[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"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[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_Correlate_Genomic_Events_Preprocess/KICH-TP/11544701/transformed.cor.cli.txt"

nPatients in clinical file=96, in cluster file=66, common to both=66
[1]  2 66
[1] "AMP PEAK 1(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
[1] "AMP PEAK 2(15Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
[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 = AMP PEAK 1(8Q11.23) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 1(8Q11.23) MUTATED   15  1
  AMP PEAK 1(8Q11.23) WILD-TYPE 42  1
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           16                            43 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                            1                             1 
$`AMP PEAK 1(8Q11.23) MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
        4311         3010         1986         1897         4622         1520 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KO-8405 
         714          788          108           18          341         2279 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
        1997         2670         2619         1739 

$`AMP PEAK 1(8Q11.23) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
        3322         4169         3127         2752         1977         2582 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
        2991         2949         1961         1364         2633         2024 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 
        2248         1815          876         1665          708         1366 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
         876         1437         3745         1553          953         3474 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 
        2674          775         1983         2211         2064          712 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
          76         1125         2727          637         2304         2339 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8416 
        2404         2820         1971         3141         2368         1873 
TCGA-KO-8417 
        1945 

  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           18                            76 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                         4622                          4169 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                       1941.5                        2024.0 
[1] "18.0 - 4622.0 (1941.5)" "76.0 - 4169.0 (2024.0)"
[1] "hr=" "2.9"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(8Q11.23) MUTATED         5        8         2        4
  AMP PEAK 1(8Q11.23) WILD-TYPE      16       17        12        2
D1V3, multiclass
           clus
vv          AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  STAGE I                             5                            16
  STAGE II                            8                            17
  STAGE III                           2                            12
  STAGE IV                            4                             2
[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
  AMP PEAK 1(8Q11.23) MUTATED    5  8     6
  AMP PEAK 1(8Q11.23) WILD-TYPE 16 17    14
D1V4, multiclass
       clus
vv      AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  T1                              5                            16
  T2                              8                            17
  T3+T4                           6                            14
[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
  AMP PEAK 1(8Q11.23) MUTATED   13     3
  AMP PEAK 1(8Q11.23) WILD-TYPE 27     2
D1V5, multiclass
       clus
vv      AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  N0                             13                            27
  N1+N2                           3                             2
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 1(8Q11.23) MUTATED    9  2  2
  AMP PEAK 1(8Q11.23) WILD-TYPE 25  0  7
D1V6, multiclass
    clus
vv   AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  M0                           9                            25
  M1                           2                             0
  MX                           2                             7
[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"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK 1(8Q11.23) MUTATED    6 13
  AMP PEAK 1(8Q11.23) WILD-TYPE 21 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) MUTATED      6   13
  AMP PEAK 1(8Q11.23) WILD-TYPE   21   26
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  FEMALE                           6                            21
  MALE                            13                            26
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(8Q11.23) MUTATED       1                         1    17
  AMP PEAK 1(8Q11.23) WILD-TYPE     1                         3    41
D1V10, multiclass
                           clus
vv                          AMP PEAK 1(8Q11.23) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              17
                           clus
vv                          AMP PEAK 1(8Q11.23) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                41
[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"
D1V11, binary
                               cls
clus                             0  1
  AMP PEAK 1(8Q11.23) MUTATED    3  9
  AMP PEAK 1(8Q11.23) WILD-TYPE  1 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) MUTATED      3    9
  AMP PEAK 1(8Q11.23) WILD-TYPE    1   23
                        clus
vv                       AMP PEAK 1(8Q11.23) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK 1(8Q11.23) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            23
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(15Q22.31) MUTATION ANALYSIS
D2V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 2(15Q22.31) MUTATED   17  2
  AMP PEAK 2(15Q22.31) WILD-TYPE 40  0
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            19                             40 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                             2                              0 
$`AMP PEAK 2(15Q22.31) MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
        4311         4169         3010         1986         1897         4622 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8435 
        1520          714         2211          108          341         2727 
TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 
         637         2279         1971         1997         2619         2368 
TCGA-KO-8415 
        1739 

$`AMP PEAK 2(15Q22.31) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
        3322         3127         2752         1977         2582         2991 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
        2949         1961         1364         2633         2024         2248 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
        1815          876         1665          708         1366          876 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
        1437         3745         1553          953         3474         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
         775          788         1983           18         2064          712 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
          76         1125         2304         2339         2404         2820 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
        2670         3141         1873         1945 

  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                           108                             18 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                          4622                           3745 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                          1997                           1980 
[1] "108.0 - 4622.0 (1997.0)" "18.0 - 3745.0 (1980.0)" 
[1] "hr="     "3.3e+09"
D2V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(15Q22.31) MUTATED         5       11         3        4
  AMP PEAK 2(15Q22.31) WILD-TYPE      16       14        11        2
D2V3, multiclass
           clus
vv          AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  STAGE I                              5                             16
  STAGE II                            11                             14
  STAGE III                            3                             11
  STAGE IV                             4                              2
[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
  AMP PEAK 2(15Q22.31) MUTATED    5 11     7
  AMP PEAK 2(15Q22.31) WILD-TYPE 16 14    13
D2V4, multiclass
       clus
vv      AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  T1                               5                             16
  T2                              11                             14
  T3+T4                            7                             13
[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
  AMP PEAK 2(15Q22.31) MUTATED   14     4
  AMP PEAK 2(15Q22.31) WILD-TYPE 26     1
D2V5, multiclass
       clus
vv      AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  N0                              14                             26
  N1+N2                            4                              1
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 2(15Q22.31) MUTATED   11  2  2
  AMP PEAK 2(15Q22.31) WILD-TYPE 23  0  7
D2V6, multiclass
    clus
vv   AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  M0                           11                             23
  M1                            2                              0
  MX                            2                              7
[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"
D2V7, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED    8 15
  AMP PEAK 2(15Q22.31) WILD-TYPE 19 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      8   15
  AMP PEAK 2(15Q22.31) WILD-TYPE   19   24
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  FEMALE                            8                             19
  MALE                             15                             24
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(15Q22.31) MUTATED       1                         1    21
  AMP PEAK 2(15Q22.31) WILD-TYPE     1                         3    37
D2V10, multiclass
                           clus
vv                          AMP PEAK 2(15Q22.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               21
                           clus
vv                          AMP PEAK 2(15Q22.31) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 37
[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"
D2V11, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED    3 11
  AMP PEAK 2(15Q22.31) WILD-TYPE  1 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      3   11
  AMP PEAK 2(15Q22.31) WILD-TYPE    1   21
                        clus
vv                       AMP PEAK 2(15Q22.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       AMP PEAK 2(15Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             21
[1] 2 2
[1] FALSE
