[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/22569433/transformed.cor.cli.txt"

nPatients in clinical file=113, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 11 to 8."
[1]  8 66
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               63 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               63 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6              60 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6              60 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
[1] "AMAC1L3 MUTATION ANALYSIS"
[1] 3
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                61 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                61 
[1] "GFM1 MUTATION ANALYSIS"
[1] 3
  GFM1 MUTATED GFM1 WILD-TYPE 
             3             63 
  GFM1 MUTATED GFM1 WILD-TYPE 
             3             63 
[1] "PABPC3 MUTATION ANALYSIS"
[1] 3
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               7               59 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               7               59 
[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 = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   16  6
  TP53 WILD-TYPE 40  3
  TP53 MUTATED TP53 WILD-TYPE 
            22             43 
  TP53 MUTATED TP53 WILD-TYPE 
             6              3 
$`TP53 MUTATED`
TCGA-KL-8339 TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       28.11       153.73        90.48        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8341 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8428 
       86.56        24.79       129.37        25.91        65.19        52.27 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 
       19.33        11.21        59.08        42.35       105.47        10.68 
TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       16.67        99.88       105.60        90.48 

$`TP53 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-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22       137.06       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       98.33        96.95        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 
       51.06        31.33        23.47        87.91        25.48       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 
        3.55         0.99        87.12         2.50       115.00       100.87 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 
      100.47       103.40        92.71       104.55       103.10        96.62 
TCGA-KO-8417 
       92.55 

  TP53 MUTATED TP53 WILD-TYPE 
         10.68           0.99 
  TP53 MUTATED TP53 WILD-TYPE 
        153.73         151.96 
  TP53 MUTATED TP53 WILD-TYPE 
        55.675         87.120 
[1] "10.7 - 153.7 (55.7)" "1.0 - 152.0 (87.1)" 
[1] "hr=" "4.4"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         5        8         5        4
  TP53 WILD-TYPE      16       17         9        2
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              5             16
  STAGE II             8             17
  STAGE III            5              9
  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
  TP53 MUTATED    5  8     9
  TP53 WILD-TYPE 16 17    11
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               5             16
  T2               8             17
  T3+T4            9             11
[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
  TP53 MUTATED   11     4
  TP53 WILD-TYPE 29     1
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0              11             29
  N1+N2            4              1
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  TP53 MUTATED   10  1
  TP53 WILD-TYPE 24  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     10    1
  TP53 WILD-TYPE   24    1
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           10             24
  1            1              1
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED    9 13
  TP53 WILD-TYPE 18 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9   13
  TP53 WILD-TYPE   18   26
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            9             18
  MALE             13             26
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus             0 1
  TP53 MUTATED   2 0
  TP53 WILD-TYPE 8 3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    0
  TP53 WILD-TYPE    8    3
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  100            2              8
  90             0              3
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         1    18
  TP53 WILD-TYPE     0                         3    40
D1V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               18             40
[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
  TP53 MUTATED    1 10
  TP53 WILD-TYPE  3 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   10
  TP53 WILD-TYPE    3   22
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10             22
[1] 2 2
[1] FALSE

Clustering(2) Variable = PTEN MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    3  3
  PTEN WILD-TYPE 53  6
  PTEN MUTATED PTEN WILD-TYPE 
             6             59 
  PTEN MUTATED PTEN WILD-TYPE 
             3              6 
$`PTEN MUTATED`
TCGA-KL-8323 TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 
       38.07        90.48        30.25        54.74        16.67        96.62 

$`PTEN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8331 
      153.73        23.84       109.22       137.06       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
       66.54        24.79        73.91        71.41        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 
      105.47        10.68       100.47       103.40        92.71       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        90.48        92.55 

  PTEN MUTATED PTEN WILD-TYPE 
         16.67           0.99 
  PTEN MUTATED PTEN WILD-TYPE 
         96.62         153.73 
  PTEN MUTATED PTEN WILD-TYPE 
        46.405         84.890 
[1] "16.7 - 96.6 (46.4)" "1.0 - 153.7 (84.9)"
[1] "hr=" "5.2"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         2        0         3        1
  PTEN WILD-TYPE      19       25        11        5
D2V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              2             19
  STAGE II             0             25
  STAGE III            3             11
  STAGE IV             1              5
[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
  PTEN MUTATED    2  0     4
  PTEN WILD-TYPE 19 25    16
D2V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T1               2             19
  T2               0             25
  T3+T4            4             16
[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
  PTEN MUTATED    3     2
  PTEN WILD-TYPE 37     3
D2V5, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  N0               3             37
  N1+N2            2              3
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus              0  1
  PTEN MUTATED    5  0
  PTEN WILD-TYPE 29  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE   29    2
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5             29
  1            0              2
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus              0  1
  PTEN MUTATED    4  2
  PTEN WILD-TYPE 23 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    2
  PTEN WILD-TYPE   23   37
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4             23
  MALE              2             37
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  PTEN MUTATED    0  0
  PTEN WILD-TYPE 10  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    0
  PTEN WILD-TYPE   10    3
D2V9, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2              9 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433     TCGA-KO-8409 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KO-8416 
"PTEN WILD-TYPE" 
D2V10, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2              6 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KM-8639 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KN-8433     TCGA-KO-8409 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         0     5
  PTEN WILD-TYPE     1                         4    53
D2V11, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5             53
[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
  PTEN MUTATED    1  1
  PTEN WILD-TYPE  3 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    1
  PTEN WILD-TYPE    3   31
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            1             31
[1] 2 2
[1] FALSE

Clustering(3) Variable = ZNF814 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  ZNF814 MUTATED    3  0
  ZNF814 WILD-TYPE 53  9
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               62 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               0                9 
$`ZNF814 MUTATED`
TCGA-KL-8333 TCGA-KL-8344 TCGA-KO-8414 
       98.33        28.80       105.60 

$`ZNF814 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67       104.55       103.10        99.88        96.62 
TCGA-KO-8416 TCGA-KO-8417 
       90.48        92.55 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
           28.80             0.99 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          105.60           153.73 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           98.33            72.66 
[1] "28.8 - 105.6 (98.3)" "1.0 - 153.7 (72.7)" 
[1] "hr="     "2.6e+07"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         0        2         1        0
  ZNF814 WILD-TYPE      21       23        13        6
D3V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                0               21
  STAGE II               2               23
  STAGE III              1               13
  STAGE IV               0                6
[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
  ZNF814 MUTATED    0  2     1
  ZNF814 WILD-TYPE 21 23    19
D3V4, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  T1                 0               21
  T2                 2               23
  T3+T4              1               19
[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
  ZNF814 MUTATED    3     0
  ZNF814 WILD-TYPE 37     5
D3V5, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  N0                 3               37
  N1+N2              0                5
[1] 2 2
[1] FALSE
D3V6, binary
                  cls
clus                0  1
  ZNF814 MUTATED    3  0
  ZNF814 WILD-TYPE 31  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3    0
  ZNF814 WILD-TYPE   31    2
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              3               31
  1              0                2
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                0  1
  ZNF814 MUTATED    1  2
  ZNF814 WILD-TYPE 26 37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      1    2
  ZNF814 WILD-TYPE   26   37
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              1               26
  MALE                2               37
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                0  1
  ZNF814 MUTATED    0  0
  ZNF814 WILD-TYPE 10  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    0
  ZNF814 WILD-TYPE   10    3
D3V9, continuous
D3V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED       0                         0     3
  ZNF814 WILD-TYPE     2                         4    55
D3V11, multiclass
                           clus
vv                          ZNF814 MUTATED ZNF814 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  3               55
[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"
D3V12, binary
                  cls
clus                0  1
  ZNF814 MUTATED    0  1
  ZNF814 WILD-TYPE  4 31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    1
  ZNF814 WILD-TYPE    4   31
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              1               31
[1] 2 2
[1] FALSE

Clustering(4) Variable = CDC27 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    5  1
  CDC27 WILD-TYPE 51  8
  CDC27 MUTATED CDC27 WILD-TYPE 
              6              59 
  CDC27 MUTATED CDC27 WILD-TYPE 
              1               8 
$`CDC27 MUTATED`
TCGA-KL-8324 TCGA-KM-8438 TCGA-KN-8435 TCGA-KO-8404 TCGA-KO-8409 TCGA-KO-8414 
      153.73       151.96       115.00        10.68       104.55       105.60 

$`CDC27 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        54.74        62.37        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 
       87.12        19.33         2.50        11.21        59.08        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47       100.47       103.40        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88        96.62        90.48        92.55 

  CDC27 MUTATED CDC27 WILD-TYPE 
          10.68            0.99 
  CDC27 MUTATED CDC27 WILD-TYPE 
         153.73          137.06 
  CDC27 MUTATED CDC27 WILD-TYPE 
         110.30           66.54 
[1] "10.7 - 153.7 (110.3)" "1.0 - 137.1 (66.5)"  
[1] "hr=" "1.1"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CDC27 MUTATED         0        5         0        1
  CDC27 WILD-TYPE      21       20        14        5
D4V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I               0              21
  STAGE II              5              20
  STAGE III             0              14
  STAGE IV              1               5
[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
  CDC27 MUTATED    0  5     1
  CDC27 WILD-TYPE 21 20    19
D4V4, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                0              21
  T2                5              20
  T3+T4             1              19
[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
  CDC27 MUTATED    3     0
  CDC27 WILD-TYPE 37     5
D4V5, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  N0                3              37
  N1+N2             0               5
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  0
  CDC27 WILD-TYPE 31  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    0
  CDC27 WILD-TYPE   31    2
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             3              31
  1             0               2
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  3
  CDC27 WILD-TYPE 24 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    3
  CDC27 WILD-TYPE   24   36
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             3              24
  MALE               3              36
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus              0 1
  CDC27 MUTATED   1 0
  CDC27 WILD-TYPE 9 3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    0
  CDC27 WILD-TYPE    9    3
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  100             1               9
  90              0               3
[1] 2 2
[1] FALSE
D4V9, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2               9 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433      TCGA-KO-8408 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-KO-8416 
"CDC27 WILD-TYPE" 
D4V10, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1               7 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         0     6
  CDC27 WILD-TYPE     2                         4    52
D4V11, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 6              52
[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"
D4V12, binary
                 cls
clus               0  1
  CDC27 MUTATED    0  5
  CDC27 WILD-TYPE  4 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    5
  CDC27 WILD-TYPE    4   27
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5              27
[1] 2 2
[1] FALSE

Clustering(5) Variable = PABPC1 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    4  3
  PABPC1 WILD-TYPE 52  6
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               58 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               3                6 
$`PABPC1 MUTATED`
TCGA-KL-8329 TCGA-KL-8341 TCGA-KL-8343 TCGA-KM-8476 TCGA-KN-8425 TCGA-KN-8427 
       90.48        24.79        71.41       123.12       104.52         0.99 
TCGA-KO-8404 
       10.68 

$`PABPC1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       153.73        23.84       109.22       137.06       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 
       44.84        86.56        66.54        73.91        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       62.37       151.96        44.91        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       59.08       115.00        42.35       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      105.60        96.62        90.48        92.55 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
            0.99             2.50 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          123.12           153.73 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           71.41            79.40 
[1] "1.0 - 123.1 (71.4)" "2.5 - 153.7 (79.4)"
[1] "hr=" "5"  
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PABPC1 MUTATED         3        0         1        3
  PABPC1 WILD-TYPE      18       25        13        3
D5V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE I                3               18
  STAGE II               0               25
  STAGE III              1               13
  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
  PABPC1 MUTATED    3  0     4
  PABPC1 WILD-TYPE 18 25    16
D5V4, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  T1                 3               18
  T2                 0               25
  T3+T4              4               16
[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
  PABPC1 MUTATED    3     2
  PABPC1 WILD-TYPE 37     3
D5V5, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  N0                 3               37
  N1+N2              2                3
[1] 2 2
[1] FALSE
D5V6, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  0
  PABPC1 WILD-TYPE 31  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    0
  PABPC1 WILD-TYPE   31    2
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              3               31
  1              0                2
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    1  6
  PABPC1 WILD-TYPE 26 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    6
  PABPC1 WILD-TYPE   26   33
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              1               26
  MALE                6               33
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus               0 1
  PABPC1 MUTATED   1 0
  PABPC1 WILD-TYPE 9 3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    0
  PABPC1 WILD-TYPE    9    3
     clus
vv    PABPC1 MUTATED PABPC1 WILD-TYPE
  100              1                9
  90               0                3
[1] 2 2
[1] FALSE
D5V9, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               10 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8345 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433       TCGA-KO-8408 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8416 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
D5V10, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1                7 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8345       TCGA-KM-8639 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED       2                         0     5
  PABPC1 WILD-TYPE     0                         4    53
D5V11, multiclass
                           clus
vv                          PABPC1 MUTATED PABPC1 WILD-TYPE
  ASIAN                                  2                0
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5               53
[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"
D5V12, binary
                  cls
clus                0  1
  PABPC1 MUTATED    0  3
  PABPC1 WILD-TYPE  4 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    3
  PABPC1 WILD-TYPE    4   29
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3               29
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMAC1L3 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  AMAC1L3 MUTATED    5  0
  AMAC1L3 WILD-TYPE 51  9
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                60 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                0                 9 
$`AMAC1L3 MUTATED`
TCGA-KL-8335 TCGA-KL-8337 TCGA-KM-8477 TCGA-KN-8431 TCGA-KN-8436 
       92.55        44.84        51.06        19.33        42.35 

$`AMAC1L3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8336 
      108.62        98.96        84.89        98.33        96.95        30.25 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
        2.50        11.21        59.08       115.00       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 

  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
            19.33              0.99 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
            92.55            153.73 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
           44.840            85.725 
[1] "19.3 - 92.5 (44.8)" "1.0 - 153.7 (85.7)"
[1] "hr="     "7.4e+07"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  AMAC1L3 MUTATED         1        3         1        0
  AMAC1L3 WILD-TYPE      20       22        13        6
D6V3, multiclass
           clus
vv          AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  STAGE I                 1                20
  STAGE II                3                22
  STAGE III               1                13
  STAGE IV                0                 6
[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
  AMAC1L3 MUTATED    1  3     1
  AMAC1L3 WILD-TYPE 20 22    19
D6V4, multiclass
       clus
vv      AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  T1                  1                20
  T2                  3                22
  T3+T4               1                19
[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
  AMAC1L3 MUTATED    2     0
  AMAC1L3 WILD-TYPE 38     5
D6V5, multiclass
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                2                43 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KN-8430        TCGA-KL-8326 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KL-8327        TCGA-KL-8329        TCGA-KL-8330        TCGA-KL-8331 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KL-8332        TCGA-KL-8333        TCGA-KL-8334        TCGA-KL-8336 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8340        TCGA-KL-8341        TCGA-KL-8342 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345        TCGA-KL-8346 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418        TCGA-KN-8419 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KO-8405        TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8410        TCGA-KO-8413        TCGA-KO-8414 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
D6V6, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    2  0
  AMAC1L3 WILD-TYPE 32  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      2    0
  AMAC1L3 WILD-TYPE   32    2
   clus
vv  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  0               2                32
  1               0                 2
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    1  4
  AMAC1L3 WILD-TYPE 26 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      1    4
  AMAC1L3 WILD-TYPE   26   35
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  FEMALE               1                26
  MALE                 4                35
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    0  1
  AMAC1L3 WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      0    1
  AMAC1L3 WILD-TYPE   10    2
     clus
vv    AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  100               0                10
  90                1                 2
[1] 2 2
[1] FALSE
D6V9, continuous
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                10 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8341        TCGA-KL-8345 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
D6V10, continuous
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                 7 
       TCGA-KL-8330        TCGA-KL-8341        TCGA-KL-8345        TCGA-KM-8639 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMAC1L3 MUTATED       0                         1     3
  AMAC1L3 WILD-TYPE     2                         3    55
D6V11, multiclass
                           clus
vv                          AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 3
  WHITE                                   3                55
[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"
D6V12, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    0  2
  AMAC1L3 WILD-TYPE  4 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      0    2
  AMAC1L3 WILD-TYPE    4   30
                        clus
vv                       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               2                30
[1] 2 2
[1] FALSE

Clustering(7) Variable = GFM1 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  GFM1 MUTATED    2  1
  GFM1 WILD-TYPE 54  8
  GFM1 MUTATED GFM1 WILD-TYPE 
             3             62 
  GFM1 MUTATED GFM1 WILD-TYPE 
             1              8 
$`GFM1 MUTATED`
TCGA-KN-8426 TCGA-KO-8406 TCGA-KO-8408 
        3.55       103.40        16.67 

$`GFM1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 
       87.91        25.48        25.91        65.19       104.52         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       92.71       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 
       90.48        92.55 

  GFM1 MUTATED GFM1 WILD-TYPE 
          3.55           0.99 
  GFM1 MUTATED GFM1 WILD-TYPE 
        103.40         153.73 
  GFM1 MUTATED GFM1 WILD-TYPE 
         16.67          79.40 
[1] "3.5 - 103.4 (16.7)" "1.0 - 153.7 (79.4)"
[1] "hr=" "5.1"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GFM1 MUTATED         1        0         1        1
  GFM1 WILD-TYPE      20       25        13        5
D7V3, multiclass
           clus
vv          GFM1 MUTATED GFM1 WILD-TYPE
  STAGE I              1             20
  STAGE II             0             25
  STAGE III            1             13
  STAGE IV             1              5
[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
  GFM1 MUTATED    1  0     2
  GFM1 WILD-TYPE 20 25    18
D7V4, multiclass
       clus
vv      GFM1 MUTATED GFM1 WILD-TYPE
  T1               1             20
  T2               0             25
  T3+T4            2             18
[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
  GFM1 MUTATED    1     1
  GFM1 WILD-TYPE 39     4
D7V5, multiclass
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             2             43 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-KL-8326 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8327     TCGA-KL-8329     TCGA-KL-8330     TCGA-KL-8331 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8332     TCGA-KL-8333     TCGA-KL-8334     TCGA-KL-8335 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8336     TCGA-KL-8337     TCGA-KL-8338     TCGA-KL-8340 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8341     TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8418     TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8423     TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8428     TCGA-KN-8429     TCGA-KO-8405     TCGA-KO-8407 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
D7V6, binary
                cls
clus              0  1
  GFM1 MUTATED    1  1
  GFM1 WILD-TYPE 33  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      1    1
  GFM1 WILD-TYPE   33    1
   clus
vv  GFM1 MUTATED GFM1 WILD-TYPE
  0            1             33
  1            1              1
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus              0  1
  GFM1 MUTATED    1  2
  GFM1 WILD-TYPE 26 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      1    2
  GFM1 WILD-TYPE   26   37
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  FEMALE            1             26
  MALE              2             37
[1] 2 2
[1] FALSE
D7V8, binary
                cls
clus              0  1
  GFM1 MUTATED    0  0
  GFM1 WILD-TYPE 10  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      0    0
  GFM1 WILD-TYPE   10    3
D7V9, continuous
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             1             10 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
D7V10, continuous
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             1              7 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8409 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GFM1 MUTATED       0                         0     3
  GFM1 WILD-TYPE     2                         4    55
D7V11, multiclass
                           clus
vv                          GFM1 MUTATED GFM1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                3             55
[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"
D7V12, binary
                cls
clus              0  1
  GFM1 MUTATED    0  2
  GFM1 WILD-TYPE  4 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      0    2
  GFM1 WILD-TYPE    4   30
                        clus
vv                       GFM1 MUTATED GFM1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2             30
[1] 2 2
[1] FALSE

Clustering(8) Variable = PABPC3 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  PABPC3 MUTATED    5  1
  PABPC3 WILD-TYPE 51  8
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               6               59 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               1                8 
$`PABPC3 MUTATED`
TCGA-KL-8345 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8407 
       54.74        11.21        59.08        42.35        10.68        92.71 

$`PABPC3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       71.41        28.80        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 
       52.27        87.12        19.33         2.50       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      105.47       100.47       103.40        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       99.88       105.60        96.62        90.48        92.55 

  PABPC3 MUTATED PABPC3 WILD-TYPE 
           10.68             0.99 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
           92.71           153.73 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
          48.545           86.560 
[1] "10.7 - 92.7 (48.5)" "1.0 - 153.7 (86.6)"
[1] "hr=" "1.6"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PABPC3 MUTATED         1        3         2        1
  PABPC3 WILD-TYPE      20       22        12        5
D8V3, multiclass
           clus
vv          PABPC3 MUTATED PABPC3 WILD-TYPE
  STAGE I                1               20
  STAGE II               3               22
  STAGE III              2               12
  STAGE IV               1                5
[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
  PABPC3 MUTATED    1  3     3
  PABPC3 WILD-TYPE 20 22    17
D8V4, multiclass
       clus
vv      PABPC3 MUTATED PABPC3 WILD-TYPE
  T1                 1               20
  T2                 3               22
  T3+T4              3               17
[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
  PABPC3 MUTATED    3     0
  PABPC3 WILD-TYPE 37     5
D8V5, multiclass
       clus
vv      PABPC3 MUTATED PABPC3 WILD-TYPE
  N0                 3               37
  N1+N2              0                5
[1] 2 2
[1] FALSE
D8V6, binary
                  cls
clus                0  1
  PABPC3 MUTATED    2  0
  PABPC3 WILD-TYPE 32  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      2    0
  PABPC3 WILD-TYPE   32    2
   clus
vv  PABPC3 MUTATED PABPC3 WILD-TYPE
  0              2               32
  1              0                2
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                0  1
  PABPC3 MUTATED    2  5
  PABPC3 WILD-TYPE 25 34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      2    5
  PABPC3 WILD-TYPE   25   34
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  FEMALE              2               25
  MALE                5               34
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus               0 1
  PABPC3 MUTATED   1 0
  PABPC3 WILD-TYPE 9 3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      1    0
  PABPC3 WILD-TYPE    9    3
     clus
vv    PABPC3 MUTATED PABPC3 WILD-TYPE
  100              1                9
  90               0                3
[1] 2 2
[1] FALSE
D8V9, continuous
[1] "Remove cluster labels:" "PABPC3 MUTATED"        
clus
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               2                9 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8428       TCGA-KO-8408       TCGA-KO-8409 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-KO-8416 
"PABPC3 WILD-TYPE" 
D8V10, continuous
[1] "Remove cluster labels:" "PABPC3 MUTATED"        
clus
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               2                6 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KM-8639 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC3 MUTATED       0                         0     7
  PABPC3 WILD-TYPE     2                         4    51
D8V11, multiclass
                           clus
vv                          PABPC3 MUTATED PABPC3 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  7               51
[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"
D8V12, binary
                  cls
clus                0  1
  PABPC3 MUTATED    0  6
  PABPC3 WILD-TYPE  4 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      0    6
  PABPC3 WILD-TYPE    4   26
                        clus
vv                       PABPC3 MUTATED PABPC3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6               26
[1] 2 2
[1] FALSE
