[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/22506450/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/22507963/transformed.cor.cli.txt"

nPatients in clinical file=113, in cluster file=66, common to both=66
[1]  2 66
[1] "AMP PEAK 1(8Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                          19                           47 
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 66 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	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=53,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'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 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 66 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=39, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=2, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=10, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=8, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(8Q23.3) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 1(8Q23.3) MUTATED   15  3
  AMP PEAK 1(8Q23.3) WILD-TYPE 41  6
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                          18                           47 
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                           3                            6 
$`AMP PEAK 1(8Q23.3) MUTATED`
TCGA-KL-8339 TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
       28.11       153.73        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       49.97        23.47        25.91         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       11.21       100.47       104.55       103.10        99.88        96.62 

$`AMP PEAK 1(8Q23.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-KL-8323 
      102.81        23.28        28.80        47.24       130.13        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       23.84       109.22       137.06        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 
       66.54        73.91        71.41        28.80        54.74        44.91 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67       105.60        90.48        92.55 

  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                        0.99                         2.50 
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                      153.73                       137.06 
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                       57.32                        84.89 
[1] "1.0 - 153.7 (57.3)" "2.5 - 137.1 (84.9)"
[1] "hr=" "1.6"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(8Q23.3) MUTATED         5        8         2        4
  AMP PEAK 1(8Q23.3) WILD-TYPE      16       17        12        2
D1V3, multiclass
           clus
vv          AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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(8Q23.3) MUTATED    5  8     6
  AMP PEAK 1(8Q23.3) WILD-TYPE 16 17    14
D1V4, multiclass
       clus
vv      AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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(8Q23.3) MUTATED   13     3
  AMP PEAK 1(8Q23.3) WILD-TYPE 27     2
D1V5, multiclass
       clus
vv      AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  N0                            13                           27
  N1+N2                          3                            2
[1] 2 2
[1] FALSE
D1V6, binary
                              cls
clus                            0  1
  AMP PEAK 1(8Q23.3) MUTATED    9  2
  AMP PEAK 1(8Q23.3) WILD-TYPE 25  0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(8Q23.3) MUTATED      9    2
  AMP PEAK 1(8Q23.3) WILD-TYPE   25    0
   clus
vv  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  0                          9                           25
  1                          2                            0
[1] 2 2
[1] FALSE
D1V7, binary
                              cls
clus                            0  1
  AMP PEAK 1(8Q23.3) MUTATED    6 13
  AMP PEAK 1(8Q23.3) WILD-TYPE 21 26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(8Q23.3) MUTATED      6   13
  AMP PEAK 1(8Q23.3) WILD-TYPE   21   26
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  FEMALE                          6                           21
  MALE                           13                           26
[1] 2 2
[1] FALSE
D1V8, binary
                              cls
clus                           0 1
  AMP PEAK 1(8Q23.3) MUTATED   3 0
  AMP PEAK 1(8Q23.3) WILD-TYPE 7 3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(8Q23.3) MUTATED      3    0
  AMP PEAK 1(8Q23.3) WILD-TYPE    7    3
     clus
vv    AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  100                          3                            7
  90                           0                            3
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(8Q23.3) MUTATED       1                         1    17
  AMP PEAK 1(8Q23.3) WILD-TYPE     1                         3    41
D1V11, multiclass
                           clus
vv                          AMP PEAK 1(8Q23.3) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             17
                           clus
vv                          AMP PEAK 1(8Q23.3) 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"
D1V12, binary
                              cls
clus                            0  1
  AMP PEAK 1(8Q23.3) MUTATED    3  9
  AMP PEAK 1(8Q23.3) WILD-TYPE  1 23
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(8Q23.3) MUTATED      3    9
  AMP PEAK 1(8Q23.3) WILD-TYPE    1   23
                        clus
vv                       AMP PEAK 1(8Q23.3) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                          9
                        clus
vv                       AMP PEAK 1(8Q23.3) 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  5
  AMP PEAK 2(15Q22.31) WILD-TYPE 39  4
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            22                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                             5                              4 
$`AMP PEAK 2(15Q22.31) MUTATED`
TCGA-KL-8339 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8341 
       28.11       153.73       137.06        98.96        30.25        24.79 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 
       62.37       151.96        49.97        23.47       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 
       52.27        11.21       115.00        42.35       100.47        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      104.55        99.88       105.60        96.62 

$`AMP PEAK 2(15Q22.31) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-KL-8323 
      102.81        23.28        28.80        47.24       130.13        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
       23.84       109.22        90.48       108.62        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
       96.95        92.55        44.84        86.56        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 
       71.41        28.80        54.74        44.91       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        87.91        25.48        25.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8437 
        0.99        87.12        19.33         2.50        59.08       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8416 
      105.47        10.68       103.40        92.71       103.10        90.48 
TCGA-KO-8417 
       92.55 

  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                          3.55                           0.99 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                        153.73                         130.13 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                        79.495                         73.910 
[1] "3.5 - 153.7 (79.5)" "1.0 - 130.1 (73.9)"
[1] "hr=" "2.6"
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
D2V6, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED   11  2
  AMP PEAK 2(15Q22.31) WILD-TYPE 23  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED     11    2
  AMP PEAK 2(15Q22.31) WILD-TYPE   23    0
   clus
vv  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  0                           11                             23
  1                            2                              0
[1] 2 2
[1] FALSE
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, binary
                                cls
clus                             0 1
  AMP PEAK 2(15Q22.31) MUTATED   3 0
  AMP PEAK 2(15Q22.31) WILD-TYPE 7 3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      3    0
  AMP PEAK 2(15Q22.31) WILD-TYPE    7    3
     clus
vv    AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  100                            3                              7
  90                             0                              3
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, 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
D2V11, 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"
D2V12, 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
