404         2820         1997 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        3141         1739         1873         1945 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
        4311         3322         3127         2752         1977         3010 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
        2582         2949         1961         1364         2633         2024 
TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 
        1986          876         1897         4622         1366         1437 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
        3474         2674          775          788         1983          108 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8408 
        2064          712           76         2727          637         1971 
TCGA-KO-8414 
        2368 

$subtype3
TCGA-KL-8333 TCGA-KL-8343 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
        2991         1815          708          876         1553          953 
TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8410 TCGA-KO-8413 
          18          341         2304         2279         2670         2619 

subtype1 subtype2 subtype3 
     714       76       18 
subtype1 subtype2 subtype3 
    4169     4622     2991 
subtype1 subtype2 subtype3 
    2104     1986     1684 
[1] "714.0 - 4169.0 (2104.0)" "76.0 - 4622.0 (1986.0)" 
[3] "18.0 - 2991.0 (1684.0)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       8        7         3        0
  subtype2       6       17         8        4
  subtype3       7        1         3        2
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          8        6        7
  STAGE II         7       17        1
  STAGE III        3        8        3
  STAGE IV         0        4        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       T1 T2 T3+T4
  subtype1  8  7     3
  subtype2  6 17    12
  subtype3  7  1     5
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           8        6        7
  T2           7       17        1
  T3+T4        3       12        5
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1 12     0
  subtype2 23     4
  subtype3  5     1
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          12       23        5
  N1+N2        0        4        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"
          vv
clus       M0 M1 MX
  subtype1 12  0  2
  subtype2 17  2  3
  subtype3  5  0  4
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       12       17        5
  M1        0        2        0
  MX        2        3        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"
D2V7, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 15 20
  subtype3  4  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   15   20
  subtype3    4    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       15        4
  MALE         10       20        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        6        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[8] "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    17
  subtype2     2                         3    28
  subtype3     0                         0    13
D2V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        1        3        0
  WHITE                           17       28       13
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2  1 12
  subtype3  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2    1   12
  subtype3    2    9
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        2
  NOT HISPANIC OR LATINO       11       12        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 17  1
  subtype2 20  0
  subtype3 11  1
  subtype4  9  0
subtype1 subtype2 subtype3 subtype4 
      18       20       12        9 
subtype1 subtype2 subtype3 subtype4 
       1        0        1        0 
$subtype1
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8338 TCGA-KL-8341 TCGA-KL-8342 
        4169         3010         2949         2633         1986         2248 
TCGA-KL-8345 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 
        1665         1520         3745         1983         1125         2727 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
        2339         2404         2820         3141         1873         1945 

$subtype2
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
        4311         1977         2582         1897         4622         1437 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8431 
         714          775          788         2211          108          712 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
          76          341         2279         1997         2670         2619 
TCGA-KO-8414 TCGA-KO-8415 
        2368         1739 

$subtype3
TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8340 
        3322         3127         2752         1961         1364         2024 
TCGA-KM-8440 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8429 TCGA-KN-8436 TCGA-KO-8408 
        1366         3474         2674         2064          637         1971 

$subtype4
TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 
        2991         1815          876          708          876         1553 
TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8437 
         953           18         2304 

subtype1 subtype2 subtype3 subtype4 
    1125       76      637       18 
subtype1 subtype2 subtype3 subtype4 
    4169     4622     3474     2991 
subtype1 subtype2 subtype3 subtype4 
  2371.5   1937.0   2044.0    953.0 
[1] "1125.0 - 4169.0 (2371.5)" "76.0 - 4622.0 (1937.0)"  
[3] "637.0 - 3474.0 (2044.0)"  "18.0 - 2991.0 (953.0)"   
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       7        6         5        1
  subtype2       8       11         2        1
  subtype3       1        7         5        2
  subtype4       5        1         2        2
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          7        8        1        5
  STAGE II         6       11        7        1
  STAGE III        5        2        5        2
  STAGE IV         1        1        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  7  6     6
  subtype2  8 11     3
  subtype3  1  7     7
  subtype4  5  1     4
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1           7        8        1        5
  T2           6       11        7        1
  T3+T4        6        3        7        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"
          vv
clus       N0 N1+N2
  subtype1 12     1
  subtype2 15     0
  subtype3 10     3
  subtype4  3     1
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          12       15       10        3
  N1+N2        1        0        3        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 13  0  2
  subtype2 11  1  2
  subtype3  7  1  1
  subtype4  3  0  4
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       13       11        7        3
  M1        0        1        1        0
  MX        2        2        1        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"
D3V7, binary
          cls
clus        0  1
  subtype1  9 10
  subtype2 11 11
  subtype3  5 10
  subtype4  2  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   10
  subtype2   11   11
  subtype3    5   10
  subtype4    2    8
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       11        5        2
  MALE         10       11       10        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        3        1        4 
 [1] "subtype2" "subtype4" "subtype4" "subtype2" "subtype1" "subtype1"
 [7] "subtype4" "subtype4" "subtype1" "subtype2"
D3V9, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       3        4        3        1 
 [1] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [7] "subtype2" "subtype3" "subtype2" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    18
  subtype2     0                         2    18
  subtype3     1                         2    12
  subtype4     0                         0    10
D3V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        0
  BLACK OR AFRICAN AMERICAN        0        2        2        0
  WHITE                           18       18       12       10
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2  4 10
  subtype3  0  5
  subtype4  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2    4   10
  subtype3    0    5
  subtype4    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        4        0        0
  NOT HISPANIC OR LATINO       10       10        5        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 17  1
  subtype2 15  0
  subtype3  5  0
  subtype4  6  0
  subtype5  6  1
  subtype6  4  0
  subtype7  4  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      18       15        5        6        7        4        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       1        0        0        0        1        0        0 
$subtype1
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
        4169         3010         2949         2024         1986         2248 
TCGA-KL-8345 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 
        1665         1520         3745         1983         1125         2727 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
        2339         2404         2820         3141         1873         1945 

$subtype2
TCGA-KL-8324 TCGA-KL-8330 TCGA-KM-8438 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
        4311         1977         4622          775          788         2211 
TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KO-8409 TCGA-KO-8410 
         108          712           76          341         1997         2670 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
        2619         2368         1739 

$subtype3
TCGA-KL-8332 TCGA-KL-8346 TCGA-KM-8442 TCGA-KN-8427 TCGA-KO-8405 
        2582         1897         1437           18         2279 

$subtype4
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8477 TCGA-KN-8419 
        3322         2991         1815          876         1553          714 

$subtype5
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8335 TCGA-KM-8440 TCGA-KN-8418 TCGA-KN-8429 
        3127         2752         1961         1366         3474         2064 
TCGA-KO-8408 
        1971 

$subtype6
TCGA-KL-8337 TCGA-KL-8338 TCGA-KN-8421 TCGA-KN-8436 
        1364         2633         2674          637 

$subtype7
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8437 
         708          876          953         2304 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1125       76       18      714     1366      637      708 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    4169     4622     2582     3322     3474     2674     2304 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  2293.5   1977.0   1897.0   1684.0   2064.0   1998.5    914.5 
[1] "1125.0 - 4169.0 (2293.5)" "76.0 - 4622.0 (1977.0)"  
[3] "18.0 - 2582.0 (1897.0)"   "714.0 - 3322.0 (1684.0)" 
[5] "1366.0 - 3474.0 (2064.0)" "637.0 - 2674.0 (1998.5)" 
[7] "708.0 - 2304.0 (914.5)"  
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       7        7         4        1
  subtype2       7        7         1        1
  subtype3       1        3         1        2
  subtype4       1        2         3        0
  subtype5       1        3         4        2
  subtype6       0        3         1        0
  subtype7       4        0         0        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          7        7        1        1        1        0        4
  STAGE II         7        7        3        2        3        3        0
  STAGE III        4        1        1        3        4        1        0
  STAGE IV         1        1        2        0        2        0        0
[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       T1 T2 T3+T4
  subtype1  7  7     5
  subtype2  7  7     2
  subtype3  1  3     3
  subtype4  1  2     3
  subtype5  1  3     6
  subtype6  0  3     1
  subtype7  4  0     0
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1           7        7        1        1        1        0        4
  T2           7        7        3        2        3        3        0
  T3+T4        5        2        3        3        6        1        0
[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"
          vv
clus       N0 N1+N2
  subtype1 12     1
  subtype2 11     0
  subtype3  3     1
  subtype4  5     0
  subtype5  6     3
  subtype6  3     0
  subtype7  0     0
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          12       11        3        5        6        3
  N1+N2        1        0        1        0        3        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 13  0  2
  subtype2  7  1  1
  subtype3  4  0  1
  subtype4  4  0  1
  subtype5  4  1  1
  subtype6  2  0  0
  subtype7  0  0  3
D4V6, multiclass
[1] "Remove cluster labels:" "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      15        9        5        5        6        2        3 
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype5"
 [7] "subtype5" "subtype2" "subtype1" "subtype3" "subtype4" "subtype1"
[13] "subtype5" "subtype5" "subtype5" "subtype1" "subtype1" "subtype1"
[19] "subtype4" "subtype4" "subtype1" "subtype3" "subtype2" "subtype7"
[25] "subtype5" "subtype7" "subtype3" "subtype1" "subtype1" "subtype4"
[31] "subtype7" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[43] "subtype1"
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype7
  M0       13        7        4        4        4        0
  M1        0        1        0        0        1        0
  MX        2        1        1        1        1        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  9 10
  subtype2 10  6
  subtype3  1  6
  subtype4  0  6
  subtype5  4  6
  subtype6  1  3
  subtype7  2  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   10
  subtype2   10    6
  subtype3    1    6
  subtype4    0    6
  subtype5    4    6
  subtype6    1    3
  subtype7    2    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        9       10        1        0        4        1        2
  MALE         10        6        6        6        6        3        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"
D4V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype7 
       3        2        1        1        1        3 
[1] "subtype7" "subtype7" "subtype1" "subtype1" "subtype7" "subtype1"
D4V9, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype5 subtype7 
       3        4        3        1 
 [1] "subtype2" "subtype2" "subtype5" "subtype1" "subtype1" "subtype5"
 [7] "subtype2" "subtype5" "subtype2" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    18
  subtype2     0                         1    14
  subtype3     0                         0     6
  subtype4     0                         1     5
  subtype5     1                         1     8
  subtype6     0                         1     3
  subtype7     0                         0     4
D4V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        1        0        1        1
  WHITE                           18       14        6        5        8
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                            3        4
[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"
D4V11, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2  2  9
  subtype3  2  1
  subtype4  0  3
  subtype5  0  3
  subtype6  0  2
  subtype7  0  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2    2    9
  subtype3    2    1
  subtype4    0    3
  subtype5    0    3
  subtype6    0    2
  subtype7    0    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        2        2        0        0        0
  NOT HISPANIC OR LATINO       10        9        1        3        3        2
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        4
[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(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 15  0
  subtype2 22  1
  subtype3 20  1
subtype1 subtype2 subtype3 
      15       23       21 
subtype1 subtype2 subtype3 
       0        1        1 
$subtype1
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8338 TCGA-KL-8343 TCGA-KL-8344 
        2991         2949         1961         2633         1815          876 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8427 
        4622          708          876         1553          953           18 
TCGA-KN-8432 TCGA-KN-8437 TCGA-KO-8405 
          76         2304         2279 

$subtype2
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 
        4311         3322         4169         3127         2752         3010 
TCGA-KL-8341 TCGA-KL-8345 TCGA-KM-8476 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8424 
        1986         1665         3745          714         2674         1983 
TCGA-KN-8426 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8406 
         108         1125         2727          637         2339         2404 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
        2820         2670         3141         1739         1873 

$subtype3
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8337 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8346 
        1977         2582         1364         2024         2248         1897 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KN-8418 TCGA-KN-8422 TCGA-KN-8423 
        1366         1437         1520         3474          775          788 
TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KO-8408 TCGA-KO-8409 
        2211         2064          712          341         1971         1997 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8417 
        2619         2368         1945 

subtype1 subtype2 subtype3 
      18      108      341 
subtype1 subtype2 subtype3 
    4622     4311     3474 
subtype1 subtype2 subtype3 
    1815     2670     1971 
[1] "18.0 - 4622.0 (1815.0)"  "108.0 - 4311.0 (2670.0)"
[3] "341.0 - 3474.0 (1971.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       6        4         7        3
  subtype2       9        9         3        3
  subtype3       6       12         4        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          6        9        6
  STAGE II         4        9       12
  STAGE III        7        3        4
  STAGE IV         3        3        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       T1 T2 T3+T4
  subtype1  6  4    10
  subtype2  9  9     6
  subtype3  6 12     4
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1           6        9        6
  T2           4        9       12
  T3+T4       10        6        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"
          vv
clus       N0 N1+N2
  subtype1 10     2
  subtype2 14     2
  subtype3 16     1
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          10       14       16
  N1+N2        2        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"
          vv
clus       M0 M1 MX
  subtype1  8  1  5
  subtype2 15  1  1
  subtype3 11  0  3
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        8       15       11
  M1        1        1        0
  MX        5        1        3
[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"
D5V7, binary
          cls
clus        0  1
  subtype1  6 14
  subtype2 11 13
  subtype3 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   14
  subtype2   11   13
  subtype3   10   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       11       10
  MALE         14       13       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       5        2        4 
[1] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[8] "subtype1" "subtype3"
D5V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    20
  subtype2     2                         1    21
  subtype3     0                         3    17
D5V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        0        1        3
  WHITE                           20       21       17
[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"
D5V11, binary
          cls
clus        0  1
  subtype1  1 11
  subtype2  1 12
  subtype3  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   11
  subtype2    1   12
  subtype3    2    9
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        2
  NOT HISPANIC OR LATINO       11       12        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 16  0
  subtype2 10  1
  subtype3 11  0
  subtype4  6  0
  subtype5  4  0
  subtype6  3  1
  subtype7  7  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      16       11       11        6        4        4        7 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       0        1        0        0        0        1        0 
$subtype1
TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8338 TCGA-KL-8342 TCGA-KL-8345 
        2752         3010         2949         2633         2248         1665 
TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 
        3745         1983         1125         2727         2339         2404 
TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
        2820         3141         1739         1873 

$subtype2
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8335 TCGA-KL-8341 TCGA-KN-8421 
        4311         4169         3127         1961         1986         2674 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8410 
         788          108           76          637         2670 

$subtype3
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8337 TCGA-KL-8340 TCGA-KL-8346 TCGA-KM-8440 
        1977         2582         1364         2024         1897         1366 
TCGA-KM-8443 TCGA-KN-8429 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 
        1520         2064         1997         2619         2368 

$subtype4
TCGA-KL-8326 TCGA-KM-8477 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8431 
        3322         1553          714          775         2211          712 

$subtype5
TCGA-KL-8333 TCGA-KM-8442 TCGA-KN-8433 TCGA-KO-8405 
        2991         1437          341         2279 

$subtype6
TCGA-KM-8438 TCGA-KN-8418 TCGA-KO-8408 TCGA-KO-8417 
        4622         3474         1971         1945 

$subtype7
TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8427 
        1815          876          708          876          953           18 
TCGA-KN-8437 
        2304 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1125       76     1364      712      341     1945       18 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    3745     4311     2619     3322     2991     4622     2304 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  2518.5   1986.0   1997.0   1164.0   1858.0   2722.5    876.0 
[1] "1125.0 - 3745.0 (2518.5)" "76.0 - 4311.0 (1986.0)"  
[3] "1364.0 - 2619.0 (1997.0)" "712.0 - 3322.0 (1164.0)" 
[5] "341.0 - 2991.0 (1858.0)"  "1945.0 - 4622.0 (2722.5)"
[7] "18.0 - 2304.0 (876.0)"   
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       7        5         5        1
  subtype2       3        5         1        2
  subtype3       2        8         2        0
  subtype4       3        2         1        0
  subtype5       1        2         2        0
  subtype6       1        2         1        1
  subtype7       4        1         2        2
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          7        3        2        3        1        1        4
  STAGE II         5        5        8        2        2        2        1
  STAGE III        5        1        2        1        2        1        2
  STAGE IV         1        2        0        0        0        1        2
[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       T1 T2 T3+T4
  subtype1  7  5     6
  subtype2  3  5     3
  subtype3  2  8     2
  subtype4  3  2     1
  subtype5  1  2     2
  subtype6  1  2     2
  subtype7  4  1     4
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1           7        3        2        3        1        1        4
  T2           5        5        8        2        2        2        1
  T3+T4        6        3        2        1        2        2        4
[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"
          vv
clus       N0 N1+N2
  subtype1 11     1
  subtype2  6     1
  subtype3 10     0
  subtype4  4     0
  subtype5  3     0
  subtype6  3     2
  subtype7  3     1
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0          11        6       10        4        3        3        3
  N1+N2        1        1        0        0        0        2        1
[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"
          vv
clus       M0 M1 MX
  subtype1 13  0  1
  subtype2  6  1  0
  subtype3  9  0  2
  subtype4  1  0  1
  subtype5  2  0  1
  subtype6  1  1  1
  subtype7  2  0  3
D6V6, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      14        7       11        2        3        3        5 
 [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [7] "subtype3" "subtype1" "subtype3" "subtype5" "subtype1" "subtype2"
[13] "subtype1" "subtype3" "subtype1" "subtype6" "subtype3" "subtype2"
[19] "subtype1" "subtype7" "subtype7" "subtype1" "subtype3" "subtype6"
[25] "subtype7" "subtype3" "subtype7" "subtype5" "subtype3" "subtype1"
[31] "subtype7" "subtype2" "subtype5" "subtype1" "subtype1" "subtype3"
[37] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[43] "subtype6"
    clus
vv   subtype1 subtype2 subtype3 subtype5 subtype6 subtype7
  M0       13        6        9        2        1        2
  M1        0        1        0        0        1        0
  MX        1        0        2        1        1        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 10  8
  subtype2  5  6
  subtype3  4  8
  subtype4  2  4
  subtype5  1  4
  subtype6  3  2
  subtype7  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    8
  subtype2    5    6
  subtype3    4    8
  subtype4    2    4
  subtype5    1    4
  subtype6    3    2
  subtype7    2    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       10        5        4        2        1        3        2
  MALE          8        6        8        4        4        2        7
[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"
D6V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
[4] "subtype5"               "subtype6"              
clus
subtype1 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        3        1        1        1        3 
[1] "subtype7" "subtype3" "subtype7" "subtype3" "subtype7" "subtype3"
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype5"               "subtype6"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype5 subtype6 subtype7 
       2        3        2        1        1        2 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    17
  subtype2     1                         0    10
  subtype3     0                         3     9
  subtype4     0                         1     4
  subtype5     0                         0     4
  subtype6     0                         0     5
  subtype7     0                         0     9
D6V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        3        1        0
  WHITE                           17       10        9        4        4
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        0        0
  WHITE                            5        9
[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"
D6V11, binary
          cls
clus       0 1
  subtype1 1 8
  subtype2 0 5
  subtype3 1 5
  subtype4 0 2
  subtype5 2 2
  subtype6 0 3
  subtype7 0 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    8
  subtype2    0    5
  subtype3    1    5
  subtype4    0    2
  subtype5    2    2
  subtype6    0    3
  subtype7    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        1        0        2        0
  NOT HISPANIC OR LATINO        8        5        5        2        2        3
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        7
[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(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 13  1
  subtype2 27  1
subtype1 subtype2 
      14       28 
subtype1 subtype2 
       1        1 
$subtype1
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8338 TCGA-KL-8343 TCGA-KL-8344 
        2991         2949         1961         2633         1815          876 
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 
         708          876          953           18          341         2304 
TCGA-KO-8405 TCGA-KO-8408 
        2279         1971 

$subtype2
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8340 
        4311         4169         3127         3010         2582         2024 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8418 
        1986         2248         1665         4622         1437         3474 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8429 
         714          775          788         1983          108         2064 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 
         712           76         1125          637         1997         2670 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        2619         1739         1873         1945 

subtype1 subtype2 
      18       76 
subtype1 subtype2 
    2991     4622 
subtype1 subtype2 
  1888.0   1984.5 
[1] "18.0 - 2991.0 (1888.0)" "76.0 - 4622.0 (1984.5)"
[1] "hr=" "2.6"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       5        2         9        3
  subtype2       9       14         3        3
D7V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          5        9
  STAGE II         2       14
  STAGE III        9        3
  STAGE IV         3        3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1  5  2    12
  subtype2  9 14     6
D7V4, multiclass
       clus
vv      subtype1 subtype2
  T1           5        9
  T2           2       14
  T3+T4       12        6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  9     3
  subtype2 20     2
D7V5, multiclass
       clus
vv      subtype1 subtype2
  N0           9       20
  N1+N2        3        2
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  9  0  3
  subtype2 15  2  2
D7V6, multiclass
    clus
vv   subtype1 subtype2
  M0        9       15
  M1        0        2
  MX        3        2
[1] 3 2
[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  6 13
  subtype2 15 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   13
  subtype2   15   14
        clus
vv       subtype1 subtype2
  FEMALE        6       15
  MALE         13       14
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    19
  subtype2     1                         1    25
D7V10, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            0        1
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                           19       25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
          cls
clus        0  1
  subtype1  1 10
  subtype2  3 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   10
  subtype2    3   10
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            1        3
  NOT HISPANIC OR LATINO       10       10
[1] 2 2
[1] FALSE

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype1 8 0
  subtype2 6 0
  subtype3 4 1
  subtype4 6 0
  subtype5 4 0
  subtype6 4 0
  subtype7 4 1
  subtype8 4 0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       8        6        5        6        4        4        5        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       0        0        1        0        0        0        1        0 
$subtype1
TCGA-KL-8331 TCGA-KL-8334 TCGA-KL-8338 TCGA-KN-8424 TCGA-KN-8426 TCGA-KO-8410 
        3010         2949         2633         1983          108         2670 
TCGA-KO-8415 TCGA-KO-8416 
        1739         1873 

$subtype2
TCGA-KL-8324 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KO-8409 TCGA-KO-8413 
        4311          714          775          788         1997         2619 

$subtype3
TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KN-8436 
        4169         1986         2248         1665          637 

$subtype4
TCGA-KL-8328 TCGA-KM-8438 TCGA-KM-8442 TCGA-KN-8418 TCGA-KN-8432 TCGA-KO-8417 
        3127         4622         1437         3474           76         1945 

$subtype5
TCGA-KL-8332 TCGA-KL-8340 TCGA-KN-8429 TCGA-KN-8434 
        2582         2024         2064         1125 

$subtype6
TCGA-KL-8333 TCGA-KL-8335 TCGA-KN-8427 TCGA-KO-8405 
        2991         1961           18         2279 

$subtype7
TCGA-KL-8343 TCGA-KL-8344 TCGA-KN-8431 TCGA-KN-8433 TCGA-KO-8408 
        1815          876          712          341         1971 

$subtype8
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8639 TCGA-KN-8437 
         708          876          953         2304 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
     108      714      637       76     1125       18      341      708 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    3010     4311     4169     4622     2582     2991     1971     2304 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  2308.0   1392.5   1986.0   2536.0   2044.0   2120.0    876.0    914.5 
[1] "108.0 - 3010.0 (2308.0)"  "714.0 - 4311.0 (1392.5)" 
[3] "637.0 - 4169.0 (1986.0)"  "76.0 - 4622.0 (2536.0)"  
[5] "1125.0 - 2582.0 (2044.0)" "18.0 - 2991.0 (2120.0)"  
[7] "341.0 - 1971.0 (876.0)"   "708.0 - 2304.0 (914.5)"  
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       3        1         4        2
  subtype2       3        3         0        0
  subtype3       1        2         1        1
  subtype4       2        5         0        1
  subtype5       1        2         1        0
  subtype6       0        2         2        2
  subtype7       0        1         4        0
  subtype8       4        0         0        0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          3        3        1        2        1        0        0
  STAGE II         1        3        2        5        2        2        1
  STAGE III        4        0        1        0        1        2        4
  STAGE IV         2        0        1        1        0        2        0
           clus
vv          subtype8
  STAGE I          4
  STAGE II         0
  STAGE III        0
  STAGE IV         0
[1] 4 8
[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  3  1     6
  subtype2  3  3     0
  subtype3  1  2     2
  subtype4  2  5     1
  subtype5  1  2     1
  subtype6  0  2     4
  subtype7  0  1     4
  subtype8  4  0     0
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1           3        3        1        2        1        0        0        4
  T2           1        3        2        5        2        2        1        0
  T3+T4        6        0        2        1        1        4        4        0
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  7     1
  subtype2  5     0
  subtype3  3     1
  subtype4  5     1
  subtype5  3     0
  subtype6  4     1
  subtype7  2     1
  subtype8  0     0
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0           7        5        3        5        3        4        2
  N1+N2        1        0        1        1        0        1        1
[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"
          vv
clus       M0 M1 MX
  subtype1  8  1  0
  subtype2  3  0  0
  subtype3  4  0  0
  subtype4  2  1  2
  subtype5  2  0  0
  subtype6  3  0  0
  subtype7  2  0  0
  subtype8  0  0  3
D8V6, multiclass
[1] "Remove cluster labels:" "subtype5"               "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       9        3        4        5        2        3        2        3 
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype1" "subtype6"
 [7] "subtype1" "subtype6" "subtype1" "subtype1" "subtype4" "subtype3"
[13] "subtype3" "subtype3" "subtype4" "subtype8" "subtype8" "subtype4"
[19] "subtype8" "subtype1" "subtype6" "subtype2" "subtype1" "subtype2"
[25] "subtype1" "subtype1" "subtype4"
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype6 subtype8
  M0        8        3        4        2        3        0
  M1        1        0        0        1        0        0
  MX        0        0        0        2        0        3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus       0 1
  subtype1 7 3
  subtype2 2 4
  subtype3 2 3
  subtype4 4 4
  subtype5 2 2
  subtype6 0 6
  subtype7 2 3
  subtype8 2 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    3
  subtype2    2    4
  subtype3    2    3
  subtype4    4    4
  subtype5    2    2
  subtype6    0    6
  subtype7    2    3
  subtype8    2    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        7        2        2        4        2        0        2
  MALE          3        4        3        4        2        6        3
        clus
vv       subtype8
  FEMALE        2
  MALE          2
[1] 2 8
[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
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype2 subtype4 subtype8 
       1        2        3 
[1] "subtype8" "subtype8" "subtype8"
D8V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype6"               "subtype7"              
[7] "subtype8"              
clus
subtype1 subtype2 subtype3 subtype6 subtype7 subtype8 
       1        2        2        2        2        1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    10
  subtype2     0                         1     5
  subtype3     1                         0     4
  subtype4     0                         0     7
  subtype5     0                         0     4
  subtype6     0                         0     6
  subtype7     0                         0     4
  subtype8     0                         0     4
D8V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        1        0        0        0
  WHITE                           10        5        4        7        4
                           clus
vv                          subtype6 subtype7 subtype8
  ASIAN                            0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        0
  WHITE                            6        4        4
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus       0 1
  subtype1 1 2
  subtype2 1 3
  subtype3 0 1
  subtype4 1 4
  subtype5 0 1
  subtype6 1 2
  subtype7 0 3
  subtype8 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    2
  subtype2    1    3
  subtype3    0    1
  subtype4    1    4
  subtype5    0    1
  subtype6    1    2
  subtype7    0    3
  subtype8    0    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        0        1        0        1
  NOT HISPANIC OR LATINO        2        3        1        4        1        2
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            0        0
  NOT HISPANIC OR LATINO        3        4
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
